Starting phenix.real_space_refine on Tue Jun 17 12:55:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b68_44249/06_2025/9b68_44249.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b68_44249/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b68_44249/06_2025/9b68_44249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b68_44249/06_2025/9b68_44249.map" model { file = "/net/cci-nas-00/data/ceres_data/9b68_44249/06_2025/9b68_44249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b68_44249/06_2025/9b68_44249.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 6, 'GLU:plan': 9, 'ARG:plan': 11, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2774 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 13, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2814 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 146 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 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: {'GLN:plan1': 1, 'GLU:plan': 9, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 2} 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: 7.27, per 1000 atoms: 0.64 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: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 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: 1.73 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: 3.57 Time building geometry restraints manager: 3.15 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: 16.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.930 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.560 ------------------------------------------------------------------------------- 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 : 6.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (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 TRP 0.040 0.002 TRP C 323 HIS 0.007 0.001 HIS C 46 PHE 0.041 0.001 PHE B 56 TYR 0.023 0.001 TYR B 26 ARG 0.004 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 5) link_NAG-ASN : angle 2.20380 ( 15) link_BETA1-4 : bond 0.00667 ( 6) link_BETA1-4 : angle 2.07215 ( 18) hydrogen bonds : bond 0.10636 ( 551) hydrogen bonds : angle 5.72060 ( 1620) SS BOND : bond 0.00236 ( 4) SS BOND : angle 2.16269 ( 8) covalent geometry : bond 0.00327 (11611) covalent geometry : angle 0.60898 (15846) *********************** 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 : 1.093 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: 0.2584 time to fit residues: 58.6839 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 : 1.189 ------------------------------------------------------------------------------- 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 124 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.136147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111993 restraints weight = 17070.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112771 restraints weight = 15284.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113990 restraints weight = 13141.182| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11626 Z= 0.164 Angle : 0.524 7.605 15887 Z= 0.272 Chirality : 0.042 0.198 1856 Planarity : 0.004 0.046 2039 Dihedral : 8.392 69.059 1826 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.87 % Allowed : 16.80 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1488 helix: 1.72 (0.21), residues: 596 sheet: -0.78 (0.34), residues: 244 loop : -1.19 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 323 HIS 0.005 0.001 HIS C 46 PHE 0.010 0.001 PHE B 41 TYR 0.016 0.002 TYR B 286 ARG 0.007 0.001 ARG C 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 5) link_NAG-ASN : angle 2.10278 ( 15) link_BETA1-4 : bond 0.00712 ( 6) link_BETA1-4 : angle 2.47880 ( 18) hydrogen bonds : bond 0.03606 ( 551) hydrogen bonds : angle 4.61443 ( 1620) SS BOND : bond 0.00175 ( 4) SS BOND : angle 1.80706 ( 8) covalent geometry : bond 0.00382 (11611) covalent geometry : angle 0.51219 (15846) *********************** 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: 21 poor density : 164 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 117 LEU cc_start: 0.8366 (tp) cc_final: 0.7809 (tt) REVERT: C 329 ILE cc_start: 0.9228 (mm) cc_final: 0.8775 (mm) REVERT: B 234 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8212 (mtmm) REVERT: D 316 LEU cc_start: 0.7525 (pp) cc_final: 0.7227 (mt) outliers start: 21 outliers final: 15 residues processed: 178 average time/residue: 0.2519 time to fit residues: 64.8297 Evaluate side-chains 165 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 140 optimal weight: 0.0170 chunk 73 optimal weight: 8.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.137177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112877 restraints weight = 17326.