Starting phenix.real_space_refine on Sun Aug 24 12:51:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b68_44249/08_2025/9b68_44249.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b68_44249/08_2025/9b68_44249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b68_44249/08_2025/9b68_44249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b68_44249/08_2025/9b68_44249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b68_44249/08_2025/9b68_44249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b68_44249/08_2025/9b68_44249.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10696 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 7261 2.51 5 N 1872 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 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11364 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2763 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 9, 'GLN:plan1': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2774 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 10, 'ASP:plan': 6, 'GLU:plan': 13, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2814 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 146 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 10, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2865 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.73, per 1000 atoms: 0.24 Number of scatterers: 11364 At special positions: 0 Unit cell: (143.5, 124.64, 89.38, 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 1872 7.00 C 7261 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: 0.86 Conformation dependent library (CDL) restraints added in 377.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 41 helices and 12 sheets defined 40.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.585A pdb=" N ILE C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 172 through 187 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 252 through 265 removed outlier: 3.703A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.888A pdb=" N TYR A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) 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 129 Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.650A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 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: 3.673A pdb=" N VAL A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 37 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 139 through 142 removed outlier: 3.615A pdb=" N GLY B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.625A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 301 Processing helix chain 'B' and resid 324 through 334 removed outlier: 4.100A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.993A pdb=" N TYR D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.538A 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 188 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.937A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.961A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.464A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.372A 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: 5.607A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR C 220 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N PHE C 245 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE C 222 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 358 " --> pdb=" O TYR C 373 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR C 373 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE C 360 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR C 373 " --> pdb=" O VAL C 381 " (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 50 removed outlier: 7.414A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.136A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.719A 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: 4.335A pdb=" N ALA B 72 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.291A 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: 5.035A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS B 364 " --> pdb=" O PRO B 368 " (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 42 through 50 removed outlier: 6.231A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 72 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 159 through 164 removed outlier: 7.442A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE D 358 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR D 373 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 339 551 hydrogen bonds defined for protein. 