Starting phenix.real_space_refine on Thu Jan 23 09:25:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b69_44250/01_2025/9b69_44250.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b69_44250/01_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_44250/01_2025/9b69_44250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b69_44250/01_2025/9b69_44250.map" model { file = "/net/cci-nas-00/data/ceres_data/9b69_44250/01_2025/9b69_44250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b69_44250/01_2025/9b69_44250.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10695 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 7264 2.51 5 N 1875 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11370 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2763 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 9, 'ARG:plan': 11, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2774 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 13, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2814 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 146 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2871 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.68, per 1000 atoms: 0.59 Number of scatterers: 11370 At special positions: 0 Unit cell: (145.14, 123.82, 94.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2195 8.00 N 1875 7.00 C 7264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 901 " - " ASN B 355 " " NAG E 1 " - " ASN C 241 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN B 241 " " NAG H 1 " - " ASN D 241 " Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 41.6% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.885A pdb=" N ILE C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 172 through 187 removed outlier: 4.045A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 252 through 265 removed outlier: 3.551A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 Processing helix chain 'C' and resid 324 through 334 removed outlier: 4.083A pdb=" N GLU C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 174 through 187 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.789A pdb=" N VAL A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.611A pdb=" N ILE B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.540A pdb=" N LYS B 172 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS B 173 " --> pdb=" O ASN B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 173' Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 232 through 237 removed outlier: 4.394A pdb=" N PHE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 Processing helix chain 'B' and resid 279 through 301 Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.732A pdb=" N ILE B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.742A pdb=" N ILE D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 143 through 157 Processing helix chain 'D' and resid 172 through 187 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 231 through 235 removed outlier: 4.050A pdb=" N LYS D 234 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 4.095A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 303 Processing helix chain 'D' and resid 325 through 335 Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.612A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 159 through 164 removed outlier: 7.414A pdb=" N LYS C 132 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ILE C 193 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA C 134 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP C 195 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 136 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 337 through 340 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 49 removed outlier: 7.229A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ASP A 48 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 164 removed outlier: 6.451A pdb=" N ALA A 134 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP A 195 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS A 364 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.617A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 47 removed outlier: 6.764A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 72 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 164 removed outlier: 4.988A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 362 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 340 Processing sheet with id=AB1, first strand: chain 'D' and resid 43 through 49 removed outlier: 6.365A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA D 72 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 159 through 164 removed outlier: 7.450A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS D 364 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 339 543 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3711 1.34 - 1.46: 2734 1.46 - 1.58: 5116 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 11617 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.05e+00 ... (remaining 11612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 15634 1.77 - 3.54: 181 3.54 - 5.30: 29 5.30 - 7.07: 8 7.07 - 8.84: 1 Bond angle restraints: 15853 Sorted by residual: angle pdb=" CA