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113386 restraints weight = 15215.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114625 restraints weight = 13885.694| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11626 Z= 0.115 Angle : 0.485 7.298 15887 Z= 0.251 Chirality : 0.041 0.203 1856 Planarity : 0.003 0.045 2039 Dihedral : 6.829 54.929 1826 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.58 % Allowed : 16.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1488 helix: 1.72 (0.21), residues: 604 sheet: -0.82 (0.34), residues: 244 loop : -1.10 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 323 HIS 0.006 0.001 HIS C 46 PHE 0.008 0.001 PHE D 36 TYR 0.018 0.001 TYR C 373 ARG 0.005 0.000 ARG C 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 5) link_NAG-ASN : angle 2.01361 ( 15) link_BETA1-4 : bond 0.00682 ( 6) link_BETA1-4 : angle 2.41524 ( 18) hydrogen bonds : bond 0.03255 ( 551) hydrogen bonds : angle 4.41000 ( 1620) SS BOND : bond 0.00339 ( 4) SS BOND : angle 1.89097 ( 8) covalent geometry : bond 0.00262 (11611) covalent geometry : angle 0.47261 (15846) *********************** 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 184 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.910 Fit side-chains revert: symmetry clash REVERT: C 117 LEU cc_start: 0.8243 (tp) cc_final: 0.7681 (tt) REVERT: C 297 ARG cc_start: 0.6936 (mtp85) cc_final: 0.6428 (mtm-85) REVERT: A 329 ILE cc_start: 0.8800 (mm) cc_final: 0.8249 (mp) REVERT: A 339 GLU cc_start: 0.6820 (tp30) cc_final: 0.6405 (mm-30) REVERT: A 380 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6887 (ttp) REVERT: D 316 LEU cc_start: 0.7528 (pp) cc_final: 0.7154 (mt) outliers start: 29 outliers final: 20 residues processed: 176 average time/residue: 0.2939 time to fit residues: 75.6147 Evaluate side-chains 155 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 C residue 336 VAL 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 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 256 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 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 64 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 100 optimal weight: 0.0570 chunk 75 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.142135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119777 restraints weight = 16738.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119438 restraints weight = 13329.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119948 restraints weight = 12004.357| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1400 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= 0.116 Angle : 0.480 9.535 15887 Z= 0.249 Chirality : 0.041 0.202 1856 Planarity : 0.003 0.044 2039 Dihedral : 5.909 54.930 1826 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.11 % Allowed : 16.44 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1488 helix: 1.81 (0.21), residues: 604 sheet: -0.80 (0.33), residues: 244 loop : -1.07 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 323 HIS 0.006 0.001 HIS C 46 PHE 0.008 0.001 PHE D 36 TYR 0.017 0.001 TYR C 373 ARG 0.004 0.000 ARG B 300 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 5) link_NAG-ASN : angle 1.92457 ( 15) link_BETA1-4 : bond 0.00675 ( 6) link_BETA1-4 : angle 2.29490 ( 18) hydrogen bonds : bond 0.03155 ( 551) hydrogen bonds : angle 4.28717 ( 1620) SS BOND : bond 0.00094 ( 4) SS BOND : angle 1.96551 ( 8) covalent geometry : bond 0.00267 (11611) covalent geometry : angle 0.46874 (15846) *********************** 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 186 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.936 Fit side-chains REVERT: C 297 ARG cc_start: 0.6932 (mtp85) cc_final: 0.6416 (mtm-85) REVERT: A 266 GLU cc_start: 0.7030 (pm20) cc_final: 0.6754 (pt0) REVERT: A 339 GLU cc_start: 0.6805 (tp30) cc_final: 0.6416 (mm-30) REVERT: A 380 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.6894 (ttp) REVERT: B 104 ASP cc_start: 0.6909 (t70) cc_final: 0.6663 (m-30) REVERT: B 300 ARG cc_start: 0.7704 (ttp-110) cc_final: 0.7467 (ttp80) REVERT: B 380 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7877 (tpp) REVERT: D 316 LEU cc_start: 0.7583 (pp) cc_final: 0.7209 (mt) outliers start: 35 outliers final: 25 residues processed: 175 average time/residue: 0.2750 time to fit residues: 70.9812 Evaluate side-chains 173 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 2.416 ------------------------------------------------------------------------------- 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 C residue 336 VAL 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 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 88 PHE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 234 LYS 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 103 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.135336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110759 restraints weight = 17162.