Starting phenix.real_space_refine on Fri Jan 17 23:44:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fjo_50507/01_2025/9fjo_50507.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fjo_50507/01_2025/9fjo_50507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fjo_50507/01_2025/9fjo_50507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fjo_50507/01_2025/9fjo_50507.map" model { file = "/net/cci-nas-00/data/ceres_data/9fjo_50507/01_2025/9fjo_50507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fjo_50507/01_2025/9fjo_50507.cif" } resolution = 3.05 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= 0.002 sd= 0.097 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 78 5.16 5 C 7234 2.51 5 N 1934 2.21 5 O 2208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 11466 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2796 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 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: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2796 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 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: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2881 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} 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: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2881 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} 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: 7.88, per 1000 atoms: 0.69 Number of scatterers: 11466 At special positions: 0 Unit cell: (99, 81, 158.4, 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 78 16.00 P 8 15.00 Mg 4 11.99 O 2208 8.00 N 1934 7.00 C 7234 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: 2.62 Conformation dependent library (CDL) restraints added in 1.4 seconds 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 22 sheets defined 51.9% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.609A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 60' Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.710A pdb=" N ILE A 75 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.639A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.565A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.785A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.735A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.641A 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 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.689A 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 removed outlier: 3.609A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.698A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.524A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.684A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.561A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.745A pdb=" N HIS B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.788A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 125 " --> pdb=" O GLN B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.936A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.595A 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 195 removed outlier: 3.768A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.603A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 257 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 289 through 295 removed outlier: 3.701A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.099A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.556A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.643A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 365 removed outlier: 3.541A pdb=" N TYR B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.783A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.552A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.573A pdb=" N LEU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.612A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.553A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.825A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.535A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.536A 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 193 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.653A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.605A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.702A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 removed outlier: 3.553A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.209A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.509A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.584A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.240A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.549A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.979A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.797A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (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 removed outlier: 3.688A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.902A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.046A 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 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 349 through 356 removed outlier: 3.507A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.108A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS D 373 " --> pdb=" O ILE D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.304A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.739A pdb=" N ASN A 162 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.739A pdb=" N ASN A 162 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.756A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.502A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.545A pdb=" N ASN B 162 " --> pdb=" O MET B 176 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.545A pdb=" N ASN B 162 " --> pdb=" O MET B 176 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 8 through 9 removed outlier: 6.835A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.614A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.504A pdb=" N ALA D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.758A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.559A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 523 hydrogen bonds defined for protein. 