LYS D 187 " pdb=" CB LYS D 187 " pdb=" CG LYS D 187 " ideal model delta sigma weight residual 114.10 120.29 -6.19 2.00e+00 2.50e-01 9.58e+00 angle pdb=" CB LYS D 187 " pdb=" CG LYS D 187 " pdb=" CD LYS D 187 " ideal model delta sigma weight residual 111.30 118.17 -6.87 2.30e+00 1.89e-01 8.93e+00 angle pdb=" C LEU D 186 " pdb=" N LYS D 187 " pdb=" CA LYS D 187 " ideal model delta sigma weight residual 122.31 116.56 5.75 2.00e+00 2.50e-01 8.27e+00 angle pdb=" N LYS D 187 " pdb=" CA LYS D 187 " pdb=" CB LYS D 187 " ideal model delta sigma weight residual 110.46 114.67 -4.21 1.54e+00 4.22e-01 7.46e+00 angle pdb=" CA LEU C 233 " pdb=" CB LEU C 233 " pdb=" CG LEU C 233 " ideal model delta sigma weight residual 116.30 125.14 -8.84 3.50e+00 8.16e-02 6.38e+00 ... (remaining 15848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 6298 21.82 - 43.65: 462 43.65 - 65.47: 74 65.47 - 87.29: 25 87.29 - 109.11: 8 Dihedral angle restraints: 6867 sinusoidal: 2543 harmonic: 4324 Sorted by residual: dihedral pdb=" CB CYS C 63 " pdb=" SG CYS C 63 " pdb=" SG CYS C 315 " pdb=" CB CYS C 315 " ideal model delta sinusoidal sigma weight residual -86.00 -48.10 -37.90 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.60 109.11 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.62 108.33 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 6864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1596 0.055 - 0.111: 223 0.111 - 0.166: 33 0.166 - 0.221: 2 0.221 - 0.276: 2 Chirality restraints: 1856 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LYS D 187 " pdb=" N LYS D 187 " pdb=" C LYS D 187 " pdb=" CB LYS D 187 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1853 not shown) Planarity restraints: 2045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO D 99 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO C 99 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 99 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.016 5.00e-02 4.00e+02 ... (remaining 2042 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 455 2.72 - 3.27: 11559 3.27 - 3.81: 19355 3.81 - 4.36: 22231 4.36 - 4.90: 39070 Nonbonded interactions: 92670 Sorted by model distance: nonbonded pdb=" OE1 GLU A 25 " pdb=" OG SER A 282 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASP C 116 " pdb=" OH TYR C 356 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR D 135 " pdb=" OD2 ASP D 195 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR B 71 " pdb=" O ILE B 306 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR D 128 " pdb=" OE2 GLU D 362 " model vdw 2.247 3.040 ... (remaining 92665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 78 or (resid 79 throu \ gh 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 through 155 or (resid 156 through 157 and (name N or name CA or name \ C or name O or name CB )) or resid 158 through 183 or (resid 184 through 190 and \ (name N or name CA or name C or name O or name CB )) or resid 191 through 199 o \ r (resid 200 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 01 through 230 or (resid 231 through 232 and (name N or name CA or name C or nam \ e O or name CB )) or resid 233 or (resid 234 through 236 and (name N or name CA \ or name C or name O or name CB )) or resid 237 through 256 or (resid 257 and (na \ me N or name CA or name C or name O or name CB )) or resid 258 through 265 or (r \ esid 266 through 269 and (name N or name CA or name C or name O or name CB )) or \ resid 270 through 273 or (resid 274 and (name N or name CA or name C or name O \ or name CB )) or resid 275 through 278 or (resid 279 and (name N or name CA or n \ ame C or name O or name CB )) or resid 280 through 296 or (resid 297 and (name N \ or name CA or name C or name O or name CB )) or resid 298 through 301 or (resid \ 302 through 303 and (name N or name CA or name C or name O or name CB )) or res \ id 304 through 333 or (resid 334 through 335 and (name N or name CA or name C or \ name O or name CB )) or resid 336 through 345 or (resid 346 and (name N or name \ CA or name C or name O or name CB )) or resid 347 through 351 or (resid 352 and \ (name N or name CA or name C or name O or name CB )) or resid 353 through 383)) \ selection = (chain 'B' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 22 or (resid 23 and (name N or nam \ e CA or name C or name O or name CB )) or resid 24 through 43 or (resid 44 and ( \ name N or name CA or name C or name O or name CB )) or resid 45 through 47 or (r \ esid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thr \ ough 103 or (resid 104 and (name N or name CA or name C or name O or name CB )) \ or resid 105 through 115 or (resid 116 and (name N or name CA or name C or name \ O or name CB )) or resid 117 through 139 or (resid 140 and (name N or name CA or \ name C or name O or name CB )) or resid 141 through 155 or (resid 156 through 1 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 158 through \ 169 or (resid 170 and (name N or name CA or name C or name O or name CB )) or r \ esid 171 through 177 or (resid 178 and (name N or name CA or name C or name O or \ name CB )) or resid 179 through 183 or (resid 184 through 190 and (name N or na \ me CA or name C or name O or name CB )) or resid 191 through 199 or (resid 200 