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111759 restraints weight = 14304.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112157 restraints weight = 12346.098| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1657 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= 0.141 Angle : 0.500 10.156 15887 Z= 0.258 Chirality : 0.042 0.207 1856 Planarity : 0.003 0.044 2039 Dihedral : 5.621 55.410 1826 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.91 % Allowed : 16.71 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1488 helix: 1.82 (0.21), residues: 596 sheet: -0.91 (0.33), residues: 244 loop : -1.00 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 323 HIS 0.006 0.001 HIS C 46 PHE 0.018 0.001 PHE A 56 TYR 0.018 0.001 TYR C 373 ARG 0.006 0.000 ARG C 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 5) link_NAG-ASN : angle 1.99995 ( 15) link_BETA1-4 : bond 0.00672 ( 6) link_BETA1-4 : angle 2.07317 ( 18) hydrogen bonds : bond 0.03307 ( 551) hydrogen bonds : angle 4.28214 ( 1620) SS BOND : bond 0.00068 ( 4) SS BOND : angle 2.10129 ( 8) covalent geometry : bond 0.00328 (11611) covalent geometry : angle 0.48978 (15846) *********************** 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 195 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.235 Fit side-chains REVERT: C 198 ARG cc_start: 0.6849 (tpp-160) cc_final: 0.5129 (ttp80) REVERT: C 297 ARG cc_start: 0.6921 (mtp85) cc_final: 0.6360 (mtm-85) REVERT: A 339 GLU cc_start: 0.6736 (tp30) cc_final: 0.6370 (mm-30) REVERT: A 380 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6946 (ttp) REVERT: B 47 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8415 (mt) REVERT: B 95 SER cc_start: 0.8913 (m) cc_final: 0.8697 (t) REVERT: B 104 ASP cc_start: 0.6910 (t0) cc_final: 0.6637 (m-30) REVERT: B 185 GLU cc_start: 0.8310 (tp30) cc_final: 0.7980 (tp30) REVERT: B 190 ARG cc_start: 0.8032 (mmp80) cc_final: 0.7615 (mmp-170) REVERT: B 300 ARG cc_start: 0.7676 (ttp-110) cc_final: 0.7465 (ttp80) REVERT: B 360 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8866 (mp) REVERT: B 380 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7934 (tpp) REVERT: D 112 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8332 (mt0) REVERT: D 316 LEU cc_start: 0.7650 (pp) cc_final: 0.7263 (mt) outliers start: 44 outliers final: 34 residues processed: 181 average time/residue: 0.2484 time to fit residues: 64.2184 Evaluate side-chains 186 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 C residue 354 ILE 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 248 VAL 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 135 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108224 restraints weight = 17490.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109289 restraints weight = 15182.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110052 restraints weight = 11612.590| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1951 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= 0.157 Angle : 0.511 10.416 15887 Z= 0.265 Chirality : 0.042 0.204 1856 Planarity : 0.003 0.044 2039 Dihedral : 5.636 56.026 1826 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.09 % Allowed : 17.16 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1488 helix: 1.75 (0.21), residues: 596 sheet: -0.92 (0.32), residues: 264 loop : -0.98 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 323 HIS 0.004 0.001 HIS B 46 PHE 0.012 0.001 PHE A 56 TYR 0.017 0.001 TYR C 373 ARG 0.004 0.000 ARG C 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 5) link_NAG-ASN : angle 2.09178 ( 15) link_BETA1-4 : bond 0.00695 ( 6) link_BETA1-4 : angle 1.96038 ( 18) hydrogen bonds : bond 0.03352 ( 551) hydrogen bonds : angle 4.29701 ( 1620) SS BOND : bond 0.00065 ( 4) SS BOND : angle 1.99961 ( 8) covalent geometry : bond 0.00367 (11611) covalent geometry : angle 0.50107 (15846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 1.224 Fit side-chains REVERT: C 198 ARG cc_start: 0.6851 (tpp-160) cc_final: 0.5174 (ttp80) REVERT: C 297 ARG cc_start: 0.6998 (mtp85) cc_final: 0.6450 (mtm-85) REVERT: A 106 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.8033 (t) REVERT: A 329 ILE cc_start: 0.8794 (mm) cc_final: 0.8270 (mp) REVERT: A 339 GLU cc_start: 0.6704 (tp30) cc_final: 0.6279 (mm-30) REVERT: A 380 