1620 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: 1.56 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3708 1.35 - 1.46: 2968 1.46 - 1.58: 4879 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 11611 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" CB ASP B 231 " pdb=" CG ASP B 231 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.76e+00 bond pdb=" CB GLU C 294 " pdb=" CG GLU C 294 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.71e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.70e+00 ... (remaining 11606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 15573 1.94 - 3.88: 230 3.88 - 5.81: 32 5.81 - 7.75: 8 7.75 - 9.69: 3 Bond angle restraints: 15846 Sorted by residual: angle pdb=" N ILE D 306 " pdb=" CA ILE D 306 " pdb=" C ILE D 306 " ideal model delta sigma weight residual 112.29 107.84 4.45 9.40e-01 1.13e+00 2.24e+01 angle pdb=" N THR C 228 " pdb=" CA THR C 228 " pdb=" C THR C 228 " ideal model delta sigma weight residual 114.75 109.33 5.42 1.26e+00 6.30e-01 1.85e+01 angle pdb=" CA CYS B 63 " pdb=" CB CYS B 63 " pdb=" SG CYS B 63 " ideal model delta sigma weight residual 114.40 122.22 -7.82 2.30e+00 1.89e-01 1.16e+01 angle pdb=" C MET A 113 " pdb=" N ARG A 114 " pdb=" CA ARG A 114 " ideal model delta sigma weight residual 121.61 116.90 4.71 1.39e+00 5.18e-01 1.15e+01 angle pdb=" N VAL A 165 " pdb=" CA VAL A 165 " pdb=" C VAL A 165 " ideal model delta sigma weight residual 113.47 110.09 3.38 1.01e+00 9.80e-01 1.12e+01 ... (remaining 15841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 6323 21.82 - 43.64: 434 43.64 - 65.46: 69 65.46 - 87.28: 27 87.28 - 109.11: 9 Dihedral angle restraints: 6862 sinusoidal: 2538 harmonic: 4324 Sorted by residual: dihedral pdb=" CB CYS B 63 " pdb=" SG CYS B 63 " pdb=" SG CYS B 315 " pdb=" CB CYS B 315 " ideal model delta sinusoidal sigma weight residual 93.00 18.39 74.61 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CB CYS D 63 " pdb=" SG CYS D 63 " pdb=" SG CYS D 315 " pdb=" CB CYS D 315 " ideal model delta sinusoidal sigma weight residual -86.00 -28.20 -57.80 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CA TRP C 323 " pdb=" C TRP C 323 " pdb=" N GLY C 324 " pdb=" CA GLY C 324 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 6859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1543 0.054 - 0.108: 271 0.108 - 0.162: 37 0.162 - 0.216: 3 0.216 - 0.269: 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 -2.54 0.27 2.00e-01 2.50e+01 1.81e+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 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN C 241 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1853 not shown) Planarity restraints: 2044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 231 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C ASP B 231 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP B 231 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 232 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 56 " 0.016 2.00e-02 2.50e+03 1.80e-02 5.65e+00 pdb=" CG PHE B 56 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 56 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 56 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 56 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 56 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 56 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 323 " 0.016 2.00e-02 2.50e+03 1.46e-02 5.34e+00 pdb=" CG TRP C 323 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 323 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 323 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 323 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 323 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 323 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 323 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 323 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 323 " 0.000 2.00e-02 2.50e+03 ... (remaining 2041 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1065 2.74 - 3.28: 11498 3.28 - 3.82: 19459 3.82 - 4.36: 21977 4.36 - 4.90: 38856 Nonbonded interactions: 92855 Sorted by model distance: nonbonded pdb=" OD1 ASP C 116 " pdb=" OH TYR C 356 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR C 228 " pdb=" NE2 GLN C 246 " model vdw 2.223 3.120 nonbonded pdb=" N GLU D 376 " pdb=" OE1 GLU D 376 " model vdw 2.285 3.120 nonbonded pdb=" OE1 GLU B 185 " pdb=" NH2 ARG B 190 " model vdw 2.312 3.120 nonbonded pdb=" N ASN A 355 " pdb=" OE2 GLU A 376 " model vdw 2.324 3.120 ... (remaining 92850 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 140 or (resid 141 and (name N or name CA or name C or name O \ or name CB )) or resid 142 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 1 \ 91 through 199 or (resid 200 and (name N or name CA or name C or name O or name \ CB )) or resid 201 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 through 236 and (na \ me N or name CA or name C or name O or name CB )) or resid 237 through 256 or (r \ esid 257 and (name N or name CA or name C or name O or name CB )) or resid 258 t \ hrough 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 273 or (resid 274 and (name N or name CA or n \ ame 