Starting phenix.real_space_refine on Mon Jan 20 04:21:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2z_42938/01_2025/8v2z_42938.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2z_42938/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v2z_42938/01_2025/8v2z_42938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2z_42938/01_2025/8v2z_42938.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2z_42938/01_2025/8v2z_42938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2z_42938/01_2025/8v2z_42938.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 8.70, per 1000 atoms: 0.59 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: 3.67 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 2.42 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: 6.14 Time building geometry restraints manager: 4.19 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: 0.03 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: 1.090 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 35.390 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.380 ------------------------------------------------------------------------------- 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= 0.301 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.002 TRP C 79 HIS 0.003 0.001 HIS B 161 PHE 0.022 0.002 PHE C 127 TYR 0.008 0.001 TYR C 362 ARG 0.005 0.000 ARG A 206 *********************** 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 : 1.598 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 1.7062 time to fit residues: 184.8830 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 : 1.740 ------------------------------------------------------------------------------- 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 156 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.0670 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 overall best weight: 2.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 225 ASN B 41 GLN D 41 GLN D 225 ASN E 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.047095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.037158 restraints weight = 42797.014| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 2.87 r_work: 0.2364 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14960 Z= 0.312 Angle : 0.608 7.210 20310 Z= 0.289 Chirality : 0.045 0.190 2250 Planarity : 0.005 0.116 2600 Dihedral : 7.700 100.959 2094 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.91 % Allowed : 14.97 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1835 helix: 0.02 (0.19), residues: 770 sheet: 0.52 (0.28), residues: 350 loop : 0.36 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.011 0.001 PHE D 262 TYR 0.009 0.001 TYR B 188 ARG 0.003 0.000 ARG A 290 *********************** 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 121 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 1.640 Fit side-chains REVERT: A 314 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: A 354 GLN cc_start: 0.8905 (pp30) cc_final: 0.8643 (pp30) REVERT: B 176 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8443 (mtp) REVERT: B 354 GLN cc_start: 0.8867 (pp30) cc_final: 0.8200 (pp30) REVERT: C 325 MET cc_start: 0.8631 (mmp) cc_final: 0.8312 (mmp) outliers start: 30 outliers final: 4 residues processed: 111 average time/residue: 1.7373 time to fit residues: 207.8248 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 : 1.834 ------------------------------------------------------------------------------- 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 153 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.047406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.037461 restraints weight = 42701.401| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 2.86 r_work: 0.2375 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14960 Z= 0.233 Angle : 0.562 7.273 20310 Z= 0.265 Chirality : 0.044 0.173 2250 Planarity : 0.004 0.085 2600 Dihedral : 7.254 95.540 2087 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.53 % Allowed : 15.