1302 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: 4.14 Time building geometry restraints manager: 3.04 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: 3726 1.34 - 1.46: 2019 1.46 - 1.57: 5819 1.57 - 1.69: 12 1.69 - 1.81: 138 Bond restraints: 11714 Sorted by residual: bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.20e+00 bond pdb=" CA ILE B 357 " pdb=" CB ILE B 357 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.17e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 ... (remaining 11709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 15560 1.37 - 2.73: 212 2.73 - 4.10: 90 4.10 - 5.47: 24 5.47 - 6.84: 14 Bond angle restraints: 15900 Sorted by residual: angle pdb=" N ILE A 64 " pdb=" CA ILE A 64 " pdb=" C ILE A 64 " ideal model delta sigma weight residual 112.29 109.65 2.64 9.40e-01 1.13e+00 7.91e+00 angle pdb=" C ILE B 76 " pdb=" N THR B 77 " pdb=" CA THR B 77 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.89e+00 angle pdb=" N GLY C 55 " pdb=" CA GLY C 55 " pdb=" C GLY C 55 " ideal model delta sigma weight residual 110.95 114.83 -3.88 1.70e+00 3.46e-01 5.20e+00 angle pdb=" CB MET B 82 " pdb=" CG MET B 82 " pdb=" SD MET B 82 " ideal model delta sigma weight residual 112.70 105.86 6.84 3.00e+00 1.11e-01 5.19e+00 angle pdb=" N ILE B 369 " pdb=" CA ILE B 369 " pdb=" C ILE B 369 " ideal model delta sigma weight residual 112.98 110.13 2.85 1.25e+00 6.40e-01 5.19e+00 ... (remaining 15895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6253 17.91 - 35.83: 595 35.83 - 53.74: 138 53.74 - 71.65: 54 71.65 - 89.56: 12 Dihedral angle restraints: 7052 sinusoidal: 2850 harmonic: 4202 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -139.43 79.43 1 2.00e+01 2.50e-03 1.96e+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 -139.13 79.13 1 2.00e+01 2.50e-03 1.95e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -127.61 67.62 1 2.00e+01 2.50e-03 1.49e+01 ... (remaining 7049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1055 0.030 - 0.060: 479 0.060 - 0.090: 113 0.090 - 0.119: 118 0.119 - 0.149: 5 Chirality restraints: 1770 Sorted by residual: chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.63 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE D 165 " pdb=" N ILE D 165 " pdb=" C ILE D 165 " pdb=" CB ILE D 165 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 1767 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 306 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO A 307 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 129 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO B 130 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 108 " 0.020 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO B 109 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 109 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 109 " 0.016 5.00e-02 4.00e+02 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 286 2.71 - 3.26: 11112 3.26 - 3.81: 17542 3.81 - 4.35: 24149 4.35 - 4.90: 40400 Nonbonded interactions: 93489 Sorted by model distance: nonbonded pdb=" O GLY C 156 " pdb=" OG1 THR C 303 " model vdw 2.165 3.040 nonbonded pdb=" OD1 ASP B 157 " pdb=" O3' ADP B 401 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASP D 157 " pdb=" O3' ADP D 401 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP C 157 " pdb=" O3' ADP C 401 " model vdw 2.225 3.040 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.227 3.040 ... (remaining 93484 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' and (resid 6 through 39 or resid 50 through 372 or resid 401 through \ 402)) selection = (chain 'D' and (resid 6 through 39 or resid 50 through 372 or resid 401 through \ 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.700 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.150 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.002 0.022 11714 Z= 0.139 Angle : 0.524 6.837 15900 Z= 0.246 Chirality : 0.042 0.149 1770 Planarity : 0.003 0.035 2028 Dihedral : 15.855 89.563 4360 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.24 % Allowed : 15.74 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1428 helix: -0.78 (0.20), residues: 580 sheet: -0.30 (0.36), residues: 232 loop : 0.65 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 340 HIS 0.006 0.001 HIS B 101 PHE 0.007 0.001 PHE C 255 TYR 0.013 0.001 TYR A 337 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 1.226 Fit side-chains REVERT: A 80 ASP cc_start: 0.7530 (t0) cc_final: 0.7020 (t0) REVERT: A 259 GLU cc_start: 0.7618 (tp30) cc_final: 0.7391 (tp30) REVERT: B 53 TYR cc_start: 0.7054 (m-80) cc_final: 0.6837 (m-80) outliers start: 3 outliers final: 2 residues processed: 141 average time/residue: 0.2629 time to fit residues: 53.7652 Evaluate side-chains 134 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 12 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 0.0470 chunk 57 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 0.0070 