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 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 throu \ gh 301 or (resid 302 through 303 and (name N or name CA or name C or name O or n \ ame CB )) or resid 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 o \ r (resid 352 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 53 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 through 141 and (name N o \ r name CA or name C or name O or name CB )) or resid 142 through 155 or (resid 1 \ 56 through 157 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 nam \ e CB )) or resid 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 name CA or name C or name O or name CB )) or resid 191 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 213 and (name N or name CA or name C or n \ ame O or name CB )) or resid 214 through 215 or (resid 216 and (name N or name C \ A or name C or name O or name CB )) or resid 217 through 230 or (resid 231 throu \ gh 232 and (name N or name CA or name C or name 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 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 name O or name CB )) or resid 280 through 293 or (resid 294 through 2 \ 95 and (name N or name CA or name C or name O or name CB )) or resid 296 through \ 298 or (resid 299 through 303 and (name N or name CA or name C or name O or nam \ e 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 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 361 or \ (resid 362 and (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 through 141 \ and (name N or name CA or name C or name O or name CB )) or resid 142 through 16 \ 9 or (resid 170 and (name N or name CA or name C or name O or name CB )) or resi \ d 171 through 184 or (resid 185 through 190 and (name N or name CA or name C or \ name O or name 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 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 resid 21 \ 7 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 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 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 or (re \ sid 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 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 351 or (resid 352 and (name N or name CA o \ r 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 through 14 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 142 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 169 or (resid 170 and (name N or name CA or name C o \ r name O or name CB )) or resid 171 through 172 or (resid 173 and (name N or nam \ e CA or name C or name O or name CB )) or resid 174 through 177 or (resid 178 an \ d (name N or name CA or name C or name O or name CB )) or resid 179 through 181 \ or (resid 182 and (name N or name CA or name C or name O or name CB )) or resid \ 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 196 or (resid 197 and (name N or name CA or name C o \ r name O or name CB )) or resid 198 through 199 or (resid 200 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 through 205 or (resid 206 an \ d (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 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 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 through 236 and (n \ ame N or name CA or name C or name O or name CB )) or resid 237 through 260 or ( \ resid 261 and (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 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 or (resid 299 throug \ h 303 and (name N or name CA or name C or name O or name CB )) or resid 304 thro \ ugh 305 or (resid 306 and (name N or name CA or name C or name O or name CB )) o \ r 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 name O or name CB )) or resid 326 through 330 or (resid 331 through 33 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 333 or (resi \ d 334 through 335 and (name N or name CA or name C or name O or name CB )) or re \ sid 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 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 37 \ 0 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.410 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 0.049 11626 Z= 0.161 Angle : 0.618 9.691 15887 Z= 0.347 Chirality : 0.043 0.269 1856 Planarity : 0.004 0.043 2039 Dihedral : 16.031 109.106 4082 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.27 % Allowed : 18.76 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.22), residues: 1488 helix: 1.48 (0.21), residues: 628 sheet: -0.82 (0.34), residues: 244 loop : -1.33 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.023 0.001 TYR B 26 PHE 0.041 0.001 PHE B 56 TRP 0.040 0.002 TRP C 323 HIS 0.007 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00327 (11611) covalent geometry : angle 0.60898 (15846) SS BOND : bond 0.00236 ( 4) SS BOND : angle 2.16269 ( 8) hydrogen bonds : bond 0.10636 ( 551) hydrogen bonds : angle 5.72060 ( 1620) link_BETA1-4 : bond 0.00667 ( 6) link_BETA1-4 : angle 2.07215 ( 18) link_NAG-ASN : bond 0.00131 ( 5) link_NAG-ASN : angle 2.20380 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 0.323 Fit side-chains REVERT: C 117 LEU cc_start: 0.8302 (tp) cc_final: 0.7781 (tt) REVERT: C 329 ILE cc_start: 0.9144 (mm) cc_final: 0.8805 (mm) REVERT: A 33 MET cc_start: 0.8050 (mmm) cc_final: 0.7808 (mmm) REVERT: B 376 GLU cc_start: 0.6813 (pm20) cc_final: 0.6586 (tp30) REVERT: D 316 LEU cc_start: 0.7475 (pp) cc_final: 0.7240 (mt) outliers start: 3 outliers final: 1 residues processed: 161 average time/residue: 0.0879 time to fit residues: 20.6313 Evaluate side-chains 149 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 HIS ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111749 restraints weight = 17262.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112296 restraints weight = 15183.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113163 restraints weight = 14127.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113709 restraints weight = 11238.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113808 restraints weight = 9883.684| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11626 Z= 0.161 Angle : 0.526 7.479 15887 Z= 0.272 Chirality : 0.043 0.207 1856 Planarity : 0.004 0.046 2039 Dihedral : 8.159 65.950 1826 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.96 % Allowed : 16.89 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.22), residues: 1488 helix: 1.72 (0.21), residues: 596 sheet: -0.79 (0.34), residues: 244 loop : -1.19 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 68 TYR 0.017 0.002 TYR B 286 PHE 0.011 0.001 PHE B 41 TRP 0.032 0.002 TRP C 323 HIS 0.005 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00377 (11611) covalent geometry : angle 0.51395 (15846) SS BOND : bond 0.00177 ( 4) SS BOND : angle 1.80703 ( 8) hydrogen bonds : bond 0.03602 ( 551) hydrogen bonds : angle 4.58570 ( 1620) link_BETA1-4 : bond 0.00609 ( 6) link_BETA1-4 : angle 2.48730 ( 18) link_NAG-ASN : bond 0.00335 ( 5) link_NAG-ASN : angle 2.11533 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: C 117 LEU cc_start: 0.8368 (tp) cc_final: 0.7802 (tt) REVERT: C 329 ILE cc_start: 0.9231 (mm) cc_final: 0.8779 (mm) REVERT: A 329 ILE cc_start: 0.8792 (mm) cc_final: 0.8226 (mp) REVERT: B 234 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8133 (mtmm) REVERT: D 316 LEU cc_start: 0.7517 (pp) cc_final: 0.7217 (mt) outliers start: 22 outliers final: 15 residues processed: 177 average time/residue: 0.0871 time to fit residues: 22.5628 Evaluate side-chains 161 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 21 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 0.0010 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116172 restraints weight = 17091.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116518 restraints weight = 14525.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117430 restraints weight = 13342.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118062 restraints weight = 10945.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118414 restraints weight = 9476.991| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11626 Z= 0.101 Angle : 0.478 7.114 15887 Z= 0.247 Chirality : 0.041 0.204 1856 Planarity : 0.003 0.044 2039 Dihedral : 6.624 54.578 1826 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.40 % Allowed : 16.80 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.22), residues: 1488 helix: 1.76 (0.21), residues: 604 sheet: -0.78 (0.34), residues: 244 loop : -1.10 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.018 0.001 TYR C 373 PHE 0.009 0.001 PHE D 36 TRP 0.032 0.002 TRP C 323 HIS 0.006 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00229 (11611) covalent geometry : angle 0.46558 (15846) SS BOND : bond 0.00307 ( 4) SS BOND : angle 1.83704 ( 8) hydrogen bonds : bond 0.03176 ( 551) hydrogen bonds : angle 4.35985 ( 1620) link_BETA1-4 : bond 0.00641 ( 6) link_BETA1-4 : angle 2.40675 ( 18) link_NAG-ASN : bond 0.00245 ( 5) link_NAG-ASN : angle 1.97935 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: C 117 LEU cc_start: 0.8179 (tp) cc_final: 0.7603 (tt) REVERT: C 297 ARG cc_start: 0.6926 (mtp85) cc_final: 0.6418 (mtm-85) REVERT: A 339 GLU cc_start: 0.6783 (tp30) cc_final: 0.6416 (mm-30) REVERT: A 380 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6811 (ttp) REVERT: D 316 LEU cc_start: 0.7503 (pp) cc_final: 0.7136 (mt) REVERT: D 328 GLU cc_start: 0.7821 (tp30) cc_final: 0.7578 (tp30) outliers start: 27 outliers final: 16 residues processed: 177 average time/residue: 0.0919 time to fit residues: 23.6029 Evaluate side-chains 163 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 57 optimal weight: 1.9990 chunk 116 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.143462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120411 restraints weight = 16787.