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.6994 (ttt) REVERT: B 47 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8479 (mt) REVERT: B 95 SER cc_start: 0.8904 (m) cc_final: 0.8695 (t) REVERT: B 104 ASP cc_start: 0.6989 (t0) cc_final: 0.6705 (m-30) REVERT: B 360 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8897 (mp) REVERT: B 380 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8009 (tpp) REVERT: D 39 SER cc_start: 0.5089 (OUTLIER) cc_final: 0.4406 (p) REVERT: D 316 LEU cc_start: 0.7740 (pp) cc_final: 0.7359 (mt) outliers start: 46 outliers final: 33 residues processed: 177 average time/residue: 0.2271 time to fit residues: 58.6240 Evaluate side-chains 185 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 C residue 354 ILE 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 106 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 248 VAL 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 12 ILE 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 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 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 41 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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** D 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108352 restraints weight = 17597.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109418 restraints weight = 14863.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110777 restraints weight = 11619.362| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2110 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= 0.147 Angle : 0.509 10.179 15887 Z= 0.264 Chirality : 0.042 0.203 1856 Planarity : 0.003 0.046 2039 Dihedral : 5.581 56.101 1826 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.18 % Allowed : 17.87 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1488 helix: 1.70 (0.21), residues: 604 sheet: -0.92 (0.32), residues: 264 loop : -0.98 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 323 HIS 0.004 0.001 HIS B 46 PHE 0.011 0.001 PHE A 56 TYR 0.018 0.001 TYR C 373 ARG 0.004 0.000 ARG C 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 5) link_NAG-ASN : angle 2.08350 ( 15) link_BETA1-4 : bond 0.00666 ( 6) link_BETA1-4 : angle 1.91050 ( 18) hydrogen bonds : bond 0.03295 ( 551) hydrogen bonds : angle 4.27279 ( 1620) SS BOND : bond 0.00087 ( 4) SS BOND : angle 2.02061 ( 8) covalent geometry : bond 0.00343 (11611) covalent geometry : angle 0.49915 (15846) *********************** 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 190 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 1.787 Fit side-chains REVERT: C 117 LEU cc_start: 0.8301 (tp) cc_final: 0.7798 (tt) REVERT: C 198 ARG cc_start: 0.6913 (tpp-160) cc_final: 0.5185 (ttp80) REVERT: C 297 ARG cc_start: 0.7028 (mtp85) cc_final: 0.6497 (mtm-85) REVERT: A 266 GLU cc_start: 0.7034 (pm20) cc_final: 0.6806 (pt0) REVERT: A 274 HIS cc_start: 0.5573 (OUTLIER) cc_final: 0.4847 (t-170) REVERT: A 329 ILE cc_start: 0.8750 (mm) cc_final: 0.8236 (mp) REVERT: A 339 GLU cc_start: 0.6634 (tp30) cc_final: 0.6226 (mm-30) REVERT: A 373 TYR cc_start: 0.7747 (p90) cc_final: 0.7314 (p90) REVERT: A 380 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.6977 (ttt) REVERT: B 47 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8488 (mt) REVERT: B 104 ASP cc_start: 0.6985 (t0) cc_final: 0.6690 (m-30) REVERT: B 300 ARG cc_start: 0.7513 (ttp80) cc_final: 0.7079 (ptm160) REVERT: B 380 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7971 (tpp) REVERT: D 39 SER cc_start: 0.5111 (OUTLIER) cc_final: 0.4571 (p) REVERT: D 112 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: D 316 LEU cc_start: 0.7753 (pp) cc_final: 0.7373 (mt) REVERT: D 380 MET cc_start: 0.7419 (tmm) cc_final: 0.7145 (ttt) outliers start: 47 outliers final: 33 residues processed: 177 average time/residue: 0.2948 time to fit residues: 77.4970 Evaluate side-chains 183 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 274 HIS 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 29 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 109 optimal weight: 0.0570 chunk 102 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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** D 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110039 restraints weight = 17416.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111643 restraints weight = 14319.