Starting phenix.real_space_refine on Sat Aug 23 21:07:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2z_42938/08_2025/8v2z_42938.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2z_42938/08_2025/8v2z_42938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v2z_42938/08_2025/8v2z_42938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2z_42938/08_2025/8v2z_42938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v2z_42938/08_2025/8v2z_42938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2z_42938/08_2025/8v2z_42938.map" } resolution = 2.72 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= 0.003 sd= 0.036 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 10 5.49 5 Mg 5 5.21 5 S 110 5.16 5 C 9230 2.51 5 N 2455 2.21 5 O 2825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14635 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, '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: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, '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: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, '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: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, '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: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, '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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.21, per 1000 atoms: 0.22 Number of scatterers: 14635 At special positions: 0 Unit cell: (105.93, 77.04, 193.67, 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 110 16.00 P 10 15.00 Mg 5 11.99 O 2825 8.00 N 2455 7.00 C 9230 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: 0.91 Conformation dependent library (CDL) restraints added in 625.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 30 sheets defined 49.2% alpha, 17.0% 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 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.596A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.799A 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 removed outlier: 3.545A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for '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 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.594A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 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 289 through 295 Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.001A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.509A pdb=" N CYS A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.667A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.795A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.514A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.540A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for '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 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.652A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 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: 3.645A pdb=" N ARG B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.990A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.556A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.837A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.531A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.539A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.731A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.540A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.680A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 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 289 through 295 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.017A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.649A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.810A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.526A pdb=" N GLY D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) 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 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.651A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 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: 3.582A pdb=" N ARG D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.018A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 91 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.720A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.790A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.523A pdb=" N GLY E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) 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 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.599A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 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: 3.597A pdb=" N ARG E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.049A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.547A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N CYS A 10 " --> 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 176 through 178 removed outlier: 6.309A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.110A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (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: 6.568A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N CYS B 10 " --> 