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1835 helix: 0.62 (0.19), residues: 770 sheet: 0.73 (0.28), residues: 355 loop : 0.58 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 PHE 0.007 0.001 PHE C 255 TYR 0.006 0.001 TYR B 188 ARG 0.002 0.000 ARG A 290 *********************** 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 119 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 1.603 Fit side-chains REVERT: A 314 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: A 354 GLN cc_start: 0.8918 (pp30) cc_final: 0.8648 (pp30) REVERT: B 314 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: B 354 GLN cc_start: 0.8864 (pp30) cc_final: 0.8261 (pp30) REVERT: C 325 MET cc_start: 0.8681 (mmp) cc_final: 0.8462 (mmp) REVERT: D 353 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8875 (mm-40) REVERT: D 354 GLN cc_start: 0.8520 (pp30) cc_final: 0.8166 (pp30) REVERT: E 176 MET cc_start: 0.8735 (mtt) cc_final: 0.8498 (mmm) outliers start: 24 outliers final: 6 residues processed: 111 average time/residue: 1.7372 time to fit residues: 208.3566 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 : 1.601 ------------------------------------------------------------------------------- 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 6 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain D residue 6 THR 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 179 optimal weight: 5.9990 chunk 26 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.2767 r_free = 0.2767 target = 0.046817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.036896 restraints weight = 42813.264| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 2.86 r_work: 0.2358 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14960 Z= 0.279 Angle : 0.574 7.342 20310 Z= 0.269 Chirality : 0.045 0.178 2250 Planarity : 0.004 0.071 2600 Dihedral : 7.179 93.746 2087 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.04 % Allowed : 14.39 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1835 helix: 0.92 (0.20), residues: 770 sheet: 1.05 (0.29), residues: 330 loop : 0.71 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 79 HIS 0.004 0.001 HIS B 161 PHE 0.007 0.001 PHE C 262 TYR 0.006 0.001 TYR A 188 ARG 0.002 0.000 ARG A 290 *********************** 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 127 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 1.666 Fit side-chains REVERT: A 314 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: A 354 GLN cc_start: 0.8894 (pp30) cc_final: 0.8602 (pp30) REVERT: A 355 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9145 (mtp) REVERT: B 95 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8155 (mtm110) REVERT: B 314 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: B 354 GLN cc_start: 0.8843 (pp30) cc_final: 0.8265 (pp30) REVERT: C 6 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8870 (p) REVERT: C 246 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8363 (mt0) REVERT: C 325 MET cc_start: 0.8743 (mmp) cc_final: 0.8480 (mmp) REVERT: D 353 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8978 (mm110) REVERT: D 354 GLN cc_start: 0.8591 (pp30) cc_final: 0.8180 (pp30) REVERT: E 6 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8832 (t) outliers start: 32 outliers final: 7 residues processed: 115 average time/residue: 1.7541 time to fit residues: 218.0831 Evaluate side-chains 109 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 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 81 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 174 optimal weight: 0.0870 chunk 44 optimal weight: 7.9990 chunk 180 optimal weight: 0.0370 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 78 optimal weight: 5.9990 chunk 69 optimal weight: 0.0060 chunk 169 optimal weight: 0.2980 chunk 133 optimal weight: 0.9990 overall best weight: 0.1652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 162 ASN B 225 ASN C 162 ASN C 225 ASN D 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.049588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.039600 restraints weight = 42414.708| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 2.89 r_work: 0.2440 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14960 Z= 0.116 Angle : 0.530 7.145 20310 Z= 0.243 Chirality : 0.042 0.147 2250 Planarity : 0.003 0.063 2600 Dihedral : 6.675 84.644 2087 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.21 % Allowed : 14.