Starting phenix.real_space_refine on Mon Dec 30 02:59:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmx_27548/12_2024/8dmx_27548.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmx_27548/12_2024/8dmx_27548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmx_27548/12_2024/8dmx_27548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmx_27548/12_2024/8dmx_27548.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmx_27548/12_2024/8dmx_27548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmx_27548/12_2024/8dmx_27548.cif" } resolution = 3.37 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= 0.001 sd= 0.032 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 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11748 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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} Time building chain proxies: 7.73, per 1000 atoms: 0.66 Number of scatterers: 11748 At special positions: 0 Unit cell: (79.299, 105.138, 170.181, 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 84 16.00 P 8 15.00 Mg 4 11.99 O 2264 8.00 N 1980 7.00 C 7408 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: 2.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 24 sheets defined 48.9% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.743A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.902A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.655A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 128 removed outlier: 3.817A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 removed outlier: 4.216A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 4.106A 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 194 removed outlier: 3.559A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.647A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.838A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.567A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.233A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.530A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 337 removed outlier: 3.512A pdb=" N TYR A 337 " --> pdb=" O GLU A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 337' Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.513A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.768A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.743A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.902A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.655A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 128 removed outlier: 3.817A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 removed outlier: 4.216A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 4.106A 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 194 removed outlier: 3.559A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.647A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.839A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.567A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.232A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.530A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 337 removed outlier: 3.512A pdb=" N TYR B 337 " --> pdb=" O GLU B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.513A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.768A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.743A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 92 removed outlier: 3.903A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.655A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 128 removed outlier: 3.817A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 removed outlier: 4.215A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 4.106A 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: 3.558A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.647A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.838A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.568A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.233A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.530A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 337 removed outlier: 3.511A pdb=" N TYR C 337 " --> pdb=" O GLU C 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 334 through 337' Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.513A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 366 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.769A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.743A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 removed outlier: 3.902A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.656A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 