Starting phenix.real_space_refine on Sat Sep 12 09:50:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5ood_3837/09_2026/5ood_3837.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ood_3837/09_2026/5ood_3837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5ood_3837/09_2026/5ood_3837.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5ood_3837/09_2026/5ood_3837.cif" model { file = "/net/cci-nas-00/data/ceres_data/5ood_3837/09_2026/5ood_3837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ood_3837/09_2026/5ood_3837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ood_3837/09_2026/5ood_3837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ood_3837/09_2026/5ood_3837.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9425 2.51 5 N 2495 2.21 5 O 2865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14910 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {' MG': 1, '9ZK': 2, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.40, per 1000 atoms: 0.23 Number of scatterers: 14910 At special positions: 0 Unit cell: (91.56, 94.83, 190.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 15 15.00 Mg 5 11.99 O 2865 8.00 N 2495 7.00 C 9425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 640.6 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 30 sheets defined 52.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.689A pdb=" N PHE A 90 " --> pdb=" O TRP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.391A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.689A pdb=" N PHE B 90 " --> pdb=" O TRP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.390A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.688A pdb=" N PHE C 90 " --> pdb=" O TRP C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.390A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 358 through 366 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.690A pdb=" N PHE D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.015A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.391A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 Processing helix chain 'D' and resid 358 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 91 removed outlier: 3.689A pdb=" N PHE E 90 " --> pdb=" O TRP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 230 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 4.390A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 356 Processing helix chain 'E' and resid 358 through 366 Processing helix chain 'E' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.217A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 5.784A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.217A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 5.784A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.217A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.785A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.216A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 5.784A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.217A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 5.784A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 750 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2460 1.28 - 1.41: 3850 1.41 - 1.54: 8730 1.54 - 1.68: 15 1.68 - 1.81: 185 Bond restraints: 15240 Sorted by residual: bond pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sigma weight residual 1.610 1.481 0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sigma weight residual 1.610 1.481 0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sigma weight residual 1.610 1.481 0.129 2.00e-02 2.50e+03 4.13e+01 bond pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sigma weight residual 1.610 1.482 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sigma weight residual 1.610 1.482 0.128 2.00e-02 2.50e+03 4.12e+01 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 18959 2.74 - 5.49: 1420 5.49 - 8.23: 226 8.23 - 10.97: 65 10.97 - 13.71: 20 Bond angle restraints: 20690 Sorted by residual: angle pdb=" C HIS C 101 " pdb=" N PRO C 102 " pdb=" CA PRO C 102 " ideal model delta sigma weight residual 120.03 128.55 -8.52 9.90e-01 1.02e+00 7.40e+01 angle pdb=" C HIS B 101 " pdb=" N PRO B 102 " pdb=" CA PRO B 102 " ideal model delta sigma weight residual 120.03 128.54 -8.51 9.90e-01 1.02e+00 7.39e+01 angle pdb=" C HIS A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 120.03 128.50 -8.47 9.90e-01 1.02e+00 7.31e+01 angle pdb=" C HIS D 101 " pdb=" N PRO D 102 " pdb=" CA PRO D 102 " ideal model delta sigma weight residual 120.03 128.49 -8.46 9.90e-01 1.02e+00 7.31e+01 angle pdb=" C HIS E 101 " pdb=" N PRO E 102 " pdb=" CA PRO E 102 " ideal model delta sigma weight residual 120.03 128.48 -8.45 9.90e-01 1.02e+00 7.29e+01 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 8895 33.06 - 66.11: 160 66.11 - 99.17: 95 99.17 - 132.23: 35 132.23 - 165.28: 55 Dihedral angle restraints: 9240 sinusoidal: 3880 harmonic: 5360 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.40 133.60 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.43 133.57 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.44 133.56 1 2.00e+01 2.50e-03 4.05e+01 ... (remaining 9237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1524 0.071 - 0.142: 650 0.142 - 0.213: 96 0.213 - 