a \ nd (name N or name CA or name C or name O or name CB )) or resid 201 through 205 \ or (resid 206 and (name N or name CA or name C or name O or name CB )) or resid \ 207 through 212 or (resid 213 and (name N or name CA or name C or name O or nam \ e CB )) or resid 214 through 215 or (resid 216 and (name N or name CA or name C \ or name O or name CB )) or resid 217 through 230 or (resid 231 through 232 and ( \ name N or name CA or name C or name O or name CB )) or resid 233 or (resid 234 t \ hrough 236 and (name N or name CA or name C or name O or name CB )) or resid 237 \ through 273 or (resid 274 and (name N or name CA or name C or name O or name CB \ )) or resid 275 through 278 or (resid 279 and (name N or name CA or name C or n \ ame O or name CB )) or resid 280 through 293 or (resid 294 through 295 and (name \ N or name CA or name C or name O or name CB )) or resid 296 through 298 or (res \ id 299 through 303 and (name N or name CA or name C or name O or name CB )) or r \ esid 304 through 305 or (resid 306 and (name N or name CA or name C or name O or \ name CB )) or resid 307 through 333 or (resid 334 through 335 and (name N or na \ me CA or name C or name O or name CB )) or resid 336 through 361 or (resid 362 a \ nd (name N or name CA or name C or name O or name CB )) or resid 363 through 368 \ or (resid 369 through 370 and (name N or name CA or name C or name O or name CB \ )) or resid 371 through 383)) selection = (chain 'C' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 22 or (resid 23 and (name N or nam \ e CA or name C or name O or name CB )) or resid 24 through 36 or (resid 37 and ( \ name N or name CA or name C or name O or name CB )) or resid 38 through 47 or (r \ esid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thr \ ough 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or \ resid 55 through 103 or (resid 104 and (name N or name CA or name C or name O o \ r name CB )) or resid 105 through 115 or (resid 116 and (name N or name CA or na \ me C or name O or name CB )) or resid 117 through 139 or (resid 140 and (name N \ or name CA or name C or name O or name CB )) or resid 141 through 169 or (resid \ 170 and (name N or name CA or name C or name O or name CB )) or resid 171 throug \ h 184 or (resid 185 through 190 and (name N or name CA or name C or name O or na \ me CB )) or resid 191 through 205 or (resid 206 and (name N or name CA or name C \ or name O or name CB )) or resid 207 through 212 or (resid 213 and (name N or n \ ame CA or name C or name O or name CB )) or resid 214 through 215 or (resid 216 \ and (name N or name CA or name C or name O or name CB )) or resid 217 through 26 \ 5 or (resid 266 through 269 and (name N or name CA or name C or name O or name C \ B )) or resid 270 through 273 or (resid 274 and (name N or name CA or name C or \ name O or name CB )) or resid 275 through 293 or (resid 294 through 295 and (nam \ e N or name CA or name C or name O or name CB )) or resid 296 or (resid 297 and \ (name N or name CA or name C or name O or name CB )) or resid 298 or (resid 299 \ through 303 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 4 through 305 or (resid 306 and (name N or name CA or name C or name O or name C \ B )) or resid 307 through 351 or (resid 352 and (name N or name CA or name C or \ name O or name CB )) or resid 353 through 383)) selection = (chain 'D' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 19 or (resid 20 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 21 through 23 and (name N or na \ me CA or name C or name O or name CB )) or resid 24 through 36 or (resid 37 and \ (name N or name CA or name C or name O or name CB )) or resid 38 through 43 or ( \ resid 44 and (name N or name CA or name C or name O or name CB )) or resid 45 th \ rough 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) o \ r resid 55 through 79 or (resid 80 and (name N or name CA or name C or name O or \ name CB )) or resid 81 through 115 or (resid 116 and (name N or name CA or name \ C or name O or name CB )) or resid 117 or (resid 118 and (name N or name CA or \ name C or name O or name CB )) or resid 119 through 139 or (resid 140 and (name \ N or name CA or name C or name O or name CB )) or resid 141 through 155 or (resi \ d 156 through 157 and (name N or name CA or name C or name O or name CB )) or re \ sid 158 through 169 or (resid 170 and (name N or name CA or name C or name O or \ name CB )) or resid 171 through 172 or (resid 173 and (name N or name CA or name \ C or name O or name CB )) or resid 174 through 177 or (resid 178 and (name N or \ name CA or name C or name O or name CB )) or resid 179 through 181 or (resid 18 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 183 or (resi \ d 184 through 190 and (name N or name CA or name C or name O or name CB )) or re \ sid 191 through 196 or (resid 197 and (name N or name CA or name C or name O or \ name CB )) or resid 198 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 205 or (resid 206 and (name N or \ name CA or name C or name O or name CB )) or resid 207 through 212 or (resid 21 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 214 through \ 215 or (resid 216 and (name N or name CA or name C or name O or name CB )) or re \ sid 217 