128 removed outlier: 3.816A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 146 removed outlier: 4.216A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 4.106A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.559A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.647A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.839A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.567A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.233A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.530A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 337 removed outlier: 3.513A pdb=" N TYR D 337 " --> pdb=" O GLU D 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 334 through 337' Processing helix chain 'D' and resid 338 through 348 removed outlier: 3.513A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.767A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.569A pdb=" N LYS A 18 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.624A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR A 166 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 160 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR A 166 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 154 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 165 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (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 31 removed outlier: 6.851A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR B 166 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 160 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR B 166 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B 154 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 165 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (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 31 removed outlier: 6.851A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.624A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR C 166 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 160 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR C 166 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP C 154 " --> pdb=" O HIS C 161 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 165 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (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 31 removed outlier: 6.851A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.624A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) 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 removed outlier: 3.608A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 160 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.608A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP D 154 " --> pdb=" O HIS D 161 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 6.740A 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 241 475 hydrogen bonds defined for protein. 1221 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: 4.03 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3824 1.34 - 1.46: 2391 1.46 - 1.58: 5629 1.58 - 1.69: 12 1.69 - 1.81: 148 Bond restraints: 12004 Sorted by residual: bond pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.15e-02 7.56e+03 8.84e+00 bond pdb=" N ILE B 71 " pdb=" CA ILE B 71 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.26e-02 6.30e+03 7.96e+00 bond pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.85e+00 bond pdb=" N ILE A 71 " pdb=" CA ILE A 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.79e+00 bond pdb=" N ILE D 71 " pdb=" CA ILE D 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.78e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 15536 1.14 - 2.29: 530 2.29 - 3.43: 151 3.43 - 4.57: 43 4.57 - 5.72: 32 Bond angle restraints: 16292 Sorted by residual: angle pdb=" CA ASN A 12 " pdb=" C ASN A 12 " pdb=" N GLY A 13 " ideal model delta sigma weight residual 115.51 120.24 -4.73 1.27e+00 6.20e-01 1.39e+01 angle pdb=" CA ASN D 296 " pdb=" C ASN D 296 " pdb=" O ASN D 296 " ideal model delta sigma weight residual 121.20 117.51 3.69 1.04e+00 9.25e-01 1.26e+01 angle pdb=" CA ASN A 296 " pdb=" C ASN A 296 " pdb=" O ASN A 296 " ideal model delta sigma weight residual 121.20 117.52 3.68 1.04e+00 9.25e-01 1.25e+01 angle pdb=" CA ASN B 296 " pdb=" C ASN B 296 " pdb=" O ASN B 296 " ideal model delta sigma weight residual 121.20 117.52 3.68 1.04e+00 9.25e-01 1.25e+01 angle pdb=" CA ASN C 296 " pdb=" C ASN C 296 " pdb=" O ASN C 296 " ideal model delta sigma weight residual 121.20 117.56 3.64 1.04e+00 9.25e-01 1.22e+01 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 6744 21.12 - 42.25: 404 42.25 - 63.37: 52 63.37 - 84.49: 12 84.49 - 