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.150143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120671 restraints weight = 13161.379| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.63 r_work: 0.3270 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11714 Z= 0.187 Angle : 0.583 6.834 15900 Z= 0.283 Chirality : 0.044 0.151 1770 Planarity : 0.004 0.036 2028 Dihedral : 5.926 82.525 1634 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.79 % Allowed : 15.82 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.24 (0.22), residues: 1428 helix: 0.09 (0.22), residues: 584 sheet: -0.36 (0.34), residues: 250 loop : 0.78 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.004 0.001 HIS D 87 PHE 0.008 0.001 PHE B 255 TYR 0.008 0.001 TYR A 337 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.342 Fit side-chains REVERT: A 95 ARG cc_start: 0.7525 (mmt-90) cc_final: 0.7096 (mmt-90) REVERT: A 259 GLU cc_start: 0.7572 (tp30) cc_final: 0.7365 (tp30) REVERT: B 100 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7177 (mp0) outliers start: 22 outliers final: 13 residues processed: 156 average time/residue: 0.2456 time to fit residues: 54.8142 Evaluate side-chains 149 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 59 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 110 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117732 restraints weight = 13454.176| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.64 r_work: 0.3229 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11714 Z= 0.298 Angle : 0.611 7.281 15900 Z= 0.293 Chirality : 0.047 0.176 1770 Planarity : 0.004 0.036 2028 Dihedral : 6.094 93.518 1632 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.53 % Allowed : 16.15 % Favored : 81.32 % 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: 0.14 (0.22), residues: 1428 helix: 0.05 (0.22), residues: 588 sheet: -0.42 (0.33), residues: 250 loop : 0.69 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.004 0.001 HIS D 87 PHE 0.012 0.001 PHE C 255 TYR 0.013 0.001 TYR A 337 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.172 Fit side-chains REVERT: A 82 MET cc_start: 0.7846 (tpt) cc_final: 0.7455 (tpt) REVERT: A 95 ARG cc_start: 0.7574 (mmt-90) cc_final: 0.7319 (mmt-90) REVERT: A 259 GLU cc_start: 0.7684 (tp30) cc_final: 0.7446 (tp30) REVERT: B 100 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: C 314 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7989 (tt0) outliers start: 31 outliers final: 21 residues processed: 167 average time/residue: 0.2499 time to fit residues: 59.0681 Evaluate side-chains 160 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 124 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114719 restraints weight = 13451.325| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.69 r_work: 0.3189 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11714 Z= 0.402 Angle : 0.654 7.328 15900 Z= 0.317 Chirality : 0.049 0.189 1770 Planarity : 0.005 0.037 2028 Dihedral : 6.438 103.573 1632 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.10 % Allowed : 16.15 % Favored : 80.75 % 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: -0.16 (0.22), residues: 1428 helix: -0.15 (0.22), residues: 576 sheet: -0.65 (0.31), residues: 260 loop : 0.50 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.005 0.001 HIS D 87 PHE 0.014 0.002 PHE C 255 TYR 0.010 0.001 TYR D 218 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 1.616 Fit side-chains REVERT: A 82 MET cc_start: 0.7792 (tpt) cc_final: 0.7366 (tpt) REVERT: A 259 GLU cc_start: 0.7725 (tp30) cc_final: 0.7461 (tp30) REVERT: B 100 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: C 53 TYR cc_start: 0.8771 (m-80) cc_final: 0.8424 (m-80) REVERT: C 314 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7942 (tt0) outliers start: 38 outliers final: 29 residues processed: 162 average time/residue: 0.2490 time to fit residues: 58.1689 Evaluate side-chains 164 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.147007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117643 restraints weight = 13232.431| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.62 r_work: 0.3228 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11714 Z= 0.172 Angle : 0.560 6.904 15900 Z= 0.265 Chirality : 0.044 0.144 1770 Planarity : 0.004 0.034 2028 Dihedral : 6.160 106.313 1632 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.53 % Allowed : 16.48 % Favored : 81.00 % 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: 0.33 (0.23), residues: 1428 helix: 0.28 (0.23), residues: 564 sheet: -0.40 (0.32), residues: 248 loop : 0.71 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.004 0.001 HIS C 161 PHE 0.010 0.001 PHE C 255 TYR 0.007 0.001 TYR A 294 ARG 0.004 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.300 Fit side-chains REVERT: A 82 MET cc_start: 0.7855 (tpt) cc_final: 0.7324 (tpt) REVERT: A 95 ARG cc_start: 0.7631 (mmt-90) cc_final: 0.7265 (mmt-90) REVERT: A 124 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: A 259 GLU cc_start: 0.7682 (tp30) cc_final: 0.7452 (tp30) REVERT: B 62 ARG cc_start: 0.6167 (ptt90) cc_final: 0.5910 (ptt180) REVERT: B 100 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: B 349 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6665 (mp) REVERT: C 53 TYR cc_start: 0.8732 (m-80) cc_final: 0.8398 (m-80) REVERT: C 289 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8089 (pt) REVERT: C 314 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7948 (tt0) outliers start: 31 outliers final: 21 residues processed: 163 average time/residue: 0.2309 time to fit residues: 54.5704 Evaluate side-chains 163 