0.284: 5 0.284 - 0.355: 5 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C25 9ZK D 404 " pdb=" C26 9ZK D 404 " pdb=" C36 9ZK D 404 " pdb=" N23 9ZK D 404 " both_signs ideal model delta sigma weight residual False 2.15 2.50 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C25 9ZK A 403 " pdb=" C26 9ZK A 403 " pdb=" C36 9ZK A 403 " pdb=" N23 9ZK A 403 " both_signs ideal model delta sigma weight residual False 2.15 2.50 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C25 9ZK A 405 " pdb=" C26 9ZK A 405 " pdb=" C36 9ZK A 405 " pdb=" N23 9ZK A 405 " both_signs ideal model delta sigma weight residual False 2.15 2.50 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 2277 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " 0.095 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO C 164 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " -0.095 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO B 164 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " 0.095 5.00e-02 4.00e+02 1.44e-01 3.34e+01 pdb=" N PRO E 164 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " 0.073 5.00e-02 4.00e+02 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 123 2.58 - 3.16: 14112 3.16 - 3.74: 22926 3.74 - 4.32: 35604 4.32 - 4.90: 54919 Nonbonded interactions: 127684 Sorted by model distance: nonbonded pdb=" O3 PO4 A 402 " pdb="MG MG A 404 " model vdw 1.995 2.170 nonbonded pdb=" O3 PO4 B 402 " pdb="MG MG B 403 " model vdw 1.995 2.170 nonbonded pdb=" O3 PO4 C 402 " pdb="MG MG C 403 " model vdw 1.995 2.170 nonbonded pdb=" O3 PO4 E 402 " pdb="MG MG E 403 " model vdw 1.996 2.170 nonbonded pdb=" O3 PO4 D 402 " pdb="MG MG D 403 " model vdw 1.997 2.170 ... (remaining 127679 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 5 through 402) selection = (chain 'B' and resid 5 through 402) selection = (chain 'C' and resid 5 through 402) selection = (chain 'D' and resid 5 through 402) selection = (chain 'E' and resid 5 through 402) } 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.170 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.017 0.129 15240 Z= 1.020 Angle : 1.689 13.713 20690 Z= 1.041 Chirality : 0.074 0.355 2280 Planarity : 0.017 0.145 2630 Dihedral : 23.090 165.281 5810 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 2.46 % Allowed : 5.52 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.19), residues: 1830 helix: -1.54 (0.16), residues: 725 sheet: -0.78 (0.31), residues: 225 loop : -0.69 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 256 TYR 0.029 0.006 TYR A 294 PHE 0.011 0.003 PHE B 90 TRP 0.027 0.006 TRP D 340 HIS 0.004 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.01705 / 1.02 (15240) covalent geometry : angle 1.68928 / 1.04 (20690) hydrogen bonds : bond 0.17104 / 11.39 ( 740) hydrogen bonds : angle 7.88416 / 5.58 ( 1845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 THR cc_start: 0.8897 (m) cc_final: 0.8642 (p) REVERT: A 291 LYS cc_start: 0.8911 (tttt) cc_final: 0.7833 (mptt) REVERT: A 349 LEU cc_start: 0.8276 (tp) cc_final: 0.7952 (mt) REVERT: B 66 THR cc_start: 0.9254 (m) cc_final: 0.8938 (p) REVERT: B 191 LYS cc_start: 0.8858 (tttt) cc_final: 0.8313 (ttpt) REVERT: B 215 LYS cc_start: 0.8369 (mttt) cc_final: 0.7914 (mtpt) REVERT: B 222 ASP cc_start: 0.7998 (t0) cc_final: 0.7723 (m-30) REVERT: B 239 SER cc_start: 0.8846 (t) cc_final: 0.8462 (p) REVERT: B 290 ARG cc_start: 0.8741 (mtm-85) cc_final: 0.8435 (mtt180) REVERT: B 291 LYS cc_start: 0.8685 (tttt) cc_final: 0.7909 (mttp) REVERT: B 314 GLN cc_start: 0.7470 (tp40) cc_final: 0.7167 (tp40) REVERT: B 340 TRP cc_start: 0.8261 (t60) cc_final: 0.7674 (t60) REVERT: C 78 ASN cc_start: 0.8432 (t0) cc_final: 0.8173 (t0) REVERT: C 87 HIS cc_start: 0.7909 (t70) cc_final: 0.7527 (t-170) REVERT: D 56 ASP cc_start: 0.7754 (m-30) cc_final: 0.7127 (t0) REVERT: D 78 ASN cc_start: 0.8371 (t0) cc_final: 0.7699 (t0) REVERT: D 214 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7882 (mt-10) REVERT: D 244 ASP cc_start: 0.7594 (p0) cc_final: 0.7374 (p0) REVERT: D 260 THR cc_start: 0.9256 (p) cc_final: 0.8194 (m) REVERT: D 283 MET cc_start: 0.8380 (mmp) cc_final: 0.7759 (ttm) REVERT: D 355 MET cc_start: 0.7844 (mmm) cc_final: 0.7406 (mmt) REVERT: D 358 THR cc_start: 0.8741 (m) cc_final: 0.8467 (p) REVERT: E 41 GLN cc_start: 0.7990 (mt0) cc_final: 0.7599 (mm-40) REVERT: E 43 VAL cc_start: 0.6549 (t) cc_final: 0.6224 (t) REVERT: E 61 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8142 (mmpt) REVERT: E 78 ASN cc_start: 0.8054 (t0) cc_final: 0.6945 (t0) REVERT: E 81 ASP cc_start: 0.8203 (m-30) cc_final: 0.7721 (m-30) REVERT: E 82 MET cc_start: 0.7751 (tpt) cc_final: 0.7423 (tpt) REVERT: E 84 LYS cc_start: 0.8400 (tptt) cc_final: 0.8163 (tttt) REVERT: E 115 ASN cc_start: 0.8737 (t0) cc_final: 0.8527 (t0) REVERT: E 276 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8676 (mt-10) REVERT: E 284 LYS cc_start: 0.7773 (mtpp) cc_final: 0.7526 (tmtt) REVERT: E 304 THR cc_start: 0.8582 (p) cc_final: 0.8265 (m) REVERT: E 336 LYS cc_start: 0.8173 (ptmt) cc_final: 0.7712 (ttpt) outliers start: 0 outliers final: 0 residues processed: 631 average time/residue: 0.1252 time to fit residues: 113.0784 Evaluate side-chains 313 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 HIS ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN C 115 ASN C 246 GLN D 87 HIS D 115 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN E 88 HIS E 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110267 restraints weight = 26749.