105.62: 8 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 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 -60.00 -165.62 105.62 1 2.00e+01 2.50e-03 3.05e+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 -165.61 105.61 1 2.00e+01 2.50e-03 3.05e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -165.60 105.59 1 2.00e+01 2.50e-03 3.05e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1127 0.032 - 0.065: 447 0.065 - 0.097: 136 0.097 - 0.130: 86 0.130 - 0.162: 12 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ILE D 71 " pdb=" N ILE D 71 " pdb=" C ILE D 71 " pdb=" CB ILE D 71 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 12 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C ASN A 12 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN A 12 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 13 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 70 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C PRO D 70 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO D 70 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE D 71 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 70 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C PRO B 70 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO B 70 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE B 71 " 0.011 2.00e-02 2.50e+03 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 121 2.66 - 3.22: 10249 3.22 - 3.78: 16075 3.78 - 4.34: 22709 4.34 - 4.90: 38454 Nonbonded interactions: 87608 Sorted by model distance: nonbonded pdb="MG MG D 400 " pdb=" O1B ADP D 401 " model vdw 2.105 2.170 nonbonded pdb="MG MG B 400 " pdb=" O1B ADP B 401 " model vdw 2.105 2.170 nonbonded pdb="MG MG A 400 " pdb=" O1B ADP A 401 " model vdw 2.105 2.170 nonbonded pdb="MG MG C 400 " pdb=" O1B ADP C 401 " model vdw 2.106 2.170 nonbonded pdb=" O ASP C 51 " pdb=" OD1 ASP C 51 " model vdw 2.144 3.040 ... (remaining 87603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.010 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.540 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12004 Z= 0.191 Angle : 0.585 5.718 16292 Z= 0.328 Chirality : 0.044 0.162 1808 Planarity : 0.005 0.052 2084 Dihedral : 13.993 105.617 4468 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: 0.17 (0.23), residues: 1468 helix: 1.05 (0.24), residues: 524 sheet: -0.19 (0.32), residues: 276 loop : -0.42 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 356 HIS 0.002 0.000 HIS C 101 PHE 0.009 0.001 PHE B 124 TYR 0.009 0.001 TYR A 294 ARG 0.013 0.001 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.244 Fit side-chains REVERT: A 326 LYS cc_start: 0.8167 (pttt) cc_final: 0.7755 (mttm) REVERT: B 47 MET cc_start: 0.4355 (ptm) cc_final: 0.4129 (ptp) REVERT: B 143 TYR cc_start: 0.7885 (m-10) cc_final: 0.7299 (m-80) REVERT: B 184 ASP cc_start: 0.8015 (m-30) cc_final: 0.7745 (m-30) REVERT: C 364 GLU cc_start: 0.8651 (tt0) cc_final: 0.8412 (tm-30) REVERT: D 47 MET cc_start: 0.3966 (ptm) cc_final: 0.3710 (ppp) REVERT: D 91 TYR cc_start: 0.7417 (m-80) cc_final: 0.6901 (m-80) REVERT: D 123 MET cc_start: 0.6921 (tpp) cc_final: 0.6677 (tpt) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2426 time to fit residues: 73.9726 Evaluate side-chains 129 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 275 HIS B 12 ASN B 275 HIS D 275 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 12004 Z= 0.515 Angle : 0.751 11.388 16292 Z= 0.380 Chirality : 0.053 0.173 1808 Planarity : 0.006 0.048 2084 Dihedral : 6.264 76.310 1672 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.39 % Allowed : 9.39 % Favored : 88.22 % 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: -0.60 (0.22), residues: 1468 helix: 0.22 (0.23), residues: 548 sheet: -0.48 (0.32), residues: 264 loop : -0.77 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 340 HIS 0.007 0.002 HIS D 161 PHE 0.014 0.002 PHE C 255 TYR 0.015 0.002 TYR B 218 ARG 0.006 0.001 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.495 Fit side-chains REVERT: A 326 LYS cc_start: 0.8415 (pttt) cc_final: 0.7699 (mttm) REVERT: C 157 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8220 (t0) REVERT: D 47 MET cc_start: 0.3639 (ptm) cc_final: 0.3306 (ppp) REVERT: D 132 MET cc_start: 0.8865 (tpp) cc_final: 0.8584 (ttm) outliers start: 30 outliers final: 21 residues processed: 130 average time/residue: 0.2196 time to fit residues: 42.7512 Evaluate side-chains 112 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12004 Z= 0.176 Angle : 0.538 6.513 16292 Z= 0.264 Chirality : 0.044 0.143 1808 Planarity : 0.005 0.050 2084 Dihedral : 5.746 65.331 1672 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.99 % Allowed : 12.26 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.43 (0.22), residues: 1468 helix: 0.18 (0.23), residues: 576 sheet: -0.51 (0.33), residues: 232 loop : -0.47 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 340 HIS 0.002 0.001 HIS D 161 PHE 0.011 0.001 PHE A 31 TYR 0.010 0.001 TYR D 69 ARG 0.002 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.383 Fit side-chains REVERT: A 326 LYS cc_start: 0.8426 (pttt) cc_final: 0.8036 (ptpp) REVERT: D 47 MET cc_start: 0.3628 (ptm) cc_final: 0.3358 (ppp) REVERT: D 355 MET cc_start: 0.8703 (mtt) cc_final: 0.8483 (mtp) outliers start: 25 outliers final: 13 residues processed: 111 average time/residue: 0.2294 time to fit residues: 38.4421 Evaluate side-chains 103 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 12004 Z= 0.449 Angle : 0.666 7.183 16292 Z= 0.335 Chirality : 0.051 0.175 1808 Planarity : 0.006 0.056 2084 Dihedral : 5.902 63.934 1672 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.79 % Allowed : 12.82 % Favored : 84.39 % 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: -0.87 (0.22), residues: 1468 helix: -0.04 (0.22), residues: 572 sheet: -0.71 (0.31), residues: 264 loop : -0.88 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 340 HIS 0.005 0.002 HIS D 161 PHE 0.014 0.002 PHE D 31 TYR 0.013 0.002 TYR B 218 ARG 0.004 0.001 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 1.285 Fit side-chains REVERT: A 261 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7782 (mp) REVERT: A 326 LYS cc_start: 0.8409 (pttt) cc_final: 0.7910 (ptpp) REVERT: C 157 ASP cc_start: 0.8348 (t0) cc_final: 0.8054 (t0) REVERT: D 25 ASP cc_start: 0.8183 (p0) cc_final: 0.7835 (m-30) outliers start: 35 outliers final: 25 residues processed: 117 average time/residue: 0.2034 time to fit residues: 37.2348 Evaluate side-chains 111 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12004 Z= 0.155 Angle : 0.533 8.934 16292 Z= 0.260 Chirality : 0.044 0.152 1808 Planarity : 0.005 0.050 2084 Dihedral : 5.483 60.326 1672 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.83 % Allowed : 14.33 % Favored : 83.84 % 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: -0.54 (0.22), residues: 1468 helix: 0.20 (0.23), residues: 576 sheet: -0.71 (0.33), residues: 232 loop : -0.59 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 340 HIS 0.002 0.001 HIS B 101 PHE 0.012 0.001 PHE D 31 TYR 0.009 0.001 TYR D 69 ARG 0.004 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.626 Fit side-chains REVERT: A 326 LYS cc_start: 0.8373 (pttt) cc_final: 0.7853 (ptpp) REVERT: D 25 ASP cc_start: 0.8151 (p0) cc_final: 0.7828 (m-30) REVERT: D 355 MET cc_start: 0.8693 (mtt) cc_final: 0.8459 (mtp) outliers start: 23 outliers final: 18 residues processed: 109 average time/residue: 0.2080 time to fit residues: 35.4552 Evaluate side-chains 105 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12004 Z= 0.414 Angle : 0.645 6.580 16292 Z= 0.323 Chirality : 0.050 0.174 1808 Planarity : 0.005 0.060 2084 Dihedral : 5.859 71.051 1672 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.47 % Allowed : 13.85 % Favored : 83.68 % 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: -0.98 (0.22), residues: 1468 helix: -0.21 (0.22), residues: 596 sheet: -0.80 (0.30), residues: 264 loop : -0.86 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 340 HIS 0.005 0.002 HIS D 161 PHE 0.015 0.002 PHE D 31 TYR 0.013 0.001 TYR B 218 ARG 0.006 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 1.508 Fit side-chains REVERT: A 261 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7796 (mp) REVERT: A 326 LYS cc_start: 0.8462 (pttt) cc_final: 0.7891 (ptpp) REVERT: B 132 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8862 (ttp) REVERT: D 25 ASP cc_start: 0.8211 (p0) cc_final: 0.7927 (m-30) outliers start: 31 outliers final: 24 residues processed: 105 average time/residue: 0.2110 time to fit residues: 34.3707 Evaluate side-chains 107 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.0370 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12004 Z= 0.192 Angle : 0.546 6.309 16292 Z= 0.269 Chirality : 0.045 0.159 1808 Planarity : 0.005 0.050 2084 Dihedral : 5.580 65.759 1672 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.83 % Allowed : 14.65 % Favored : 83.52 % 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: -0.78 (0.22), residues: 1468 helix: -0.07 (0.22), residues: 600 sheet: -0.86 (0.33), residues: 232 loop : -0.66 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 340 HIS 0.003 0.001 HIS C 101 PHE 0.012 0.001 PHE D 31 TYR 0.010 0.001 TYR D 69 ARG 0.004 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 1.441 Fit