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112772 restraints weight = 11176.479| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2175 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= 0.102 Angle : 0.480 10.238 15887 Z= 0.248 Chirality : 0.041 0.197 1856 Planarity : 0.003 0.046 2039 Dihedral : 5.439 55.323 1826 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.93 % Allowed : 19.56 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.23), residues: 1488 helix: 1.96 (0.22), residues: 596 sheet: -0.92 (0.31), residues: 272 loop : -0.88 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 323 HIS 0.004 0.001 HIS B 46 PHE 0.010 0.001 PHE D 36 TYR 0.019 0.001 TYR C 373 ARG 0.005 0.000 ARG A 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 1.89819 ( 15) link_BETA1-4 : bond 0.00649 ( 6) link_BETA1-4 : angle 1.86282 ( 18) hydrogen bonds : bond 0.03014 ( 551) hydrogen bonds : angle 4.15331 ( 1620) SS BOND : bond 0.00083 ( 4) SS BOND : angle 1.91459 ( 8) covalent geometry : bond 0.00234 (11611) covalent geometry : angle 0.47100 (15846) *********************** 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 185 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 2.147 Fit side-chains REVERT: C 117 LEU cc_start: 0.8169 (tp) cc_final: 0.7709 (tt) REVERT: C 198 ARG cc_start: 0.6883 (tpp-160) cc_final: 0.5197 (ttp80) REVERT: C 297 ARG cc_start: 0.7009 (mtp85) cc_final: 0.6523 (mtm-85) REVERT: A 274 HIS cc_start: 0.5682 (OUTLIER) cc_final: 0.4999 (t-170) REVERT: A 329 ILE cc_start: 0.8739 (mm) cc_final: 0.8227 (mp) REVERT: A 339 GLU cc_start: 0.6561 (tp30) cc_final: 0.6188 (mm-30) REVERT: A 380 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6918 (ttp) REVERT: B 47 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8394 (mt) REVERT: B 300 ARG cc_start: 0.7454 (ttp80) cc_final: 0.6889 (ptm160) REVERT: B 360 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8835 (mp) REVERT: B 380 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7943 (tpp) REVERT: D 112 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8176 (mt0) REVERT: D 316 LEU cc_start: 0.7754 (pp) cc_final: 0.7365 (mt) REVERT: D 380 MET cc_start: 0.7449 (tmm) cc_final: 0.7145 (ttt) outliers start: 33 outliers final: 24 residues processed: 172 average time/residue: 0.2970 time to fit residues: 74.3858 Evaluate side-chains 177 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 274 HIS 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 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 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 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 15 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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** D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107323 restraints weight = 17566.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108425 restraints weight = 14915.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109839 restraints weight = 11524.382| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2342 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= 0.172 Angle : 0.528 9.983 15887 Z= 0.274 Chirality : 0.043 0.201 1856 Planarity : 0.003 0.050 2039 Dihedral : 5.611 56.209 1826 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.11 % Allowed : 19.64 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1488 helix: 1.78 (0.21), residues: 596 sheet: -0.98 (0.31), residues: 264 loop : -0.90 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 323 HIS 0.007 0.001 HIS A 46 PHE 0.011 0.001 PHE A 56 TYR 0.018 0.002 TYR B 286 ARG 0.004 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 5) link_NAG-ASN : angle 2.11139 ( 15) link_BETA1-4 : bond 0.00626 ( 6) link_BETA1-4 : angle 1.82144 ( 18) hydrogen bonds : bond 0.03385 ( 551) hydrogen bonds : angle 4.28632 ( 1620) SS BOND : bond 0.00107 ( 4) SS BOND : angle 2.28062 ( 8) covalent geometry : bond 0.00407 (11611) covalent geometry : angle 0.51831 (15846) *********************** 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 172 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.276 Fit side-chains REVERT: C 198 ARG cc_start: 0.6894 (tpp-160) cc_final: 0.5172 (ttp80) REVERT: C 297 ARG cc_start: 0.7025 (mtp85) cc_final: 0.6510 (mtm-85) REVERT: A 274 HIS cc_start: 0.5733 (OUTLIER) cc_final: 0.5076 (t70) REVERT: A 329 ILE cc_start: 0.8722 (mm) cc_final: 0.8227 (mp) REVERT: A 339 GLU cc_start: 0.6653 (tp30) cc_final: 0.6266 (mm-30) REVERT: A 380 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7056 (ttt) REVERT: B 47 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8495 (mt) REVERT: B 300 ARG cc_start: 0.7430 (ttp80) cc_final: 0.6884 (ptm160) REVERT: B 360 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8920 (mp) REVERT: B 380 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7983 (tpp) REVERT: D 112 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: D 316 LEU cc_start: 0.7821 (pp) cc_final: 0.7410 (mt) REVERT: D 380 MET cc_start: 0.7650 (tmm) cc_final: 0.7308 (ttt) outliers start: 35 outliers final: 27 residues processed: 161 average time/residue: 0.2709 time to fit residues: 62.8121 Evaluate side-chains 170 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 274 HIS 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 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 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 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 109 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** D 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107558 restraints weight = 17411.