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 176 through 178 removed outlier: 6.344A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.127A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (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: 6.574A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N CYS C 10 " --> 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 176 through 178 removed outlier: 6.452A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 4.207A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (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: 6.520A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N CYS D 10 " --> 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: 6.388A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (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: 6.505A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N CYS E 10 " --> 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: 6.381A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 732 hydrogen bonds defined for protein. 1887 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: 2.28 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4707 1.34 - 1.46: 3390 1.46 - 1.58: 6662 1.58 - 1.70: 16 1.70 - 1.83: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.35e+00 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 20055 2.92 - 5.85: 215 5.85 - 8.77: 31 8.77 - 11.69: 5 11.69 - 14.62: 4 Bond angle restraints: 20310 Sorted by residual: angle pdb=" CA PRO C 367 " pdb=" N PRO C 367 " pdb=" CD PRO C 367 " ideal model delta sigma weight residual 112.00 99.68 12.32 1.40e+00 5.10e-01 7.75e+01 angle pdb=" CA PRO E 367 " pdb=" N PRO E 367 " pdb=" CD PRO E 367 " ideal model delta sigma weight residual 112.00 104.89 7.11 1.40e+00 5.10e-01 2.58e+01 angle pdb=" CB MET B 227 " pdb=" CG MET B 227 " pdb=" SD MET B 227 " ideal model delta sigma weight residual 112.70 127.32 -14.62 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CB GLN A 354 " pdb=" CG GLN A 354 " pdb=" CD GLN A 354 " ideal model delta sigma weight residual 112.60 120.56 -7.96 1.70e+00 3.46e-01 2.19e+01 angle pdb=" CA GLN A 354 " pdb=" CB GLN A 354 " pdb=" CG GLN A 354 " ideal model delta sigma weight residual 114.10 123.18 -9.08 2.00e+00 2.50e-01 2.06e+01 ... (remaining 20305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 8394 24.54 - 49.07: 545 49.07 - 73.61: 53 73.61 - 98.14: 3 98.14 - 122.68: 5 Dihedral angle restraints: 9000 sinusoidal: 3625 harmonic: 5375 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 177.32 122.68 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -173.21 113.21 1 2.00e+01 2.50e-03 3.35e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 -172.01 112.00 1 2.00e+01 2.50e-03 3.30e+01 ... (remaining 8997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1982 0.082 - 0.164: 260 0.164 - 0.247: 3 0.247 - 0.329: 3 0.329 - 0.411: 2 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CB ILE A 287 " pdb=" CA ILE A 287 " pdb=" CG1 ILE A 287 " pdb=" CG2 ILE A 287 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB ILE C 287 " pdb=" CA ILE C 287 " pdb=" CG1 ILE C 287 " pdb=" CG2 ILE C 287 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2247 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 366 " 0.133 5.00e-02 4.00e+02 1.91e-01 5.85e+01 pdb=" N PRO C 367 " -0.330 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 366 " 0.108 5.00e-02 4.00e+02 1.60e-01 4.12e+01 pdb=" N PRO E 367 " -0.277 5.00e-02 4.00e+02 pdb=" CA PRO E 367 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO E 367 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 366 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO D 367 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " -0.040 5.00e-02 4.00e+02 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 801 2.73 - 3.27: 13248 3.27 - 3.81: 24604 3.81 - 4.36: 31508 4.36 - 4.90: 52777 Nonbonded interactions: 122938 Sorted by model distance: nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.186 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.237 2.170 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.272 3.040 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.273 2.170 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.280 3.040 ... (remaining 122933 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 individual isotropic 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.900 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 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 : 0.005 0.116 14960 Z= 0.206 Angle : 0.777 14.616 20310 Z= 0.399 Chirality : 0.052 0.411 2250 Planarity : 0.008 0.191 2600 Dihedral : 15.424 122.676 5560 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.51 % Allowed : 17.52 % Favored : 81.97 % 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 aren not related in a simple way. whole: -1.04 (0.19), residues: 1835 helix: -1.57 (0.16), residues: 730 sheet: 0.41 (0.28), residues: 355 loop : -0.04 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 206 TYR 0.008 0.001 TYR C 362 PHE 0.022 0.002 PHE C 127 TRP 0.022 0.002 TRP C 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00471 (14960) covalent geometry : angle 0.77700 (20310) hydrogen bonds : bond 0.17217 ( 716) hydrogen bonds : angle 7.16647 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.394 