through 230 or (resid 231 through 232 and (name N or name CA or name C o \ r name O or name CB )) or resid 233 or (resid 234 through 236 and (name N or nam \ e CA or name C or name O or name CB )) or resid 237 through 260 or (resid 261 an \ d (name N or name CA or name C or name O or name CB )) or resid 262 through 265 \ or (resid 266 through 269 and (name N or name CA or name C or name O or name CB \ )) or resid 270 through 278 or (resid 279 and (name N or name CA or name C or na \ me O or name CB )) or resid 280 through 296 or (resid 297 and (name N or name CA \ or name C or name O or name CB )) or resid 298 or (resid 299 through 303 and (n \ ame N or name CA or name C or name O or name CB )) or resid 304 through 305 or ( \ resid 306 and (name N or name CA or name C or name O or name CB )) or resid 307 \ or (resid 308 through 309 and (name N or name CA or name C or name O or name CB \ )) or resid 310 through 324 or (resid 325 and (name N or name CA or name C or na \ me O or name CB )) or resid 326 through 330 or (resid 331 through 332 and (name \ N or name CA or name C or name O or name CB )) or resid 333 or (resid 334 throug \ h 335 and (name N or name CA or name C or name O or name CB )) or resid 336 thro \ ugh 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) o \ r resid 347 through 351 or (resid 352 and (name N or name CA or name C or name O \ or name CB )) or resid 353 through 361 or (resid 362 and (name N or name CA or \ name C or name O or name CB )) or resid 363 through 369 or (resid 370 and (name \ N or name CA or name C or name O or name CB )) or resid 371 through 383)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.920 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.640 ------------------------------------------------------------------------------- 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 11617 Z= 0.180 Angle : 0.492 8.841 15853 Z= 0.255 Chirality : 0.041 0.276 1856 Planarity : 0.003 0.037 2040 Dihedral : 16.281 109.115 4087 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.36 % Allowed : 20.34 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1488 helix: 2.10 (0.22), residues: 604 sheet: -0.99 (0.33), residues: 252 loop : -0.42 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.004 0.001 HIS A 46 PHE 0.010 0.001 PHE D 181 TYR 0.011 0.001 TYR A 77 ARG 0.007 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 1.313 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: 0.2860 time to fit residues: 56.1126 Evaluate side-chains 141 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain D residue 13 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 GLN A 24 GLN B 207 GLN D 107 HIS D 170 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099637 restraints weight = 18119.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098491 restraints weight = 15115.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099395 restraints weight = 13986.569| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 11617 Z= 0.442 Angle : 0.605 6.343 15853 Z= 0.317 Chirality : 0.045 0.159 1856 Planarity : 0.004 0.043 2040 Dihedral : 8.583 59.510 1834 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.55 % Allowed : 18.03 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1488 helix: 1.39 (0.21), residues: 612 sheet: -1.38 (0.32), residues: 260 loop : -0.61 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 323 HIS 0.007 0.002 HIS D 93 PHE 0.014 0.002 PHE D 76 TYR 0.022 0.002 TYR C 77 ARG 0.007 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8746 (mt) REVERT: C 180 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7449 (tp) REVERT: C 267 GLU cc_start: 0.8004 (tp30) cc_final: 0.7631 (tp30) REVERT: C 280 TYR cc_start: 0.7050 (p90) cc_final: 0.6703 (p90) REVERT: C 323 TRP cc_start: 0.7645 (OUTLIER) cc_final: 0.7442 (p-90) REVERT: C 339 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7215 (tm-30) REVERT: C 359 ASN cc_start: 0.8375 (t0) cc_final: 0.8129 (m-40) REVERT: A 202 ASN cc_start: 0.7687 (m110) cc_final: 0.7078 (t0) REVERT: D 318 ASN cc_start: 0.7944 (p0) cc_final: 0.7711 (p0) REVERT: D 344 ASN cc_start: 0.7990 (t0) cc_final: 0.7777 (t0) REVERT: D 380 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7945 (tpp) outliers start: 40 outliers final: 22 residues processed: 185 average time/residue: 0.2605 time to fit residues: 67.4339 Evaluate side-chains 168 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 380 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS A 290 GLN B 112 GLN D 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103485 restraints weight = 18230.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105133 restraints weight = 13339.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105876 restraints weight = 11299.654| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11617 Z= 0.154 Angle : 0.457 7.002 15853 Z= 0.241 Chirality : 0.041 0.141 1856 Planarity : 0.003 0.040 2040 Dihedral : 6.580 59.424 1826 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.13 % Allowed : 18.