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.21), residues: 1835 helix: 1.26 (0.20), residues: 765 sheet: 0.87 (0.29), residues: 345 loop : 0.79 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.009 0.001 HIS A 40 PHE 0.007 0.001 PHE E 255 TYR 0.008 0.001 TYR D 306 ARG 0.002 0.000 ARG A 206 *********************** 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 119 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.659 Fit side-chains REVERT: A 354 GLN cc_start: 0.8801 (pp30) cc_final: 0.8549 (pp30) REVERT: B 354 GLN cc_start: 0.8784 (pp30) cc_final: 0.8256 (pp30) REVERT: C 325 MET cc_start: 0.8689 (mmp) cc_final: 0.8392 (mmp) REVERT: D 246 GLN cc_start: 0.8956 (mt0) cc_final: 0.8688 (mt0) REVERT: D 353 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8976 (mm110) REVERT: D 354 GLN cc_start: 0.8532 (pp30) cc_final: 0.8323 (pp30) outliers start: 19 outliers final: 4 residues processed: 112 average time/residue: 1.7318 time to fit residues: 210.0662 Evaluate side-chains 100 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain E residue 127 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 168 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 246 GLN B 41 GLN D 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.045821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.035976 restraints weight = 43772.894| |-----------------------------------------------------------------------------| r_work (start): 0.2471 rms_B_bonded: 2.86 r_work: 0.2325 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 14960 Z= 0.434 Angle : 0.625 8.995 20310 Z= 0.296 Chirality : 0.048 0.177 2250 Planarity : 0.004 0.063 2600 Dihedral : 6.998 92.459 2087 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.97 % Allowed : 14.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1835 helix: 1.19 (0.20), residues: 770 sheet: 1.13 (0.29), residues: 330 loop : 0.81 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 79 HIS 0.005 0.001 HIS B 161 PHE 0.009 0.001 PHE C 262 TYR 0.012 0.001 TYR B 188 ARG 0.002 0.000 ARG B 39 *********************** 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 126 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 1.661 Fit side-chains REVERT: A 314 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: A 354 GLN cc_start: 0.8881 (pp30) cc_final: 0.8591 (pp30) REVERT: A 355 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9135 (mtp) REVERT: B 95 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8300 (mtm110) REVERT: B 107 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: B 176 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8351 (mtp) REVERT: B 314 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7709 (tp40) REVERT: B 354 GLN cc_start: 0.8798 (pp30) cc_final: 0.8223 (pp30) REVERT: C 246 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8452 (mt0) REVERT: C 325 MET cc_start: 0.8884 (mmp) cc_final: 0.8638 (mmp) REVERT: C 353 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8936 (mp10) REVERT: C 354 GLN cc_start: 0.9009 (mp10) cc_final: 0.8685 (mp10) REVERT: D 353 GLN cc_start: 0.9264 (mm-40) cc_final: 0.8967 (mm110) REVERT: D 354 GLN cc_start: 0.8626 (pp30) cc_final: 0.8200 (pp30) REVERT: E 99 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8814 (pm20) outliers start: 31 outliers final: 6 residues processed: 114 average time/residue: 1.7292 time to fit residues: 213.2250 Evaluate side-chains 108 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 45 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 107 GLU 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 C residue 353 GLN Chi-restraints excluded: chain E residue 99 GLU 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 126 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.2785 r_free = 0.2785 target = 0.047513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.037616 restraints weight = 43084.625| |-----------------------------------------------------------------------------| r_work (start): 0.2517 rms_B_bonded: 2.87 r_work: 0.2375 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 0.036 14960 Z= 0.185 Angle : 0.557 8.132 20310 Z= 0.257 Chirality : 0.044 0.164 2250 Planarity : 0.004 0.060 2600 Dihedral : 6.716 89.392 2087 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.34 % Allowed : 14.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.21), residues: 1835 helix: 1.34 (0.20), residues: 770 sheet: 1.14 (0.29), residues: 330 loop : 0.85 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS A 40 PHE 0.007 0.001 PHE B 127 TYR 0.005 0.001 TYR E 69 ARG 0.002 0.000 ARG A 290 *********************** 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 115 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.840 Fit side-chains REVERT: A 314 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: A 354 GLN cc_start: 0.8819 (pp30) cc_final: 0.8544 (pp30) REVERT: B 314 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7653 (tp40) REVERT: B 354 GLN cc_start: 0.8795 (pp30) cc_final: 0.8246 (pp30) REVERT: C 325 MET cc_start: 0.8770 (mmp) cc_final: 0.8550 (mmp) REVERT: C 354 GLN cc_start: 0.9045 (mp10) cc_final: 0.8696 (mp10) REVERT: D 314 