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120599 restraints weight = 14796.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121109 restraints weight = 13887.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121581 restraints weight = 11718.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122137 restraints weight = 10671.193| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11626 Z= 0.109 Angle : 0.476 9.251 15887 Z= 0.247 Chirality : 0.041 0.205 1856 Planarity : 0.003 0.043 2039 Dihedral : 5.840 54.785 1826 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.11 % Allowed : 16.98 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.22), residues: 1488 helix: 1.86 (0.21), residues: 604 sheet: -0.76 (0.33), residues: 244 loop : -1.06 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 300 TYR 0.017 0.001 TYR C 373 PHE 0.009 0.001 PHE D 36 TRP 0.028 0.001 TRP C 323 HIS 0.006 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00250 (11611) covalent geometry : angle 0.46441 (15846) SS BOND : bond 0.00124 ( 4) SS BOND : angle 1.90980 ( 8) hydrogen bonds : bond 0.03122 ( 551) hydrogen bonds : angle 4.25257 ( 1620) link_BETA1-4 : bond 0.00675 ( 6) link_BETA1-4 : angle 2.27598 ( 18) link_NAG-ASN : bond 0.00222 ( 5) link_NAG-ASN : angle 1.87290 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.380 Fit side-chains REVERT: C 294 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 297 ARG cc_start: 0.6929 (mtp85) cc_final: 0.6437 (mtm-85) REVERT: A 266 GLU cc_start: 0.7001 (pm20) cc_final: 0.6711 (pt0) REVERT: A 339 GLU cc_start: 0.6683 (tp30) cc_final: 0.6313 (mm-30) REVERT: A 380 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.6827 (ttp) REVERT: B 104 ASP cc_start: 0.6876 (t0) cc_final: 0.6629 (m-30) REVERT: B 300 ARG cc_start: 0.7699 (ttp-110) cc_final: 0.7489 (ttp80) REVERT: B 380 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7855 (tpp) REVERT: D 316 LEU cc_start: 0.7559 (pp) cc_final: 0.7194 (mt) outliers start: 35 outliers final: 24 residues processed: 182 average time/residue: 0.0884 time to fit residues: 23.6493 Evaluate side-chains 169 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 91 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 113 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113504 restraints weight = 17201.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114161 restraints weight = 13617.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115059 restraints weight = 11888.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115474 restraints weight = 10249.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115609 restraints weight = 9407.557| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11626 Z= 0.107 Angle : 0.477 10.714 15887 Z= 0.246 Chirality : 0.041 0.202 1856 Planarity : 0.003 0.042 2039 Dihedral : 5.512 54.676 1826 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.93 % Allowed : 17.33 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.22), residues: 1488 helix: 1.96 (0.21), residues: 596 sheet: -0.92 (0.32), residues: 252 loop : -0.94 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 68 TYR 0.019 0.001 TYR C 373 PHE 0.010 0.001 PHE D 36 TRP 0.037 0.002 TRP C 323 HIS 0.006 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00247 (11611) covalent geometry : angle 0.46746 (15846) SS BOND : bond 0.00081 ( 4) SS BOND : angle 1.93880 ( 8) hydrogen bonds : bond 0.03034 ( 551) hydrogen bonds : angle 4.17680 ( 1620) link_BETA1-4 : bond 0.00636 ( 6) link_BETA1-4 : angle 2.05077 ( 18) link_NAG-ASN : bond 0.00200 ( 5) link_NAG-ASN : angle 1.81839 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.393 Fit side-chains REVERT: C 198 ARG cc_start: 0.6837 (tpp-160) cc_final: 0.5164 (ttp80) REVERT: C 294 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7669 (tm-30) REVERT: C 297 ARG cc_start: 0.6923 (mtp85) cc_final: 0.6445 (mtm-85) REVERT: A 266 GLU cc_start: 0.6920 (pm20) cc_final: 0.6719 (pt0) REVERT: A 339 GLU cc_start: 0.6672 (tp30) cc_final: 0.6354 (mm-30) REVERT: A 380 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.6874 (ttp) REVERT: B 95 SER cc_start: 0.8964 (m) cc_final: 0.8688 (t) REVERT: B 104 ASP cc_start: 0.6786 (t0) cc_final: 0.6573 (m-30) REVERT: B 185 GLU cc_start: 0.8239 (tp30) cc_final: 0.7911 (tp30) REVERT: B 190 ARG cc_start: 0.7886 (mmp80) cc_final: 0.7518 (mmp-170) REVERT: B 380 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7894 (tpp) REVERT: D 316 LEU cc_start: 0.7591 (pp) cc_final: 0.7247 (mt) outliers start: 33 outliers final: 27 residues processed: 175 average time/residue: 0.1000 time to fit residues: 24.9949 Evaluate side-chains 180 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 60 optimal weight: 0.0470 chunk 90 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN A 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112589 restraints weight = 17355.