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 0.7466 time to fit residues: 80.5532 Evaluate side-chains 95 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain D residue 260 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.046974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.037054 restraints weight = 42997.555| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 2.87 r_work: 0.2365 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14960 Z= 0.216 Angle : 0.615 7.152 20310 Z= 0.294 Chirality : 0.046 0.191 2250 Planarity : 0.005 0.118 2600 Dihedral : 7.739 101.789 2094 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.85 % Allowed : 14.97 % Favored : 83.18 % 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 aren not related in a simple way. whole: 0.16 (0.20), residues: 1835 helix: -0.05 (0.19), residues: 770 sheet: 0.52 (0.28), residues: 350 loop : 0.35 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.009 0.001 TYR B 188 PHE 0.011 0.001 PHE D 262 TRP 0.010 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00502 (14960) covalent geometry : angle 0.61474 (20310) hydrogen bonds : bond 0.03708 ( 716) hydrogen bonds : angle 4.97768 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.712 Fit side-chains REVERT: A 314 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: A 354 GLN cc_start: 0.8903 (pp30) cc_final: 0.8627 (pp30) REVERT: B 176 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: B 354 GLN cc_start: 0.8872 (pp30) cc_final: 0.8207 (pp30) REVERT: C 325 MET cc_start: 0.8643 (mmp) cc_final: 0.8329 (mmp) outliers start: 29 outliers final: 4 residues processed: 110 average time/residue: 0.7814 time to fit residues: 92.6621 Evaluate side-chains 97 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 168 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.046870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.036885 restraints weight = 43245.700| |-----------------------------------------------------------------------------| r_work (start): 0.2498 rms_B_bonded: 2.88 r_work: 0.2357 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14960 Z= 0.185 Angle : 0.580 7.221 20310 Z= 0.274 Chirality : 0.045 0.182 2250 Planarity : 0.004 0.088 2600 Dihedral : 7.331 96.668 2087 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.97 % Allowed : 14.78 % Favored : 83.25 % 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 aren not related in a simple way. whole: 0.84 (0.20), residues: 1835 helix: 0.60 (0.19), residues: 770 sheet: 0.97 (0.29), residues: 330 loop : 0.55 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 116 TYR 0.007 0.001 TYR B 188 PHE 0.008 0.001 PHE C 262 TRP 0.011 0.001 TRP B 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00432 (14960) covalent geometry : angle 0.57989 (20310) hydrogen bonds : bond 0.03157 ( 716) hydrogen bonds : angle 4.62863 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.536 Fit side-chains REVERT: A 314 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: A 354 GLN cc_start: 0.8919 (pp30) cc_final: 0.8629 (pp30) REVERT: A 355 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9163 (mtp) REVERT: B 176 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8450 (mtp) REVERT: B 314 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7695 (tp40) REVERT: B 354 GLN cc_start: 0.8860 (pp30) cc_final: 0.8257 (pp30) REVERT: C 6 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8878 (p) REVERT: C 325 MET cc_start: 0.8707 (mmp) cc_final: 0.8462 (mmp) REVERT: D 353 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8891 (mm-40) REVERT: D 354 GLN cc_start: 0.8538 (pp30) cc_final: 0.8178 (pp30) outliers start: 31 outliers final: 7 residues processed: 115 average time/residue: 0.8195 time to fit residues: 101.5988 Evaluate side-chains 105 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 0.0870 chunk 180 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.046793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.036877 restraints weight = 43090.468| |-----------------------------------------------------------------------------| r_work (start): 0.2497 rms_B_bonded: 2.86 r_work: 0.2356 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14960 Z= 0.178 Angle : 0.573 7.339 20310 Z= 0.269 Chirality : 0.045 0.179 2250 Planarity : 0.004 0.072 2600 Dihedral : 7.216 93.962 2087 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.10 % Allowed : 14.14 % Favored : 83.76 % 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 aren not related in a simple way. whole: 1.12 (0.21), residues: 1835 helix: 0.91 (0.20), residues: 770 sheet: 1.05 (0.29), residues: 330 loop : 0.64 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.006 0.001 TYR A 188 PHE 0.007 0.001 PHE C 255 TRP 0.011 0.001 TRP A 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00418 (14960) covalent geometry : angle 0.57288 (20310) hydrogen bonds : bond 0.02946 ( 716) hydrogen bonds : angle 4.48389 ( 1887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.634 Fit side-chains REVERT: A 314 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: A 354 GLN cc_start: 0.8879 (pp30) cc_final: 0.8628 (pp30) REVERT: A 355 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8989 (mtm) REVERT: B 95 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8268 (mtm110) REVERT: B 314 