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1488 helix: 1.83 (0.21), residues: 608 sheet: -1.21 (0.32), residues: 252 loop : -0.59 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 262 HIS 0.005 0.001 HIS A 214 PHE 0.008 0.001 PHE D 133 TYR 0.021 0.001 TYR A 127 ARG 0.007 0.000 ARG A 198 *********************** 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 179 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8692 (mt) REVERT: C 339 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 71 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6337 (m-10) REVERT: A 190 ARG cc_start: 0.6997 (tpp80) cc_final: 0.6718 (mmm-85) REVERT: A 202 ASN cc_start: 0.7431 (m110) cc_final: 0.7074 (t0) REVERT: B 68 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.7291 (ttp-170) REVERT: B 259 ILE cc_start: 0.7939 (mt) cc_final: 0.7678 (mm) REVERT: D 318 ASN cc_start: 0.7901 (p0) cc_final: 0.7644 (p0) outliers start: 24 outliers final: 14 residues processed: 172 average time/residue: 0.2712 time to fit residues: 64.9298 Evaluate side-chains 157 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 123 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102111 restraints weight = 18156.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101759 restraints weight = 14032.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.102785 restraints weight = 15024.556| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11617 Z= 0.326 Angle : 0.511 5.297 15853 Z= 0.270 Chirality : 0.042 0.143 1856 Planarity : 0.003 0.037 2040 Dihedral : 6.263 58.286 1826 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.00 % Allowed : 18.83 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1488 helix: 1.65 (0.21), residues: 612 sheet: -1.51 (0.31), residues: 268 loop : -0.54 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 323 HIS 0.005 0.001 HIS D 46 PHE 0.013 0.001 PHE B 258 TYR 0.017 0.002 TYR A 128 ARG 0.007 0.001 ARG A 198 *********************** 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 196 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8722 (mt) REVERT: C 339 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7245 (tm-30) REVERT: A 202 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.7127 (t0) REVERT: A 380 MET cc_start: 0.6246 (ttp) cc_final: 0.5982 (ttp) REVERT: B 274 HIS cc_start: 0.5395 (OUTLIER) cc_final: 0.3569 (t70) REVERT: B 380 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7741 (ttt) REVERT: D 304 ILE cc_start: 0.8635 (mm) cc_final: 0.8350 (mt) REVERT: D 318 ASN cc_start: 0.7989 (p0) cc_final: 0.7771 (p0) outliers start: 45 outliers final: 30 residues processed: 181 average time/residue: 0.2650 time to fit residues: 66.7527 Evaluate side-chains 178 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 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 95 SER 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 70 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 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 14 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 127 optimal weight: 0.0980 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101652 restraints weight = 18059.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104259 restraints weight = 13412.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104905 restraints weight = 12249.986| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11617 Z= 0.217 Angle : 0.471 6.215 15853 Z= 0.249 Chirality : 0.041 0.163 1856 Planarity : 0.003 0.034 2040 Dihedral : 6.080 58.771 1826 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.00 % Allowed : 18.83 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1488 helix: 1.78 (0.21), residues: 612 sheet: -1.25 (0.32), residues: 252 loop : -0.64 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.006 0.001 HIS D 46 PHE 0.009 0.001 PHE D 133 TYR 0.015 0.001 TYR A 128 ARG 0.008 0.001 ARG A 198 *********************** 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 201 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8650 (mt) REVERT: C 339 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7307 (tm-30) REVERT: A 47 ILE cc_start: 0.9000 (mm) cc_final: 0.8612 (pt) REVERT: A 50 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6155 (pp) REVERT: A 71 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.5901 (m-10) REVERT: A 190 ARG cc_start: 0.6840 (mmm-85) cc_final: 0.6243 (mmm-85) REVERT: A 202 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.7059 (t0) REVERT: A 380 MET cc_start: 0.6230 (ttp) cc_final: 0.5767 (ttp) REVERT: B 68 ARG cc_start: 0.7410 (ttp-170) cc_final: 0.7181 (ttt180) REVERT: B 274 HIS cc_start: 0.5354 (OUTLIER) cc_final: 0.3509 (t70) REVERT: B 380 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7750 (ttp) REVERT: D 304 ILE cc_start: 0.8630 (mm) cc_final: 0.8353 (mt) REVERT: D 318 ASN cc_start: 0.7991 (p0) cc_final: 0.7731 (p0) outliers start: 45 outliers final: 28 residues processed: 186 average time/residue: 0.2607 time to fit residues: 67.5465 Evaluate side-chains 178 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 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 50 LEU 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 160 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 202 ASN 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 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.132915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103960 restraints weight = 18163.