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113339 restraints weight = 13127.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115383 restraints weight = 7860.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116757 restraints weight = 5391.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117583 restraints weight = 4071.876| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15240 Z= 0.151 Angle : 0.772 9.192 20690 Z= 0.384 Chirality : 0.047 0.218 2280 Planarity : 0.008 0.064 2630 Dihedral : 29.424 171.002 2330 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.32 % Favored : 95.36 % Rotamer: Outliers : 1.98 % Allowed : 10.67 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.20), residues: 1830 helix: -0.02 (0.18), residues: 800 sheet: -0.46 (0.27), residues: 295 loop : -0.35 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 147 TYR 0.020 0.001 TYR E 306 PHE 0.033 0.002 PHE C 352 TRP 0.027 0.002 TRP A 340 HIS 0.010 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (15240) covalent geometry : angle 0.77207 / 0.38 (20690) hydrogen bonds : bond 0.03734 / 2.47 ( 740) hydrogen bonds : angle 5.57653 / 3.99 ( 1845) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 409 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8937 (t0) cc_final: 0.7863 (t0) REVERT: A 81 ASP cc_start: 0.8291 (m-30) cc_final: 0.7771 (m-30) REVERT: A 206 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8102 (ttm170) REVERT: A 249 THR cc_start: 0.8902 (m) cc_final: 0.8346 (p) REVERT: A 259 GLU cc_start: 0.8027 (tp30) cc_final: 0.7711 (tp30) REVERT: A 291 LYS cc_start: 0.8699 (tttt) cc_final: 0.7860 (mptt) REVERT: A 314 GLN cc_start: 0.7938 (tt0) cc_final: 0.7600 (mt0) REVERT: A 340 TRP cc_start: 0.8735 (t60) cc_final: 0.7693 (t60) REVERT: A 344 SER cc_start: 0.8781 (m) cc_final: 0.8180 (p) REVERT: B 66 THR cc_start: 0.8991 (m) cc_final: 0.8694 (t) REVERT: B 191 LYS cc_start: 0.8854 (tttt) cc_final: 0.8296 (ttmt) REVERT: B 291 LYS cc_start: 0.8354 (tttt) cc_final: 0.7574 (mttt) REVERT: B 305 MET cc_start: 0.7735 (mtp) cc_final: 0.7459 (mtp) REVERT: B 314 GLN cc_start: 0.7388 (tp40) cc_final: 0.7065 (tp40) REVERT: B 325 MET cc_start: 0.5517 (mmt) cc_final: 0.5309 (mmt) REVERT: B 337 TYR cc_start: 0.6785 (m-10) cc_final: 0.6569 (m-10) REVERT: C 68 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8615 (mmmm) REVERT: C 87 HIS cc_start: 0.7593 (t70) cc_final: 0.7021 (t-90) REVERT: C 283 MET cc_start: 0.8868 (mmm) cc_final: 0.8642 (mmm) REVERT: D 56 ASP cc_start: 0.7476 (m-30) cc_final: 0.7099 (t0) REVERT: D 59 GLN cc_start: 0.8871 (mm110) cc_final: 0.8670 (mm110) REVERT: D 78 ASN cc_start: 0.7591 (t0) cc_final: 0.7341 (t0) REVERT: D 191 LYS cc_start: 0.8887 (tttt) cc_final: 0.8429 (mtpp) REVERT: D 201 VAL cc_start: 0.8724 (m) cc_final: 0.8516 (p) REVERT: D 283 MET cc_start: 0.7928 (mmp) cc_final: 0.7393 (ttm) REVERT: D 360 GLN cc_start: 0.8139 (pp30) cc_final: 0.6971 (pp30) REVERT: E 84 LYS cc_start: 0.8224 (tptt) cc_final: 0.7747 (tptt) REVERT: E 205 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7659 (mt-10) REVERT: E 292 ASP cc_start: 0.8149 (t70) cc_final: 0.7557 (t70) outliers start: 31 outliers final: 19 residues processed: 431 average time/residue: 0.1065 time to fit residues: 69.6009 Evaluate side-chains 322 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 303 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 130 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 61 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS B 92 ASN B 225 ASN C 87 HIS C 115 ASN C 128 ASN C 225 ASN D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 101 HIS E 246 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101801 restraints weight = 27479.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104739 restraints weight = 13687.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106671 restraints weight = 8270.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107966 restraints weight = 5719.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108755 restraints weight = 4366.092| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15240 Z= 0.204 Angle : 0.754 7.371 20690 Z= 0.372 Chirality : 0.048 0.238 2280 Planarity : 0.006 0.060 2630 Dihedral : 28.199 178.986 2330 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.97 % Favored : 94.75 % Rotamer: Outliers : 2.94 % Allowed : 12.78 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1830 helix: 0.40 (0.18), residues: 780 sheet: -0.62 (0.28), residues: 305 loop : 0.39 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 335 TYR 0.023 0.002 TYR A 133 PHE 0.029 0.002 PHE C 352 TRP 0.022 0.002 TRP B 79 HIS 0.006 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (15240) covalent geometry : angle 0.75434 / 0.37 (20690) hydrogen bonds : bond 0.03892 / 2.56 ( 740) hydrogen bonds : angle 5.29412 / 3.81 ( 1845) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 324 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8848 (t0) cc_final: 0.8389 (t0) REVERT: A 117 