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7694 (tp40) REVERT: B 354 GLN cc_start: 0.8856 (pp30) cc_final: 0.8276 (pp30) REVERT: C 107 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8666 (tm-30) REVERT: C 246 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8430 (mt0) REVERT: C 325 MET cc_start: 0.8743 (mmp) cc_final: 0.8478 (mmp) REVERT: D 353 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8984 (mm110) REVERT: D 354 GLN cc_start: 0.8602 (pp30) cc_final: 0.8188 (pp30) REVERT: E 6 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8841 (t) outliers start: 33 outliers final: 8 residues processed: 116 average time/residue: 0.8132 time to fit residues: 101.7741 Evaluate side-chains 110 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 12 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.046798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.036866 restraints weight = 43169.399| |-----------------------------------------------------------------------------| r_work (start): 0.2495 rms_B_bonded: 2.87 r_work: 0.2354 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14960 Z= 0.171 Angle : 0.571 7.331 20310 Z= 0.267 Chirality : 0.045 0.178 2250 Planarity : 0.004 0.063 2600 Dihedral : 7.123 92.449 2087 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.97 % Allowed : 14.08 % Favored : 83.95 % 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 aren not related in a simple way. whole: 1.28 (0.21), residues: 1835 helix: 1.09 (0.20), residues: 770 sheet: 1.09 (0.29), residues: 330 loop : 0.69 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.005 0.001 TYR A 188 PHE 0.008 0.001 PHE E 127 TRP 0.011 0.001 TRP A 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00403 (14960) covalent geometry : angle 0.57067 (20310) hydrogen bonds : bond 0.02882 ( 716) hydrogen bonds : angle 4.42279 ( 1887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.605 Fit side-chains REVERT: A 314 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: A 354 GLN cc_start: 0.8859 (pp30) cc_final: 0.8553 (pp30) REVERT: A 355 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.9145 (mtp) REVERT: B 95 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8319 (mtm110) REVERT: B 314 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.7689 (tp40) REVERT: B 354 GLN cc_start: 0.8829 (pp30) cc_final: 0.8229 (pp30) REVERT: C 6 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8881 (p) REVERT: C 107 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8691 (tm-30) REVERT: C 246 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8455 (mt0) REVERT: C 325 MET cc_start: 0.8778 (mmp) cc_final: 0.8488 (mmp) REVERT: D 47 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7866 (pmm) REVERT: D 353 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8952 (mm110) REVERT: D 354 GLN cc_start: 0.8594 (pp30) cc_final: 0.8168 (pp30) REVERT: E 6 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8879 (t) REVERT: E 99 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8842 (pm20) outliers start: 31 outliers final: 9 residues processed: 114 average time/residue: 0.7849 time to fit residues: 96.5232 Evaluate side-chains 112 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 142 optimal weight: 4.9990 chunk 35 optimal weight: 0.0370 chunk 183 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 overall best weight: 2.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN B 162 ASN D 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.046629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.036697 restraints weight = 43203.026| |-----------------------------------------------------------------------------| r_work (start): 0.2491 rms_B_bonded: 2.86 r_work: 0.2350 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14960 Z= 0.171 Angle : 0.571 7.339 20310 Z= 0.266 Chirality : 0.045 0.177 2250 Planarity : 0.003 0.056 2600 Dihedral : 7.044 91.778 2087 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.85 % Allowed : 14.20 % Favored : 83.95 % 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 aren not related in a simple way. whole: 1.41 (0.20), residues: 1835 helix: 1.20 (0.20), residues: 770 sheet: 1.11 (0.29), residues: 330 loop : 0.78 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.005 0.001 TYR A 188 PHE 0.007 0.001 PHE E 127 TRP 0.011 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00404 (14960) covalent geometry : angle 0.57071 (20310) hydrogen bonds : bond 0.02852 ( 716) hydrogen bonds : angle 4.39524 ( 1887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.613 Fit side-chains REVERT: A 246 GLN cc_start: 0.8969 (mt0) cc_final: 0.8695 (mt0) REVERT: A 314 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: A 354 GLN cc_start: 0.8844 (pp30) cc_final: 0.8562 (pp30) REVERT: A 355 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9136 (mtp) REVERT: B 95 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8325 (mtm110) REVERT: B 176 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8325 (mtp) REVERT: B 314 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7691 (tp40) REVERT: B 354 GLN cc_start: 0.8809 (pp30) cc_final: 0.8241 (pp30) REVERT: C 107 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8767 (tm-30) REVERT: C 246 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8465 (mt0) REVERT: C 325 