side-chains REVERT: A 326 LYS cc_start: 0.8423 (pttt) cc_final: 0.7842 (ptpp) REVERT: B 132 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8721 (ttp) REVERT: D 25 ASP cc_start: 0.8164 (p0) cc_final: 0.7904 (m-30) REVERT: D 355 MET cc_start: 0.8693 (mtt) cc_final: 0.8452 (mtp) outliers start: 23 outliers final: 16 residues processed: 101 average time/residue: 0.2188 time to fit residues: 34.1362 Evaluate side-chains 102 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12004 Z= 0.238 Angle : 0.557 6.628 16292 Z= 0.274 Chirality : 0.046 0.159 1808 Planarity : 0.005 0.054 2084 Dihedral : 5.537 65.378 1672 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.15 % Allowed : 14.41 % Favored : 83.44 % 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: -0.75 (0.22), residues: 1468 helix: -0.06 (0.22), residues: 600 sheet: -0.85 (0.32), residues: 236 loop : -0.61 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 340 HIS 0.003 0.001 HIS D 161 PHE 0.013 0.001 PHE D 31 TYR 0.009 0.001 TYR D 69 ARG 0.006 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 1.384 Fit side-chains REVERT: A 326 LYS cc_start: 0.8379 (pttt) cc_final: 0.7802 (ptpp) REVERT: B 132 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8732 (ttp) REVERT: D 25 ASP cc_start: 0.8171 (p0) cc_final: 0.7920 (m-30) REVERT: D 261 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7764 (mp) REVERT: D 355 MET cc_start: 0.8678 (mtt) cc_final: 0.8439 (mtp) outliers start: 27 outliers final: 19 residues processed: 108 average time/residue: 0.2037 time to fit residues: 34.2579 Evaluate side-chains 107 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12004 Z= 0.240 Angle : 0.560 6.357 16292 Z= 0.276 Chirality : 0.046 0.157 1808 Planarity : 0.005 0.051 2084 Dihedral : 5.512 64.748 1672 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.15 % Allowed : 13.93 % Favored : 83.92 % 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: -0.75 (0.22), residues: 1468 helix: -0.07 (0.22), residues: 600 sheet: -0.86 (0.32), residues: 236 loop : -0.60 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 340 HIS 0.003 0.001 HIS D 161 PHE 0.012 0.001 PHE D 31 TYR 0.009 0.001 TYR D 69 ARG 0.007 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 1.306 Fit side-chains REVERT: A 326 LYS cc_start: 0.8367 (pttt) cc_final: 0.7784 (ptpp) REVERT: B 132 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8732 (ttp) outliers start: 27 outliers final: 22 residues processed: 106 average time/residue: 0.2056 time to fit residues: 33.7915 Evaluate side-chains 109 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 216 LEU 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 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 125 optimal weight: 0.0970 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12004 Z= 0.129 Angle : 0.510 7.572 16292 Z= 0.246 Chirality : 0.043 0.164 1808 Planarity : 0.005 0.050 2084 Dihedral : 5.110 55.286 1672 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.67 % Allowed : 14.41 % Favored : 83.92 % 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: -0.35 (0.22), residues: 1468 helix: 0.33 (0.23), residues: 580 sheet: -0.65 (0.33), residues: 236 loop : -0.44 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 356 HIS 0.003 0.001 HIS C 101 PHE 0.011 0.001 PHE D 31 TYR 0.008 0.001 TYR B 69 ARG 0.008 0.000 ARG B 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 1.313 Fit side-chains REVERT: A 326 LYS cc_start: 0.8361 (pttt) cc_final: 0.7772 (ptpp) REVERT: D 325 MET cc_start: 0.7853 (ptp) cc_final: 0.7648 (ptp) outliers start: 21 outliers final: 18 residues processed: 105 average time/residue: 0.2121 time to fit residues: 34.9972 Evaluate side-chains 107 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.096631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.087040 restraints weight = 17425.478| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.26 r_work: 0.2871 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12004 Z= 0.188 Angle : 0.530 7.027 16292 Z= 0.258 Chirality : 0.045 0.153 1808 Planarity : 0.005 0.052 2084 Dihedral : 5.113 56.300 1672 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.75 % Allowed : 14.57 % Favored : 83.68 % 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: -0.49 (0.22), residues: 1468 helix: 0.09 (0.23), residues: 604 sheet: -0.64 (0.33), residues: 236 loop : -0.43 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 340 HIS 0.003 0.001 HIS C 101 PHE 0.011 0.001 PHE D 31 TYR 0.007 0.001 TYR D 69 ARG 0.008 0.000 ARG A 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2270.24 seconds wall clock time: 42 minutes 19.29 seconds (2539.29 seconds total)