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113286 restraints weight = 13875.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113771 restraints weight = 12390.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114147 restraints weight = 10473.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114579 restraints weight = 9500.692| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11626 Z= 0.125 Angle : 0.483 10.417 15887 Z= 0.249 Chirality : 0.041 0.203 1856 Planarity : 0.003 0.043 2039 Dihedral : 5.479 55.058 1826 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.56 % Allowed : 17.42 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.23), residues: 1488 helix: 1.93 (0.21), residues: 596 sheet: -0.74 (0.32), residues: 264 loop : -0.93 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 30 TYR 0.018 0.001 TYR C 373 PHE 0.007 0.001 PHE D 36 TRP 0.028 0.001 TRP C 323 HIS 0.003 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00292 (11611) covalent geometry : angle 0.47407 (15846) SS BOND : bond 0.00082 ( 4) SS BOND : angle 1.95977 ( 8) hydrogen bonds : bond 0.03127 ( 551) hydrogen bonds : angle 4.16813 ( 1620) link_BETA1-4 : bond 0.00648 ( 6) link_BETA1-4 : angle 1.95728 ( 18) link_NAG-ASN : bond 0.00189 ( 5) link_NAG-ASN : angle 1.85969 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.335 Fit side-chains REVERT: C 198 ARG cc_start: 0.6849 (tpp-160) cc_final: 0.5168 (ttp80) REVERT: C 294 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7628 (tm-30) REVERT: C 297 ARG cc_start: 0.6965 (mtp85) cc_final: 0.6466 (mtm-85) REVERT: A 339 GLU cc_start: 0.6612 (tp30) cc_final: 0.6309 (mm-30) REVERT: A 380 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6902 (ttp) REVERT: B 47 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8391 (mt) REVERT: B 104 ASP cc_start: 0.6817 (t0) cc_final: 0.6587 (m-30) REVERT: B 185 GLU cc_start: 0.8292 (tp30) cc_final: 0.7941 (tp30) REVERT: B 190 ARG cc_start: 0.7977 (mmp80) cc_final: 0.7525 (mmp-170) REVERT: B 380 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7906 (tpp) REVERT: D 112 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: D 316 LEU cc_start: 0.7642 (pp) cc_final: 0.7324 (mt) REVERT: D 380 MET cc_start: 0.7313 (tmm) cc_final: 0.7028 (ttt) outliers start: 40 outliers final: 30 residues processed: 188 average time/residue: 0.0891 time to fit residues: 24.5897 Evaluate side-chains 187 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 79 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110112 restraints weight = 17379.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111132 restraints weight = 15102.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112267 restraints weight = 12758.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112521 restraints weight = 9955.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112628 restraints weight = 9176.561| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11626 Z= 0.164 Angle : 0.528 9.825 15887 Z= 0.273 Chirality : 0.042 0.206 1856 Planarity : 0.003 0.046 2039 Dihedral : 5.593 55.977 1826 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.91 % Allowed : 17.78 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.22), residues: 1488 helix: 1.82 (0.21), residues: 596 sheet: -0.85 (0.32), residues: 264 loop : -0.94 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 300 TYR 0.022 0.002 TYR A 177 PHE 0.011 0.001 PHE C 296 TRP 0.047 0.002 TRP C 323 HIS 0.005 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00384 (11611) covalent geometry : angle 0.51938 (15846) SS BOND : bond 0.00065 ( 4) SS BOND : angle 2.00317 ( 8) hydrogen bonds : bond 0.03406 ( 551) hydrogen bonds : angle 4.27229 ( 1620) link_BETA1-4 : bond 0.00647 ( 6) link_BETA1-4 : angle 1.87808 ( 18) link_NAG-ASN : bond 0.00236 ( 5) link_NAG-ASN : angle 2.08678 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.329 Fit side-chains REVERT: C 47 ILE cc_start: 0.8192 (mm) cc_final: 0.7516 (tt) REVERT: C 198 ARG cc_start: 0.6848 (tpp-160) cc_final: 0.5151 (ttp80) REVERT: C 297 ARG cc_start: 0.7034 (mtp85) cc_final: 0.6538 (mtm-85) REVERT: A 274 HIS cc_start: 0.5485 (OUTLIER) cc_final: 0.4745 (t-170) REVERT: A 329 ILE cc_start: 0.8766 (mm) cc_final: 0.8250 (mp) REVERT: A 339 GLU cc_start: 0.6636 (tp30) cc_final: 0.6278 (mm-30) REVERT: A 373 TYR cc_start: 0.7783 (p90) cc_final: 0.7357 (p90) REVERT: A 380 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6966 (ttp) REVERT: B 47 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8437 (mt) REVERT: B 300 ARG cc_start: 0.7549 (ttp-110) cc_final: 0.7329 (ttp80) REVERT: B 360 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8906 (mp) REVERT: B 380 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7973 (tpp) REVERT: D 112 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: D 316 LEU cc_start: 0.7706 (pp) cc_final: 0.7364 (mt) outliers start: 44 outliers final: 28 residues processed: 180 average time/residue: 0.0909 time to fit residues: 23.8666 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 : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 81 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 121 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.134029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109717 restraints weight = 17272.