MET cc_start: 0.8795 (mmp) cc_final: 0.8591 (mmp) REVERT: D 353 GLN cc_start: 0.9249 (mm-40) cc_final: 0.9011 (mm110) REVERT: D 354 GLN cc_start: 0.8608 (pp30) cc_final: 0.8174 (pp30) REVERT: E 6 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8892 (t) outliers start: 29 outliers final: 11 residues processed: 113 average time/residue: 0.7235 time to fit residues: 88.5804 Evaluate side-chains 112 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 45 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 127 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 134 optimal weight: 0.0030 chunk 126 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.047418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.037511 restraints weight = 42725.143| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 2.86 r_work: 0.2376 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14960 Z= 0.120 Angle : 0.557 7.916 20310 Z= 0.257 Chirality : 0.044 0.164 2250 Planarity : 0.003 0.052 2600 Dihedral : 6.838 89.203 2087 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.85 % Allowed : 14.14 % Favored : 84.01 % 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 aren not related in a simple way. whole: 1.52 (0.20), residues: 1835 helix: 1.32 (0.20), residues: 770 sheet: 1.14 (0.29), residues: 330 loop : 0.82 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.005 0.001 TYR B 188 PHE 0.007 0.001 PHE D 127 TRP 0.011 0.001 TRP B 79 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00283 (14960) covalent geometry : angle 0.55702 (20310) hydrogen bonds : bond 0.02579 ( 716) hydrogen bonds : angle 4.33157 ( 1887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.635 Fit side-chains REVERT: A 246 GLN cc_start: 0.8980 (mt0) cc_final: 0.8686 (mt0) REVERT: A 354 GLN cc_start: 0.8823 (pp30) cc_final: 0.8559 (pp30) REVERT: A 355 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.9115 (mtp) REVERT: B 95 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8325 (mtm110) REVERT: B 176 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8318 (mtp) REVERT: B 314 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7661 (tp40) REVERT: B 354 GLN cc_start: 0.8787 (pp30) cc_final: 0.8238 (pp30) REVERT: C 325 MET cc_start: 0.8791 (mmp) cc_final: 0.8550 (mmp) REVERT: D 246 GLN cc_start: 0.8882 (mt0) cc_final: 0.8622 (mt0) REVERT: D 353 GLN cc_start: 0.9246 (mm-40) cc_final: 0.9022 (mm110) REVERT: D 354 GLN cc_start: 0.8619 (pp30) cc_final: 0.8381 (pp30) REVERT: E 99 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8826 (pm20) outliers start: 29 outliers final: 10 residues processed: 116 average time/residue: 0.8001 time to fit residues: 100.1035 Evaluate side-chains 110 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 178 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 102 optimal weight: 0.0980 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.047407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.037531 restraints weight = 42932.903| |-----------------------------------------------------------------------------| r_work (start): 0.2515 rms_B_bonded: 2.85 r_work: 0.2375 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14960 Z= 0.130 Angle : 0.557 8.373 20310 Z= 0.256 Chirality : 0.044 0.163 2250 Planarity : 0.003 0.048 2600 Dihedral : 6.652 88.240 2087 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.72 % Allowed : 14.59 % Favored : 83.69 % 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 aren not related in a simple way. whole: 1.59 (0.21), residues: 1835 helix: 1.38 (0.20), residues: 770 sheet: 1.16 (0.29), residues: 330 loop : 0.86 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 254 TYR 0.005 0.001 TYR B 188 PHE 0.007 0.001 PHE E 127 TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00307 (14960) covalent geometry : angle 0.55714 (20310) hydrogen bonds : bond 0.02600 ( 716) hydrogen bonds : angle 4.30135 ( 1887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.509 Fit side-chains REVERT: A 314 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: A 354 GLN cc_start: 0.8810 (pp30) cc_final: 0.8552 (pp30) REVERT: A 355 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.9105 (mtp) REVERT: B 95 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8297 (mtm110) REVERT: B 176 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8331 (mtp) REVERT: B 314 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7664 (tp40) REVERT: B 354 GLN cc_start: 0.8766 (pp30) cc_final: 0.8234 (pp30) REVERT: C 325 MET cc_start: 0.8864 (mmp) cc_final: 0.8603 (mmp) REVERT: D 246 GLN cc_start: 0.8896 (mt0) cc_final: 0.8634 (mt0) REVERT: D 314 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: D 353 GLN cc_start: 0.9254 (mm-40) cc_final: 0.9017 (mm110) REVERT: D 354 GLN cc_start: 0.8623 (pp30) cc_final: 0.8379 (pp30) REVERT: E 99 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8831 (pm20) outliers start: 27 outliers final: 13 residues processed: 116 average time/residue: 0.7655 time to fit residues: 95.7008 Evaluate side-chains 116 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 134 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.046562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.036644 restraints weight = 43516.845| |-----------------------------------------------------------------------------| r_work (start): 0.2491 rms_B_bonded: 2.87 r_work: 0.2350 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14960 Z= 0.188 Angle : 0.592 9.118 20310 Z= 0.276 Chirality : 0.045 0.175 2250 Planarity : 0.003 0.045 2600 Dihedral : 6.722 90.337 2087 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.66 % Allowed : 14.46 % Favored : 83.89 % 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 aren not related in a simple way. whole: 1.54 (0.21), residues: 1835 helix: 1.33 (0.20), residues: 770 sheet: 1.12 (0.29), residues: 330 loop : 0.83 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 254 TYR 0.008 0.001 TYR B 188 PHE 0.008 0.001 PHE E 127 TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00444 (14960) covalent geometry : angle 0.59191 (20310) hydrogen bonds : bond 0.02912 ( 716) hydrogen bonds : angle 4.36455 ( 1887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.426 Fit side-chains REVERT: A 314 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: A 354 GLN cc_start: 0.8836 (pp30) cc_final: 0.8581 (pp30) REVERT: A 355 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9115 (mtp) REVERT: B 95 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8327 (mtm110) REVERT: B 176 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8319 (mtp) REVERT: B 314 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7688 (tp40) REVERT: B 354 GLN cc_start: 0.8769 (pp30) cc_final: 0.8224 (pp30) REVERT: C 314 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7887 (tp40) REVERT: C 325 MET cc_start: 0.8888 (mmp) cc_final: 0.8624 (mmp) REVERT: D 314 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8093 (tp40) REVERT: D 353 GLN cc_start: 0.9262 (mm-40) cc_final: 0.9011 (mm110) REVERT: E 6 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.8887 (t) outliers start: 26 outliers final: 14 residues processed: 115 average time/residue: 0.8192 time to fit residues: 101.4912 Evaluate side-chains 116 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.046563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.036703 restraints weight = 43204.967| |-----------------------------------------------------------------------------| r_work (start): 0.2488 rms_B_bonded: 2.86 r_work: 0.2346 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14960 Z= 0.201 Angle : 0.595 10.012 20310 Z= 0.277 Chirality : 0.046 0.176 2250 Planarity : 0.003 0.044 2600 Dihedral : 6.735 91.130 2087 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.53 % Allowed : 14.59 % Favored : 83.89 % 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 aren not related in a simple way. whole: 1.53 (0.21), residues: 1835 helix: 1.34 (0.20), residues: 770 sheet: 1.11 (0.29), residues: 330 loop : 0.83 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 254 TYR 0.007 0.001 TYR B 188 PHE 0.008 0.001 PHE E 127 TRP 0.010 0.001 TRP B 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00473 (14960) covalent geometry : angle 0.59460 (20310) hydrogen bonds : bond 0.02938 ( 716) hydrogen bonds : angle 4.37376 ( 1887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.635 Fit side-chains REVERT: A 314 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: A 354 GLN cc_start: 0.8836 (pp30) cc_final: 0.8581 (pp30) REVERT: A 355 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9119 (mtp) REVERT: B 95 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8317 (mtm110) REVERT: B 176 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8337 (mtp) REVERT: B 314 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7706 (tp40) REVERT: B 354 GLN cc_start: 0.8774 (pp30) cc_final: 0.8224 (pp30) REVERT: C 314 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7882 (tp40) REVERT: C 325 MET cc_start: 0.8890 (mmp) cc_final: 0.8646 (mmp) REVERT: D 314 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8128 (tp40) REVERT: D 353 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8991 (mm110) REVERT: E 6 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8894 (t) outliers start: 24 outliers final: 14 residues processed: 114 average time/residue: 0.7090 time to fit residues: 87.5421 Evaluate side-chains 116 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 102 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.047431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.037594 restraints weight = 42638.354| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 2.85 r_work: 0.2373 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14960 Z= 0.130 Angle : 0.574 10.226 20310 Z= 0.265 Chirality : 0.044 0.165 2250 Planarity : 0.003 0.044 2600 Dihedral : 6.552 89.088 2087 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.53 % Allowed : 14.65 % Favored : 83.82 % 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 aren not related in a simple way. whole: 1.60 (0.21), residues: 1835 helix: 1.41 (0.20), residues: 770 sheet: 1.13 (0.29), residues: 330 loop : 0.85 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 372 TYR 0.005 0.001 TYR E 69 PHE 0.007 0.001 PHE D 127 TRP 0.011 0.001 TRP E 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00311 (14960) covalent geometry : angle 0.57371 (20310) hydrogen bonds : bond 0.02610 ( 716) hydrogen bonds : angle 4.30515 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3276.36 seconds wall clock time: 57 minutes 10.69 seconds (3430.69 seconds total)