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: D 353 GLN cc_start: 0.9238 (mm-40) cc_final: 0.9006 (mm110) REVERT: D 354 GLN cc_start: 0.8600 (pp30) cc_final: 0.8242 (pp30) REVERT: E 355 MET cc_start: 0.9246 (mtp) cc_final: 0.8856 (mtm) outliers start: 21 outliers final: 7 residues processed: 109 average time/residue: 1.7019 time to fit residues: 201.2049 Evaluate side-chains 105 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 45 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 314 GLN 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 80 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 246 GLN B 41 GLN D 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.046330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.036421 restraints weight = 43462.702| |-----------------------------------------------------------------------------| r_work (start): 0.2485 rms_B_bonded: 2.88 r_work: 0.2341 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14960 Z= 0.328 Angle : 0.597 9.250 20310 Z= 0.278 Chirality : 0.046 0.177 2250 Planarity : 0.004 0.054 2600 Dihedral : 6.782 91.224 2087 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.59 % Allowed : 14.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.20), residues: 1835 helix: 1.32 (0.20), residues: 770 sheet: 1.11 (0.28), residues: 330 loop : 0.84 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.004 0.001 HIS B 161 PHE 0.007 0.001 PHE B 127 TYR 0.009 0.001 TYR B 188 ARG 0.002 0.000 ARG C 254 *********************** 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 120 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 2.049 Fit side-chains REVERT: A 314 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: A 325 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7677 (mtp) REVERT: A 354 GLN cc_start: 0.8890 (pp30) cc_final: 0.8610 (pp30) REVERT: A 355 MET cc_start: 0.9382 (mtm) cc_final: 0.9137 (mtp) REVERT: B 95 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8314 (mtm110) REVERT: B 132 MET cc_start: 0.9197 (ppp) cc_final: 0.8980 (OUTLIER) REVERT: B 176 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8342 (mtp) REVERT: B 314 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7701 (tp40) REVERT: B 354 GLN cc_start: 0.8786 (pp30) cc_final: 0.8238 (pp30) REVERT: C 325 MET cc_start: 0.8876 (mmp) cc_final: 0.8639 (mmp) REVERT: C 353 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8948 (mp10) REVERT: C 354 GLN cc_start: 0.9051 (mp10) cc_final: 0.8705 (mp10) REVERT: D 314 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8130 (tp40) REVERT: D 353 GLN cc_start: 0.9260 (mm-40) cc_final: 0.9026 (mm110) REVERT: D 354 GLN cc_start: 0.8749 (pp30) cc_final: 0.8504 (pp30) REVERT: E 99 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8825 (pm20) outliers start: 25 outliers final: 9 residues processed: 113 average time/residue: 1.7844 time to fit residues: 217.9033 Evaluate side-chains 110 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.809 ------------------------------------------------------------------------------- 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 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 353 GLN 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 169 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 158 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.2785 r_free = 0.2785 target = 0.047547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.037709 restraints weight = 42588.235| |-----------------------------------------------------------------------------| r_work (start): 0.2520 rms_B_bonded: 2.86 r_work: 0.2378 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14960 Z= 0.192 Angle : 0.563 9.487 20310 Z= 0.259 Chirality : 0.044 0.162 2250 Planarity : 0.003 0.054 2600 Dihedral : 6.548 88.509 2087 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.21 % Allowed : 15.