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104442 restraints weight = 14507.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105732 restraints weight = 12635.125| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11617 Z= 0.215 Angle : 0.471 6.257 15853 Z= 0.249 Chirality : 0.041 0.164 1856 Planarity : 0.003 0.034 2040 Dihedral : 5.997 57.685 1826 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.44 % Allowed : 18.65 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1488 helix: 1.77 (0.21), residues: 616 sheet: -1.23 (0.32), residues: 252 loop : -0.63 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.005 0.001 HIS D 46 PHE 0.010 0.001 PHE D 133 TYR 0.012 0.001 TYR A 77 ARG 0.009 0.001 ARG A 198 *********************** 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 201 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8649 (mt) REVERT: A 50 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6206 (pp) REVERT: A 380 MET cc_start: 0.6239 (ttp) cc_final: 0.5903 (ttp) REVERT: B 274 HIS cc_start: 0.5297 (OUTLIER) cc_final: 0.3445 (t70) REVERT: B 380 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7750 (ttp) REVERT: D 304 ILE cc_start: 0.8631 (mm) cc_final: 0.8345 (mt) outliers start: 50 outliers final: 34 residues processed: 190 average time/residue: 0.2545 time to fit residues: 68.1646 Evaluate side-chains 179 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 336 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 123 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 18 optimal weight: 0.0170 chunk 56 optimal weight: 0.9980 chunk 100 optimal weight: 0.0470 chunk 25 optimal weight: 0.0040 chunk 28 optimal weight: 0.9990 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS B 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.135485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106349 restraints weight = 18261.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107525 restraints weight = 13246.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108560 restraints weight = 11617.031| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 0.037 11617 Z= 0.135 Angle : 0.451 7.210 15853 Z= 0.237 Chirality : 0.040 0.155 1856 Planarity : 0.003 0.034 2040 Dihedral : 5.766 57.129 1826 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.46 % Allowed : 19.72 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1488 helix: 1.92 (0.22), residues: 616 sheet: -1.18 (0.32), residues: 252 loop : -0.55 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 262 HIS 0.005 0.001 HIS D 46 PHE 0.011 0.001 PHE D 76 TYR 0.009 0.001 TYR A 77 ARG 0.010 0.001 ARG A 198 *********************** 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 192 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8586 (mt) REVERT: A 47 ILE cc_start: 0.8895 (mm) cc_final: 0.8415 (pt) REVERT: A 279 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7426 (mtmt) REVERT: B 274 HIS cc_start: 0.5167 (OUTLIER) cc_final: 0.3435 (t70) REVERT: D 304 ILE cc_start: 0.8618 (mm) cc_final: 0.8319 (mt) outliers start: 39 outliers final: 31 residues processed: 184 average time/residue: 0.2739 time to fit residues: 69.9258 Evaluate side-chains 175 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 215 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 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 82 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 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 282 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 141 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 136 optimal weight: 0.0570 chunk 94 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.134066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105108 restraints weight = 18176.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105676 restraints weight = 14631.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106756 restraints weight = 12774.703| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11617 Z= 0.194 Angle : 0.467 7.164 15853 Z= 0.246 Chirality : 0.041 0.160 1856 Planarity : 0.003 0.048 2040 Dihedral : 5.781 59.505 1826 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.73 % Allowed : 20.25 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1488 helix: 1.89 (0.22), residues: 616 sheet: -1.11 (0.32), residues: 252 loop : -0.55 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.005 0.001 HIS B 46 PHE 0.015 0.001 PHE A 181 TYR 0.012 0.001 TYR A 77 ARG 0.011 0.001 ARG C 141 *********************** 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 189 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8605 (mt) REVERT: A 47 ILE cc_start: 0.8909 (mm) cc_final: 0.8404 (pt) REVERT: A 279 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7510 (mtmt) REVERT: A 380 MET cc_start: 0.6206 (ttp) cc_final: 0.5900 (ttp) REVERT: B 274 HIS cc_start: 0.5165 (OUTLIER) cc_final: 0.3326 (t-170) REVERT: D 304 ILE cc_start: 0.8619 (mm) cc_final: 0.8315 (mt) outliers start: 42 outliers final: 35 residues processed: 179 average time/residue: 0.2675 time to fit residues: 66.8594 Evaluate side-chains 180 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 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 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 279 LYS 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 159 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 282 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 113 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 146 optimal weight: 0.0970 chunk 90 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.131444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102550 restraints weight = 18304.