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111347 restraints weight = 14515.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112046 restraints weight = 10775.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112437 restraints weight = 9326.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112655 restraints weight = 8773.105| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11626 Z= 0.138 Angle : 0.509 10.092 15887 Z= 0.264 Chirality : 0.042 0.203 1856 Planarity : 0.003 0.045 2039 Dihedral : 5.530 55.969 1826 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.56 % Allowed : 17.96 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.23), residues: 1488 helix: 1.86 (0.21), residues: 596 sheet: -0.88 (0.32), residues: 264 loop : -0.91 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 300 TYR 0.018 0.001 TYR C 373 PHE 0.009 0.001 PHE D 36 TRP 0.034 0.002 TRP C 323 HIS 0.004 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00323 (11611) covalent geometry : angle 0.49968 (15846) SS BOND : bond 0.00273 ( 4) SS BOND : angle 1.94438 ( 8) hydrogen bonds : bond 0.03234 ( 551) hydrogen bonds : angle 4.21762 ( 1620) link_BETA1-4 : bond 0.00673 ( 6) link_BETA1-4 : angle 1.85239 ( 18) link_NAG-ASN : bond 0.00185 ( 5) link_NAG-ASN : angle 2.01700 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.291 Fit side-chains REVERT: C 117 LEU cc_start: 0.8255 (tp) cc_final: 0.7765 (tt) REVERT: C 198 ARG cc_start: 0.6929 (tpp-160) cc_final: 0.5230 (ttp80) REVERT: C 250 TYR cc_start: 0.5947 (m-80) cc_final: 0.5694 (m-80) REVERT: C 297 ARG cc_start: 0.6974 (mtp85) cc_final: 0.6500 (mtm-85) REVERT: A 329 ILE cc_start: 0.8747 (mm) cc_final: 0.8230 (mp) REVERT: A 339 GLU cc_start: 0.6624 (tp30) cc_final: 0.6285 (mm-30) REVERT: A 373 TYR cc_start: 0.7745 (p90) cc_final: 0.7315 (p90) REVERT: A 380 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.6983 (ttt) REVERT: B 47 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8450 (mt) REVERT: B 360 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8882 (mp) REVERT: B 380 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7960 (tpp) REVERT: D 39 SER cc_start: 0.5286 (OUTLIER) cc_final: 0.4681 (p) REVERT: D 112 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8214 (mt0) REVERT: D 316 LEU cc_start: 0.7752 (pp) cc_final: 0.7375 (mt) REVERT: D 380 MET cc_start: 0.7451 (tmm) cc_final: 0.7141 (ttt) outliers start: 40 outliers final: 29 residues processed: 173 average time/residue: 0.0832 time to fit residues: 21.3497 Evaluate side-chains 174 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 13 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110155 restraints weight = 17234.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111362 restraints weight = 14578.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112119 restraints weight = 11190.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112603 restraints weight = 9429.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112792 restraints weight = 8930.156| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11626 Z= 0.126 Angle : 0.507 9.770 15887 Z= 0.263 Chirality : 0.042 0.199 1856 Planarity : 0.003 0.045 2039 Dihedral : 5.496 55.717 1826 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.11 % Allowed : 18.84 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.23), residues: 1488 helix: 1.92 (0.21), residues: 596 sheet: -0.88 (0.31), residues: 272 loop : -0.85 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 300 TYR 0.019 0.001 TYR C 373 PHE 0.009 0.001 PHE D 36 TRP 0.035 0.002 TRP C 323 HIS 0.004 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00297 (11611) covalent geometry : angle 0.49873 (15846) SS BOND : bond 0.00209 ( 4) SS BOND : angle 1.99879 ( 8) hydrogen bonds : bond 0.03168 ( 551) hydrogen bonds : angle 4.16874 ( 1620) link_BETA1-4 : bond 0.00665 ( 6) link_BETA1-4 : angle 1.82559 ( 18) link_NAG-ASN : bond 0.00175 ( 5) link_NAG-ASN : angle 1.94962 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.398 Fit side-chains REVERT: C 117 LEU cc_start: 0.8221 (tp) cc_final: 0.7732 (tt) REVERT: C 198 ARG cc_start: 0.6897 (tpp-160) cc_final: 0.5214 (ttp80) REVERT: C 250 TYR cc_start: 0.5677 (m-80) cc_final: 0.5453 (m-80) REVERT: C 297 ARG cc_start: 0.6999 (mtp85) cc_final: 0.6508 (mtm-85) REVERT: A 329 ILE cc_start: 0.8735 (mm) cc_final: 0.8241 (mp) REVERT: A 339 GLU cc_start: 0.6609 (tp30) cc_final: 0.6291 (mm-30) REVERT: A 380 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6975 (ttt) REVERT: B 47 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8386 (mt) REVERT: B 104 ASP cc_start: 0.6945 (t0) cc_final: 0.6743 (m-30) REVERT: B 300 ARG cc_start: 0.7561 (ttp-110) cc_final: 0.7356 (ttp80) REVERT: B 360 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8871 (mp) REVERT: B 380 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7954 (tpp) REVERT: D 112 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: D 316 LEU cc_start: 0.7747 (pp) cc_final: 0.7378 (mt) REVERT: D 380 MET cc_start: 0.7537 (tmm) cc_final: 0.7189 (ttt) outliers start: 35 outliers final: 29 residues processed: 172 average time/residue: 0.0939 time to fit residues: 23.8057 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 : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 336 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 0.0070 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110755 restraints weight = 17433.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111890 restraints weight = 15210.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112828 restraints weight = 11615.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113507 restraints weight = 9407.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113659 restraints weight = 8562.810| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11626 Z= 0.108 Angle : 0.496 10.001 15887 Z= 0.257 Chirality : 0.041 0.195 1856 Planarity : 0.003 0.044 2039 Dihedral : 5.429 55.209 1826 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.67 % Allowed : 19.29 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.23), residues: 1488 helix: 1.99 (0.22), residues: 596 sheet: -0.83 (0.31), residues: 272 loop : -0.77 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 300 TYR 0.026 0.001 TYR A 177 PHE 0.012 0.001 PHE D 36 TRP 0.033 0.001 TRP C 323 HIS 0.005 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00252 (11611) covalent geometry : angle 0.48751 (15846) SS BOND : bond 0.00128 ( 4) SS BOND : angle 2.06684 ( 8) hydrogen bonds : bond 0.03019 ( 551) hydrogen bonds : angle 4.10186 ( 1620) link_BETA1-4 : bond 0.00667 ( 6) link_BETA1-4 : angle 1.79852 ( 18) link_NAG-ASN : bond 0.00167 ( 5) link_NAG-ASN : angle 1.84382 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: C 117 LEU cc_start: 0.8152 (tp) cc_final: 0.7630 (tt) REVERT: C 198 ARG cc_start: 0.6887 (tpp-160) cc_final: 0.5233 (ttp80) REVERT: C 297 ARG cc_start: 0.6976 (mtp85) cc_final: 0.6488 (mtm-85) REVERT: A 380 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6886 (ttp) REVERT: B 47 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8415 (mt) REVERT: B 360 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8858 (mp) REVERT: B 380 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7931 (tpp) REVERT: D 112 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: D 316 LEU cc_start: 0.7720 (pp) cc_final: 0.7340 (mt) REVERT: D 380 MET cc_start: 0.7466 (tmm) cc_final: 0.7174 (ttt) outliers start: 30 outliers final: 24 residues processed: 169 average time/residue: 0.0878 time to fit residues: 21.9610 Evaluate side-chains 173 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 112 GLN 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 275 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.0770 chunk 46 optimal weight: 0.0470 chunk 26 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 109 optimal weight: 0.0980 chunk 56 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 141 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112495 restraints weight = 17379.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113587 restraints weight = 14620.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114377 restraints weight = 11356.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114842 restraints weight = 9634.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115091 restraints weight = 8944.173| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11626 Z= 0.092 Angle : 0.482 10.872 15887 Z= 0.250 Chirality : 0.041 0.187 1856 Planarity : 0.003 0.041 2039 Dihedral : 5.320 54.181 1826 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.67 % Allowed : 19.11 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.23), residues: 1488 helix: 2.17 (0.22), residues: 596 sheet: -0.69 (0.32), residues: 272 loop : -0.72 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.021 0.001 TYR C 373 PHE 0.013 0.001 PHE D 36 TRP 0.034 0.002 TRP C 323 HIS 0.004 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00211 (11611) covalent geometry : angle 0.47476 (15846) SS BOND : bond 0.00072 ( 4) SS BOND : angle 1.82145 ( 8) hydrogen bonds : bond 0.02844 ( 551) hydrogen bonds : angle 3.99116 ( 1620) link_BETA1-4 : bond 0.00628 ( 6) link_BETA1-4 : angle 1.77384 ( 18) link_NAG-ASN : bond 0.00176 ( 5) link_NAG-ASN : angle 1.66164 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1592.26 seconds wall clock time: 28 minutes 14.91 seconds (1694.91 seconds total)