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 120 THR cc_start: 0.9494 (OUTLIER) cc_final: 0.9085 (p) REVERT: A 249 THR cc_start: 0.8963 (m) cc_final: 0.8536 (p) REVERT: A 291 LYS cc_start: 0.8951 (tttt) cc_final: 0.7890 (mptt) REVERT: A 314 GLN cc_start: 0.7995 (tt0) cc_final: 0.7519 (mt0) REVERT: A 340 TRP cc_start: 0.8855 (t60) cc_final: 0.8066 (t60) REVERT: A 344 SER cc_start: 0.9085 (m) cc_final: 0.8628 (p) REVERT: B 291 LYS cc_start: 0.8421 (tttt) cc_final: 0.7581 (mttt) REVERT: B 314 GLN cc_start: 0.7580 (tp40) cc_final: 0.7152 (tp40) REVERT: C 68 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8672 (mmmm) REVERT: C 78 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8109 (t0) REVERT: C 87 HIS cc_start: 0.7467 (t-90) cc_final: 0.7083 (t-90) REVERT: C 191 LYS cc_start: 0.8877 (tttt) cc_final: 0.8577 (tttp) REVERT: C 238 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8536 (mmmm) REVERT: C 325 MET cc_start: 0.8759 (mmm) cc_final: 0.8529 (mmm) REVERT: D 56 ASP cc_start: 0.7498 (m-30) cc_final: 0.7035 (t0) REVERT: D 191 LYS cc_start: 0.8786 (tttt) cc_final: 0.8581 (ttpp) REVERT: D 226 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8202 (mm-30) REVERT: D 283 MET cc_start: 0.8176 (mmp) cc_final: 0.7436 (ttm) REVERT: D 305 MET cc_start: 0.8185 (mtp) cc_final: 0.7958 (mtt) REVERT: E 79 TRP cc_start: 0.8610 (m100) cc_final: 0.8363 (m100) REVERT: E 84 LYS cc_start: 0.8097 (tptt) cc_final: 0.7586 (tptt) REVERT: E 119 MET cc_start: 0.8285 (ttp) cc_final: 0.7953 (ttm) REVERT: E 225 ASN cc_start: 0.8195 (m-40) cc_final: 0.7865 (t0) REVERT: E 292 ASP cc_start: 0.8282 (t70) cc_final: 0.7726 (t0) outliers start: 46 outliers final: 29 residues processed: 355 average time/residue: 0.1008 time to fit residues: 56.0608 Evaluate side-chains 309 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 278 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 202 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 120 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 155 optimal weight: 0.0470 chunk 97 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 87 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN E 88 HIS ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102781 restraints weight = 27153.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105711 restraints weight = 13588.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107665 restraints weight = 8211.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108933 restraints weight = 5684.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109842 restraints weight = 4352.732| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15240 Z= 0.162 Angle : 0.698 7.207 20690 Z= 0.339 Chirality : 0.047 0.214 2280 Planarity : 0.005 0.052 2630 Dihedral : 27.367 176.883 2330 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.03 % Favored : 94.75 % Rotamer: Outliers : 3.58 % Allowed : 13.67 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1830 helix: 0.39 (0.18), residues: 795 sheet: -0.57 (0.27), residues: 305 loop : 0.44 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 335 TYR 0.014 0.001 TYR A 133 PHE 0.033 0.002 PHE C 352 TRP 0.017 0.002 TRP A 340 HIS 0.020 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (15240) covalent geometry : angle 0.69822 / 0.34 (20690) hydrogen bonds : bond 0.03387 / 2.22 ( 740) hydrogen bonds : angle 5.09810 / 3.67 ( 1845) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 302 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8787 (t0) cc_final: 0.8029 (t0) REVERT: A 81 ASP cc_start: 0.8202 (m-30) cc_final: 0.7622 (m-30) REVERT: A 117 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 226 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 249 THR cc_start: 0.8945 (m) cc_final: 0.8581 (p) REVERT: A 291 LYS cc_start: 0.8936 (tttt) cc_final: 0.7887 (mptt) REVERT: A 314 GLN cc_start: 0.8059 (tt0) cc_final: 0.7648 (mt0) REVERT: B 191 LYS cc_start: 0.8831 (tttt) cc_final: 0.8184 (ttmt) REVERT: B 207 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7401 (tm-30) REVERT: B 291 LYS cc_start: 0.8408 (tttt) cc_final: 0.7628 (mttp) REVERT: B 314 GLN cc_start: 0.7549 (tp40) cc_final: 0.7270 (tp40) REVERT: C 44 MET cc_start: 0.6518 (mmm) cc_final: 0.6251 (mmm) REVERT: C 68 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8681 (mmmm) REVERT: C 87 HIS cc_start: 0.7447 (t70) cc_final: 0.7034 (t-90) REVERT: C 132 MET cc_start: 0.8431 (ppp) cc_final: 0.8202 (ppp) REVERT: C 191 LYS cc_start: 0.8902 (tttt) cc_final: 0.8626 (tttp) REVERT: C 201 VAL cc_start: 0.8752 (m) cc_final: 0.8528 (p) REVERT: C 325 MET cc_start: 0.8878 (mmm) cc_final: 0.8619 (mmm) REVERT: D 56 ASP cc_start: 0.7436 (m-30) cc_final: 0.7026 (t0) REVERT: D 283 MET cc_start: 0.8173 (mmp) cc_final: 0.7297 (ttm) REVERT: D 305 MET cc_start: 0.8240 (mtp) cc_final: 0.8017 (mtt) REVERT: D 325 MET cc_start: 0.8255 (mmm) cc_final: 0.7814 (mmp) REVERT: E 21 PHE cc_start: 0.7700 (m-80) cc_final: 0.7215 (m-80) REVERT: E 84 LYS cc_start: 0.8107 (tptt) cc_final: 0.7574 (tptt) REVERT: E 119 MET cc_start: 0.8250 (ttp) cc_final: 0.8033 (ttp) REVERT: E 211 ASP cc_start: 0.8547 (t70) cc_final: 0.8296 (t70) REVERT: E 225 ASN cc_start: 0.8083 (m-40) cc_final: 0.7844 (t0) REVERT: E 280 ASN cc_start: 0.8888 (m110) cc_final: 0.8640 (m110) REVERT: E 292 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7844 (t70) outliers start: 56 outliers final: 39 residues processed: 336 average time/residue: 0.0992 time to fit residues: 52.1530 Evaluate side-chains 308 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 357 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN E 12 ASN E 88 HIS E 101 HIS E 263 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.097739 restraints weight = 27789.