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108770 restraints weight = 14718.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110004 restraints weight = 11482.297| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11626 Z= 0.145 Angle : 0.524 10.050 15887 Z= 0.272 Chirality : 0.042 0.200 1856 Planarity : 0.003 0.052 2039 Dihedral : 5.586 56.420 1826 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.84 % Allowed : 20.09 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1488 helix: 1.74 (0.21), residues: 604 sheet: -1.01 (0.32), residues: 244 loop : -0.93 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 323 HIS 0.005 0.001 HIS A 46 PHE 0.009 0.001 PHE A 56 TYR 0.018 0.001 TYR C 373 ARG 0.004 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 5) link_NAG-ASN : angle 2.03443 ( 15) link_BETA1-4 : bond 0.00657 ( 6) link_BETA1-4 : angle 1.80785 ( 18) hydrogen bonds : bond 0.03247 ( 551) hydrogen bonds : angle 4.23583 ( 1620) SS BOND : bond 0.00218 ( 4) SS BOND : angle 2.27561 ( 8) covalent geometry : bond 0.00341 (11611) covalent geometry : angle 0.51458 (15846) ********************** 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 165 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.226 Fit side-chains REVERT: C 117 LEU cc_start: 0.8331 (tp) cc_final: 0.7861 (tt) REVERT: C 198 ARG cc_start: 0.6865 (tpp-160) cc_final: 0.5148 (ttp80) REVERT: C 297 ARG cc_start: 0.7029 (mtp85) cc_final: 0.6499 (mtm-85) REVERT: A 274 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.5086 (t70) REVERT: A 329 ILE cc_start: 0.8709 (mm) cc_final: 0.8210 (mp) REVERT: A 339 GLU cc_start: 0.6591 (tp30) cc_final: 0.6240 (mm-30) REVERT: A 380 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7020 (ttt) REVERT: B 47 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8460 (mt) REVERT: B 300 ARG cc_start: 0.7450 (ttp80) cc_final: 0.6896 (ptm160) REVERT: B 360 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8876 (mp) REVERT: B 380 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7973 (tpp) REVERT: D 112 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8239 (mt0) REVERT: D 316 LEU cc_start: 0.7758 (pp) cc_final: 0.7357 (mt) REVERT: D 380 MET cc_start: 0.7641 (tmm) cc_final: 0.7340 (ttt) outliers start: 32 outliers final: 25 residues processed: 155 average time/residue: 0.2231 time to fit residues: 50.7809 Evaluate side-chains 163 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 274 HIS 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 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 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 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 111 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** B 219 HIS D 46 HIS ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108660 restraints weight = 17302.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109073 restraints weight = 16294.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110059 restraints weight = 13648.870| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11626 Z= 0.221 Angle : 0.583 9.815 15887 Z= 0.304 Chirality : 0.044 0.206 1856 Planarity : 0.004 0.055 2039 Dihedral : 5.873 57.663 1826 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.20 % Allowed : 19.91 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1488 helix: 1.56 (0.21), residues: 596 sheet: -1.18 (0.32), residues: 244 loop : -0.99 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 323 HIS 0.006 0.002 HIS A 46 PHE 0.011 0.002 PHE B 76 TYR 0.023 0.002 TYR B 286 ARG 0.004 0.001 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 5) link_NAG-ASN : angle 2.38759 ( 15) link_BETA1-4 : bond 0.00704 ( 6) link_BETA1-4 : angle 1.81869 ( 18) hydrogen bonds : bond 0.03686 ( 551) hydrogen bonds : angle 4.45200 ( 1620) SS BOND : bond 0.00321 ( 4) SS BOND : angle 2.46363 ( 8) covalent geometry : bond 0.00520 (11611) covalent geometry : angle 0.57341 (15846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4335.49 seconds wall clock time: 80 minutes 18.32 seconds (4818.32 seconds total)