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102021 restraints weight = 13116.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103168 restraints weight = 15691.371| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11617 Z= 0.333 Angle : 0.541 6.552 15853 Z= 0.286 Chirality : 0.043 0.166 1856 Planarity : 0.004 0.060 2040 Dihedral : 5.992 58.377 1826 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.64 % Allowed : 20.34 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1488 helix: 1.67 (0.21), residues: 616 sheet: -1.18 (0.32), residues: 252 loop : -0.65 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 323 HIS 0.003 0.001 HIS D 46 PHE 0.017 0.001 PHE A 181 TYR 0.016 0.002 TYR A 77 ARG 0.009 0.001 ARG C 141 *********************** 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 184 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8671 (mt) REVERT: A 47 ILE cc_start: 0.8927 (mm) cc_final: 0.8471 (pt) REVERT: A 214 HIS cc_start: 0.6687 (OUTLIER) cc_final: 0.6361 (p90) REVERT: A 279 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7515 (mtmt) REVERT: A 380 MET cc_start: 0.6268 (ttp) cc_final: 0.5979 (ttp) REVERT: B 274 HIS cc_start: 0.5364 (OUTLIER) cc_final: 0.3735 (t-170) REVERT: D 304 ILE cc_start: 0.8652 (mm) cc_final: 0.8366 (mt) outliers start: 41 outliers final: 33 residues processed: 175 average time/residue: 0.2814 time to fit residues: 68.8872 Evaluate side-chains 179 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 82 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 CYS 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 82 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 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 4 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 128 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.132974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103956 restraints weight = 18137.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103967 restraints weight = 12825.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105179 restraints weight = 12077.309| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11617 Z= 0.190 Angle : 0.494 6.870 15853 Z= 0.261 Chirality : 0.041 0.168 1856 Planarity : 0.003 0.049 2040 Dihedral : 5.807 58.378 1826 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.29 % Allowed : 20.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1488 helix: 1.78 (0.21), residues: 616 sheet: -1.15 (0.32), residues: 252 loop : -0.62 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 262 HIS 0.005 0.001 HIS A 214 PHE 0.014 0.001 PHE A 181 TYR 0.012 0.001 TYR A 77 ARG 0.009 0.001 ARG C 141 ********************** 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: 37 poor density : 146 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8648 (mt) REVERT: A 47 ILE cc_start: 0.8925 (mm) cc_final: 0.8459 (pt) REVERT: A 190 ARG cc_start: 0.6837 (mmm-85) cc_final: 0.6276 (mmm-85) REVERT: A 214 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.6079 (p90) REVERT: A 279 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7458 (mtmt) REVERT: A 380 MET cc_start: 0.6224 (ttp) cc_final: 0.5903 (ttp) REVERT: B 274 HIS cc_start: 0.5293 (OUTLIER) cc_final: 0.3425 (t-170) REVERT: D 304 ILE cc_start: 0.8636 (mm) cc_final: 0.8348 (mt) outliers start: 37 outliers final: 32 residues processed: 176 average time/residue: 0.2713 time to fit residues: 66.6384 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 : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 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 82 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 THR 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 159 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 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 58 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102899 restraints weight = 18232.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102640 restraints weight = 14779.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103899 restraints weight = 14431.598| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11617 Z= 0.277 Angle : 0.517 6.561 15853 Z= 0.273 Chirality : 0.042 0.165 1856 Planarity : 0.003 0.050 2040 Dihedral : 5.827 58.235 1826 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.37 % Allowed : 20.87 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1488 helix: 1.70 (0.21), residues: 616 sheet: -1.15 (0.32), residues: 252 loop : -0.65 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 323 HIS 0.009 0.001 HIS A 214 PHE 0.012 0.001 PHE B 258 TYR 0.015 0.001 TYR A 77 ARG 0.009 0.001 ARG B 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3114.61 seconds wall clock time: 56 minutes 53.54 seconds (3413.54 seconds total)