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100565 restraints weight = 13947.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.102405 restraints weight = 8491.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103540 restraints weight = 5941.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104419 restraints weight = 4659.790| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 15240 Z= 0.267 Angle : 0.780 8.265 20690 Z= 0.382 Chirality : 0.050 0.262 2280 Planarity : 0.006 0.054 2630 Dihedral : 27.644 176.205 2330 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 4.22 % Allowed : 14.44 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1830 helix: 0.50 (0.19), residues: 755 sheet: -0.69 (0.28), residues: 305 loop : 0.29 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 335 TYR 0.014 0.002 TYR A 133 PHE 0.024 0.003 PHE B 90 TRP 0.018 0.002 TRP A 340 HIS 0.008 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.27 (15240) covalent geometry : angle 0.77970 / 0.38 (20690) hydrogen bonds : bond 0.04028 / 2.64 ( 740) hydrogen bonds : angle 5.37229 / 3.87 ( 1845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 274 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8737 (t0) cc_final: 0.8411 (t0) REVERT: A 91 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6957 (t80) REVERT: A 117 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 249 THR cc_start: 0.8972 (m) cc_final: 0.8593 (p) REVERT: A 291 LYS cc_start: 0.8976 (tttt) cc_final: 0.7817 (mptt) REVERT: A 314 GLN cc_start: 0.8123 (tt0) cc_final: 0.7716 (mt0) REVERT: A 356 TRP cc_start: 0.8834 (m100) cc_final: 0.8613 (m100) REVERT: B 257 CYS cc_start: 0.8626 (t) cc_final: 0.7892 (p) REVERT: B 290 ARG cc_start: 0.8885 (mtm-85) cc_final: 0.8268 (mtt180) REVERT: B 291 LYS cc_start: 0.8542 (tttt) cc_final: 0.7552 (mttt) REVERT: B 314 GLN cc_start: 0.7755 (tp40) cc_final: 0.7520 (tp40) REVERT: C 87 HIS cc_start: 0.7489 (t70) cc_final: 0.7060 (t-90) REVERT: C 284 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7431 (mmtp) REVERT: C 325 MET cc_start: 0.9063 (mmm) cc_final: 0.8673 (mmm) REVERT: D 56 ASP cc_start: 0.7308 (m-30) cc_final: 0.6874 (t0) REVERT: D 191 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7926 (mtpp) REVERT: D 283 MET cc_start: 0.8256 (mmp) cc_final: 0.7337 (ttm) REVERT: D 297 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8485 (m-40) REVERT: E 12 ASN cc_start: 0.8584 (p0) cc_final: 0.8352 (p0) REVERT: E 28 ARG cc_start: 0.6423 (mtm180) cc_final: 0.6212 (mtm180) REVERT: E 84 LYS cc_start: 0.8230 (tptt) cc_final: 0.7632 (tptt) REVERT: E 124 PHE cc_start: 0.7586 (m-10) cc_final: 0.7334 (m-10) REVERT: E 211 ASP cc_start: 0.8531 (t70) cc_final: 0.8284 (t70) REVERT: E 225 ASN cc_start: 0.8111 (m-40) cc_final: 0.7863 (t0) REVERT: E 280 ASN cc_start: 0.8896 (m110) cc_final: 0.8539 (m110) REVERT: E 292 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7930 (t0) outliers start: 66 outliers final: 44 residues processed: 320 average time/residue: 0.0987 time to fit residues: 48.7124 Evaluate side-chains 292 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 317 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 0.2980 chunk 117 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 155 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN E 101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.117455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103375 restraints weight = 27150.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106302 restraints weight = 13434.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108243 restraints weight = 8092.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109505 restraints weight = 5598.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110340 restraints weight = 4301.308| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15240 Z= 0.115 Angle : 0.657 7.423 20690 Z= 0.316 Chirality : 0.044 0.183 2280 Planarity : 0.005 0.047 2630 Dihedral : 26.909 174.361 2330 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.14 % Favored : 94.81 % Rotamer: Outliers : 2.81 % Allowed : 16.81 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1830 helix: 0.53 (0.19), residues: 785 sheet: -0.77 (0.27), residues: 310 loop : 0.61 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 116 TYR 0.012 0.001 TYR A 133 PHE 0.017 0.001 PHE C 31 TRP 0.016 0.002 TRP C 340 HIS 0.015 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (15240) covalent geometry : angle 0.65689 / 0.32 (20690) hydrogen bonds : bond 0.03076 / 2.03 ( 740) hydrogen bonds : angle 5.05325 / 3.63 ( 1845) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8586 (t0) cc_final: 0.7860 (t0) REVERT: A 81 ASP cc_start: 0.8081 (m-30) cc_final: 0.7785 (m-30) REVERT: A 117 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7559 (mt-10) REVERT: A 249 THR cc_start: 0.8906 (m) cc_final: 0.8612 (p) REVERT: A 291 LYS cc_start: 0.8898 (tttt) cc_final: 0.7805 (mptt) REVERT: A 314 GLN cc_start: 0.8053 (tt0) cc_final: 0.7634 (mt0) REVERT: A 336 LYS cc_start: 0.8256 (ptmt) cc_final: 0.7689 (pttp) REVERT: B 191 LYS cc_start: 0.8811 (tttt) cc_final: 0.8150 (ttmt) REVERT: B 207 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7226 (tm-30) REVERT: B 257 CYS cc_start: 0.8542 (t) cc_final: 0.7798 (p) REVERT: B 291 LYS cc_start: 0.8419 (tttt) cc_final: 0.7594 (mttt) REVERT: B 314 GLN cc_start: 0.7693 (tp40) cc_final: 0.7302 (tp40) REVERT: C 68 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8259 (mttt) REVERT: C 87 HIS cc_start: 0.7383 (t70) cc_final: 0.6985 (t70) REVERT: C 201 VAL cc_start: 0.8864 (m) cc_final: 0.8610 (p) REVERT: C 325 MET cc_start: 0.8902 (mmm) cc_final: 0.8583 (mmm) REVERT: D 56 ASP cc_start: 0.7091 (m-30) cc_final: 0.6759 (t0) REVERT: D 283 MET cc_start: 0.8156 (mmp) cc_final: 0.7424 (ttm) REVERT: E 84 LYS cc_start: 0.8180 (tptt) cc_final: 0.7567 (tptt) REVERT: E 125 GLU cc_start: 0.8424 (mp0) cc_final: 0.8152 (mp0) REVERT: E 211 ASP cc_start: 0.8558 (t70) cc_final: 0.8332 (t70) REVERT: E 292 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7946 (t70) REVERT: E 355 MET cc_start: 0.7218 (mmm) cc_final: 0.6996 (mmm) outliers start: 44 outliers final: 31 residues processed: 309 average time/residue: 0.1071 time to fit residues: 50.5924 Evaluate side-chains 285 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 7 optimal weight: 0.0470 chunk 154 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 123 optimal weight: 0.0270 chunk 160 optimal weight: 0.3980 chunk 104 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.8938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN C 115 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104420 restraints weight = 27033.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107371 restraints weight = 13463.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109247 restraints weight = 8130.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110561 restraints weight = 5667.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111338 restraints weight = 4324.316| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15240 Z= 0.115 Angle : 0.647 7.601 20690 Z= 0.310 Chirality : 0.045 0.246 2280 Planarity : 0.005 0.045 2630 Dihedral : 26.168 165.381 2330 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.97 % Favored : 94.92 % Rotamer: Outliers : 3.51 % Allowed : 17.25 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.20), residues: 1830 helix: 0.41 (0.19), residues: 810 sheet: -0.69 (0.27), residues: 300 loop : 0.76 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 28 TYR 0.012 0.001 TYR A 133 PHE 0.037 0.001 PHE C 352 TRP 0.021 0.002 TRP E 79 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (15240) covalent geometry : angle 0.64668 / 0.31 (20690) hydrogen bonds : bond 0.03036 / 2.01 ( 740) hydrogen bonds : angle 4.94801 / 3.55 ( 1845) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 274 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8555 (t0) cc_final: 0.7707 (t0) REVERT: A 81 ASP cc_start: 0.8174 (m-30) cc_final: 0.7693 (m-30) REVERT: A 117 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 291 LYS cc_start: 0.8874 (tttt) cc_final: 0.7915 (mptt) REVERT: A 336 LYS cc_start: 0.8267 (ptmt) cc_final: 0.7769 (pttp) REVERT: A 372 ARG cc_start: 0.7207 (mmt180) cc_final: 0.6656 (ptt180) REVERT: B 191 LYS cc_start: 0.8777 (tttt) cc_final: 0.8132 (ttmt) REVERT: B 257 CYS cc_start: 0.8539 (t) cc_final: 0.7856 (p) REVERT: B 291 LYS cc_start: 0.8433 (tttt) cc_final: 0.7444 (mttt) REVERT: C 44 MET cc_start: 0.5711 (mmm) cc_final: 0.5200 (mmm) REVERT: C 68 LYS cc_start: 0.8525 (mmmm) cc_final: 0.8212 (mttt) REVERT: C 87 HIS cc_start: 0.7429 (t70) cc_final: 0.7053 (t70) REVERT: C 132 MET cc_start: 0.8479 (ppp) cc_final: 0.7988 (ppp) REVERT: C 325 MET cc_start: 0.8936 (mmm) cc_final: 0.8666 (mmm) REVERT: D 56 ASP cc_start: 0.7020 (m-30) cc_final: 0.6752 (t0) REVERT: D 59 GLN cc_start: 0.9051 (mm110) cc_final: 0.8795 (tp40) REVERT: D 123 MET cc_start: 0.8714 (mmm) cc_final: 0.8408 (mmm) REVERT: D 283 MET cc_start: 0.8222 (mmp) cc_final: 0.7442 (ttm) REVERT: D 305 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.8025 (mtt) REVERT: E 84 LYS cc_start: 0.8191 (tptt) cc_final: 0.7584 (tptt) REVERT: E 124 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7086 (m-10) REVERT: E 169 TYR cc_start: 0.7616 (m-80) cc_final: 0.7391 (m-80) REVERT: E 217 CYS cc_start: 0.8940 (m) cc_final: 0.8551 (m) REVERT: E 292 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7521 (t70) REVERT: E 355 MET cc_start: 0.7244 (mmm) cc_final: 0.6983 (mmm) outliers start: 55 outliers final: 35 residues processed: 306 average time/residue: 0.1055 time to fit residues: 49.7851 Evaluate side-chains 284 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 169 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 41 GLN E 101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103178 restraints weight = 27352.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106084 restraints weight = 13685.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107987 restraints weight = 8310.