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.21), residues: 1835 helix: 1.41 (0.20), residues: 770 sheet: 1.14 (0.29), residues: 330 loop : 0.87 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 79 HIS 0.003 0.001 HIS C 161 PHE 0.007 0.001 PHE B 127 TYR 0.005 0.001 TYR E 69 ARG 0.001 0.000 ARG B 290 *********************** 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 115 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.938 Fit side-chains REVERT: A 44 MET cc_start: 0.9192 (mmm) cc_final: 0.6668 (pmt) REVERT: A 314 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: A 325 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7658 (mtp) REVERT: A 354 GLN cc_start: 0.8853 (pp30) cc_final: 0.8589 (pp30) REVERT: A 355 MET cc_start: 0.9318 (mtm) cc_final: 0.9102 (mtp) REVERT: B 95 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8308 (mtm110) REVERT: B 314 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7669 (tp40) REVERT: B 354 GLN cc_start: 0.8770 (pp30) cc_final: 0.8247 (pp30) REVERT: C 325 MET cc_start: 0.8856 (mmp) cc_final: 0.8615 (mmp) REVERT: C 354 GLN cc_start: 0.9073 (mp10) cc_final: 0.8699 (mp10) REVERT: D 246 GLN cc_start: 0.8939 (mt0) cc_final: 0.8687 (mt0) REVERT: D 353 GLN cc_start: 0.9247 (mm-40) cc_final: 0.9015 (mm110) REVERT: D 354 GLN cc_start: 0.8690 (pp30) cc_final: 0.8349 (pp30) REVERT: D 355 MET cc_start: 0.9466 (mtm) cc_final: 0.9199 (mtm) outliers start: 19 outliers final: 8 residues processed: 112 average time/residue: 1.7312 time to fit residues: 209.5704 Evaluate side-chains 107 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 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 132 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D 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 159 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 246 GLN B 41 GLN D 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.047290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.037416 restraints weight = 42946.349| |-----------------------------------------------------------------------------| r_work (start): 0.2512 rms_B_bonded: 2.86 r_work: 0.2370 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1577 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= 0.210 Angle : 0.566 10.284 20310 Z= 0.260 Chirality : 0.044 0.164 2250 Planarity : 0.003 0.053 2600 Dihedral : 6.478 88.032 2087 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.83 % Allowed : 15.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.21), residues: 1835 helix: 1.45 (0.20), residues: 770 sheet: 1.14 (0.29), residues: 330 loop : 0.88 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.003 0.001 HIS B 161 PHE 0.007 0.001 PHE B 127 TYR 0.006 0.001 TYR B 188 ARG 0.001 0.000 ARG C 254 ********************** 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 109 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.792 Fit side-chains REVERT: A 44 MET cc_start: 0.9196 (mmm) cc_final: 0.6726 (pmt) REVERT: A 314 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: A 325 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7654 (mtp) REVERT: A 354 GLN cc_start: 0.8857 (pp30) cc_final: 0.8598 (pp30) REVERT: A 355 MET cc_start: 0.9333 (mtm) cc_final: 0.9102 (mtp) REVERT: B 95 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8277 (mtm110) REVERT: B 314 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7664 (tp40) REVERT: B 354 GLN cc_start: 0.8771 (pp30) cc_final: 0.8204 (pp30) REVERT: C 325 MET cc_start: 0.8855 (mmp) cc_final: 0.8603 (mmp) REVERT: C 354 GLN cc_start: 0.9091 (mp10) cc_final: 0.8703 (mp10) REVERT: D 246 GLN cc_start: 0.8934 (mt0) cc_final: 0.8670 (mt0) REVERT: D 353 GLN cc_start: 0.9252 (mm-40) cc_final: 0.9018 (mm110) REVERT: D 354 GLN cc_start: 0.8680 (pp30) cc_final: 0.8434 (pp30) REVERT: E 99 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8844 (pm20) outliers start: 13 outliers final: 7 residues processed: 108 average time/residue: 1.7831 time to fit residues: 210.0080 Evaluate side-chains 106 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 12 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.0030 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- 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 = 0.2804 r_free = 0.2804 target = 0.048218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.038382 restraints weight = 42554.559| |-----------------------------------------------------------------------------| r_work (start): 0.2541 rms_B_bonded: 2.87 r_work: 0.2401 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14960 Z= 0.162 Angle : 0.557 10.302 20310 Z= 0.255 Chirality : 0.043 0.155 2250 Planarity : 0.003 0.052 2600 Dihedral : 6.277 85.129 2087 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.89 % Allowed : 15.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.21), residues: 1835 helix: 1.51 (0.20), residues: 770 sheet: 1.18 (0.29), residues: 330 loop : 0.91 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 79 HIS 0.002 0.000 HIS B 161 PHE 0.006 0.001 PHE B 127 TYR 0.007 0.001 TYR B 133 ARG 0.002 0.000 ARG C 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7121.08 seconds wall clock time: 127 minutes 19.28 seconds (7639.28 seconds total)