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109279 restraints weight = 5765.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110067 restraints weight = 4410.377| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15240 Z= 0.145 Angle : 0.674 8.950 20690 Z= 0.324 Chirality : 0.046 0.225 2280 Planarity : 0.005 0.043 2630 Dihedral : 26.110 163.439 2330 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.75 % Rotamer: Outliers : 3.19 % Allowed : 18.27 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1830 helix: 0.63 (0.19), residues: 775 sheet: -0.65 (0.28), residues: 300 loop : 0.52 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 290 TYR 0.011 0.001 TYR A 133 PHE 0.026 0.002 PHE C 352 TRP 0.020 0.002 TRP E 79 HIS 0.008 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15240) covalent geometry : angle 0.67403 / 0.32 (20690) hydrogen bonds : bond 0.03164 / 2.09 ( 740) hydrogen bonds : angle 4.98335 / 3.58 ( 1845) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8568 (t0) cc_final: 0.7755 (t0) REVERT: A 81 ASP cc_start: 0.8253 (m-30) cc_final: 0.7729 (m-30) REVERT: A 117 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7530 (mt-10) REVERT: A 291 LYS cc_start: 0.8401 (tttt) cc_final: 0.7664 (mptt) REVERT: A 336 LYS cc_start: 0.8230 (ptmt) cc_final: 0.7724 (pttp) REVERT: A 372 ARG cc_start: 0.7199 (mmt180) cc_final: 0.6653 (ptt180) REVERT: B 191 LYS cc_start: 0.8789 (tttt) cc_final: 0.8169 (ttmt) REVERT: B 291 LYS cc_start: 0.8447 (tttt) cc_final: 0.7473 (mttt) REVERT: C 44 MET cc_start: 0.6142 (mmm) cc_final: 0.5647 (mmm) REVERT: C 68 LYS cc_start: 0.8544 (mmmm) cc_final: 0.8208 (mttt) REVERT: C 87 HIS cc_start: 0.7448 (t70) cc_final: 0.7135 (t70) REVERT: C 284 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7306 (mmtp) REVERT: C 325 MET cc_start: 0.8924 (mmm) cc_final: 0.8679 (mmm) REVERT: D 56 ASP cc_start: 0.7018 (m-30) cc_final: 0.6712 (t0) REVERT: D 191 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7908 (mtpp) REVERT: D 283 MET cc_start: 0.8184 (mmp) cc_final: 0.7397 (ttm) REVERT: E 21 PHE cc_start: 0.7461 (m-80) cc_final: 0.6992 (m-80) REVERT: E 84 LYS cc_start: 0.8204 (tptt) cc_final: 0.7601 (tptt) REVERT: E 124 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7105 (m-10) REVERT: E 125 GLU cc_start: 0.8457 (mp0) cc_final: 0.8190 (mp0) REVERT: E 211 ASP cc_start: 0.8438 (t70) cc_final: 0.8230 (t70) REVERT: E 214 GLU cc_start: 0.8504 (pt0) cc_final: 0.8299 (pt0) REVERT: E 252 ASN cc_start: 0.7915 (p0) cc_final: 0.7413 (m-40) REVERT: E 292 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7421 (t70) REVERT: E 355 MET cc_start: 0.7344 (mmm) cc_final: 0.7064 (mmm) outliers start: 50 outliers final: 40 residues processed: 286 average time/residue: 0.1051 time to fit residues: 46.5272 Evaluate side-chains 274 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 109 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN E 12 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.094249 restraints weight = 28455.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.096928 restraints weight = 14382.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098710 restraints weight = 8856.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099902 restraints weight = 6238.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100668 restraints weight = 4842.742| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.101 15240 Z= 0.400 Angle : 0.920 8.963 20690 Z= 0.457 Chirality : 0.055 0.306 2280 Planarity : 0.007 0.060 2630 Dihedral : 27.668 176.913 2330 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.17 % Favored : 93.66 % Rotamer: Outliers : 4.28 % Allowed : 17.51 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 1830 helix: 0.22 (0.18), residues: 760 sheet: -1.22 (0.29), residues: 270 loop : -0.02 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 183 TYR 0.017 0.002 TYR C 337 PHE 0.034 0.003 PHE B 90 TRP 0.018 0.003 TRP E 79 HIS 0.008 0.002 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00945 / 0.40 (15240) covalent geometry : angle 0.91968 / 0.46 (20690) hydrogen bonds : bond 0.04782 / 3.12 ( 740) hydrogen bonds : angle 5.70066 / 4.08 ( 1845) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 234 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8742 (t0) cc_final: 0.8482 (t0) REVERT: A 91 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6791 (t80) REVERT: A 117 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 291 LYS cc_start: 0.8905 (tttt) cc_final: 0.7922 (mptt) REVERT: A 325 MET cc_start: 0.7883 (tpp) cc_final: 0.7656 (tpt) REVERT: B 291 LYS cc_start: 0.8645 (tttt) cc_final: 0.7611 (mptt) REVERT: B 349 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7987 (mp) REVERT: C 87 HIS cc_start: 0.7558 (t70) cc_final: 0.7204 (t-90) REVERT: C 284 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7497 (mmtp) REVERT: C 325 MET cc_start: 0.9023 (mmm) cc_final: 0.8784 (mmm) REVERT: D 56 ASP cc_start: 0.7241 (m-30) cc_final: 0.6862 (t0) REVERT: D 191 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7964 (mtpp) REVERT: D 239 SER cc_start: 0.8722 (t) cc_final: 0.8210 (p) REVERT: D 283 MET cc_start: 0.8141 (mmp) cc_final: 0.7393 (ttm) REVERT: D 346 LEU cc_start: 0.9030 (tp) cc_final: 0.8779 (tp) REVERT: E 44 MET cc_start: 0.1422 (tpt) cc_final: 0.1163 (tpt) REVERT: E 84 LYS cc_start: 0.8203 (tptt) cc_final: 0.7623 (tptt) REVERT: E 124 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7229 (m-10) REVERT: E 217 CYS cc_start: 0.8730 (m) cc_final: 0.8476 (m) REVERT: E 292 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8079 (t70) REVERT: E 336 LYS cc_start: 0.8682 (pttm) cc_final: 0.7896 (mtpt) REVERT: E 355 MET cc_start: 0.7440 (mmm) cc_final: 0.7124 (mmm) outliers start: 67 outliers final: 50 residues processed: 280 average time/residue: 0.0991 time to fit residues: 43.5375 Evaluate side-chains 275 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 0.0010 chunk 96 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 88 HIS E 101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.095021 restraints weight = 28168.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097724 restraints weight = 14224.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.099487 restraints weight = 8696.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.100656 restraints weight = 6126.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101379 restraints weight = 4765.958| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.178 15240 Z= 0.307 Angle : 1.062 59.200 20690 Z= 0.560 Chirality : 0.054 0.718 2280 Planarity : 0.007 0.057 2630 Dihedral : 27.681 176.616 2330 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.07 % Favored : 93.77 % Rotamer: Outliers : 3.83 % Allowed : 18.27 % Favored : 77.89 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1830 helix: 0.21 (0.18), residues: 760 sheet: -1.26 (0.29), residues: 270 loop : -0.10 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 147 TYR 0.014 0.002 TYR C 337 PHE 0.042 0.003 PHE E 223 TRP 0.019 0.002 TRP E 79 HIS 0.008 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.31 (15240) covalent geometry : angle 1.06179 / 0.56 (20690) hydrogen bonds : bond 0.04620 / 3.02 ( 740) hydrogen bonds : angle 5.66683 / 4.05 ( 1845) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8663 (t0) cc_final: 0.8433 (t0) REVERT: A 91 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6852 (t80) REVERT: A 117 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7619 (mt-10) REVERT: A 291 LYS cc_start: 0.8928 (tttt) cc_final: 0.7907 (mptt) REVERT: A 325 MET cc_start: 0.7888 (tpp) cc_final: 0.7625 (tpt) REVERT: B 291 LYS cc_start: 0.8627 (tttt) cc_final: 0.7571 (mptt) REVERT: B 349 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7964 (mp) REVERT: C 87 HIS cc_start: 0.7575 (t70) cc_final: 0.7281 (t-90) REVERT: C 284 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7443 (mmtp) REVERT: C 325 MET cc_start: 0.9058 (mmm) cc_final: 0.8821 (mmm) REVERT: D 56 ASP cc_start: 0.7232 (m-30) cc_final: 0.6879 (t0) REVERT: D 191 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7879 (mtpp) REVERT: D 239 SER cc_start: 0.8730 (t) cc_final: 0.8216 (p) REVERT: D 283 MET cc_start: 0.8138 (mmp) cc_final: 0.7387 (ttm) REVERT: D 346 LEU cc_start: 0.8990 (tp) cc_final: 0.8730 (tp) REVERT: E 44 MET cc_start: 0.1355 (tpt) cc_final: 0.1130 (tpt) REVERT: E 84 LYS cc_start: 0.8214 (tptt) cc_final: 0.7625 (tptt) REVERT: E 124 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7229 (m-10) REVERT: E 217 CYS cc_start: 0.8760 (m) cc_final: 0.8493 (m) REVERT: E 292 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8059 (t70) REVERT: E 336 LYS cc_start: 0.8608 (pttm) cc_final: 0.7863 (mtpt) REVERT: E 355 MET cc_start: 0.7457 (mmm) cc_final: 0.7124 (mmm) outliers start: 60 outliers final: 50 residues processed: 264 average time/residue: 0.0993 time to fit residues: 40.9919 Evaluate side-chains 272 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 217 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 76 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 96 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 297 ASN E 12 ASN E 101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101302 restraints weight = 27364.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104157 restraints weight = 13616.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106038 restraints weight = 8248.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107259 restraints weight = 5726.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108055 restraints weight = 4399.078| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15240 Z= 0.137 Angle : 0.714 10.976 20690 Z= 0.348 Chirality : 0.046 0.211 2280 Planarity : 0.005 0.064 2630 Dihedral : 27.313 177.577 2330 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.14 % Favored : 94.64 % Rotamer: Outliers : 2.68 % Allowed : 19.23 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1830 helix: 0.45 (0.19), residues: 770 sheet: -1.14 (0.29), residues: 270 loop : 0.22 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 312 TYR 0.013 0.001 TYR A 133 PHE 0.022 0.001 PHE C 352 TRP 0.020 0.002 TRP C 340 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (15240) covalent geometry : angle 0.71369 / 0.35 (20690) hydrogen bonds : bond 0.03316 / 2.21 ( 740) hydrogen bonds : angle 5.25247 / 3.75 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.97 seconds wall clock time: 39 minutes 23.41 seconds (2363.41 seconds total)