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119564 restraints weight = 13344.817| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.64 r_work: 0.3230 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11714 Z= 0.175 Angle : 0.554 6.891 15900 Z= 0.260 Chirality : 0.044 0.142 1770 Planarity : 0.004 0.033 2028 Dihedral : 6.049 110.593 1632 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.02 % Allowed : 16.39 % Favored : 80.59 % 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: 0.47 (0.23), residues: 1428 helix: 0.43 (0.23), residues: 568 sheet: -0.32 (0.32), residues: 248 loop : 0.75 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE C 255 TYR 0.015 0.001 TYR A 337 ARG 0.004 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.300 Fit side-chains REVERT: A 82 MET cc_start: 0.7857 (tpt) cc_final: 0.7311 (tpt) REVERT: A 95 ARG cc_start: 0.7626 (mmt-90) cc_final: 0.7224 (mmt-90) REVERT: A 117 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6614 (mm-30) REVERT: A 259 GLU cc_start: 0.7687 (tp30) cc_final: 0.7486 (tp30) REVERT: B 62 ARG cc_start: 0.6152 (ptt90) cc_final: 0.5866 (ptt180) REVERT: C 53 TYR cc_start: 0.8735 (m-80) cc_final: 0.8406 (m-80) REVERT: C 289 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8072 (pt) REVERT: C 314 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: D 82 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7828 (tpt) outliers start: 37 outliers final: 24 residues processed: 171 average time/residue: 0.2562 time to fit residues: 62.2178 Evaluate side-chains 169 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 141 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 31 optimal weight: 0.0000 chunk 118 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 overall best weight: 2.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115319 restraints weight = 13533.759| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.64 r_work: 0.3180 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11714 Z= 0.393 Angle : 0.650 7.612 15900 Z= 0.314 Chirality : 0.049 0.171 1770 Planarity : 0.004 0.035 2028 Dihedral : 6.409 124.723 1630 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.77 % Allowed : 16.72 % Favored : 80.51 % 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: 0.03 (0.23), residues: 1428 helix: 0.05 (0.22), residues: 568 sheet: -0.52 (0.31), residues: 268 loop : 0.54 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.005 0.001 HIS D 87 PHE 0.012 0.001 PHE C 255 TYR 0.021 0.001 TYR A 337 ARG 0.004 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 1.361 Fit side-chains REVERT: A 82 MET cc_start: 0.7904 (tpt) cc_final: 0.7397 (tpt) REVERT: A 259 GLU cc_start: 0.7829 (tp30) cc_final: 0.7595 (tp30) REVERT: C 53 TYR cc_start: 0.8790 (m-80) cc_final: 0.8465 (m-80) REVERT: D 82 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7869 (tpt) outliers start: 34 outliers final: 28 residues processed: 160 average time/residue: 0.2524 time to fit residues: 58.2435 Evaluate side-chains 163 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 108 optimal weight: 0.0010 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119908 restraints weight = 13261.719| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.64 r_work: 0.3240 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11714 Z= 0.146 Angle : 0.551 6.771 15900 Z= 0.261 Chirality : 0.043 0.140 1770 Planarity : 0.004 0.033 2028 Dihedral : 6.140 127.000 1630 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.45 % Allowed : 17.13 % Favored : 80.42 % 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: 0.47 (0.23), residues: 1428 helix: 0.47 (0.23), residues: 568 sheet: -0.37 (0.31), residues: 262 loop : 0.76 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.004 0.001 HIS C 161 PHE 0.010 0.001 PHE C 255 TYR 0.013 0.001 TYR A 337 ARG 0.004 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.342 Fit side-chains REVERT: A 82 MET cc_start: 0.7839 (tpt) cc_final: 0.7329 (tpt) REVERT: A 95 ARG cc_start: 0.7611 (mmt-90) cc_final: 0.7235 (mmt-90) REVERT: A 259 GLU cc_start: 0.7684 (tp30) cc_final: 0.7459 (tp30) REVERT: B 62 ARG cc_start: 0.6131 (ptt90) cc_final: 0.5913 (ptt180) REVERT: C 53 TYR cc_start: 0.8776 (m-80) cc_final: 0.8497 (m-80) REVERT: C 314 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7928 (tt0) outliers start: 30 outliers final: 25 residues processed: 161 average time/residue: 0.2421 time to fit residues: 55.8537 Evaluate side-chains 166 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 11 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 115 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120199 restraints weight = 13420.083| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.64 r_work: 0.3235 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11714 Z= 0.163 Angle : 0.551 6.673 15900 Z= 0.259 Chirality : 0.044 0.145 1770 Planarity : 0.004 0.033 2028 Dihedral : 6.067 127.661 1630 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.37 % Allowed : 17.54 % Favored : 80.10 % 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: 0.59 (0.23), residues: 1428 helix: 0.55 (0.23), residues: 570 sheet: -0.36 (0.31), residues: 266 loop : 0.91 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.008 0.001 HIS B 101 PHE 0.009 0.001 PHE C 255 TYR 0.018 0.001 TYR A 337 ARG 0.005 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.249 Fit side-chains REVERT: A 82 MET cc_start: 0.7852 (tpt) cc_final: 0.7342 (tpt) REVERT: A 95 ARG cc_start: 0.7618 (mmt-90) cc_final: 0.7231 (mmt-90) REVERT: A 259 GLU cc_start: 0.7716 (tp30) cc_final: 0.7498 (tp30) REVERT: B 62 ARG cc_start: 0.6187 (ptt90) cc_final: 0.5935 (ptt180) REVERT: C 53 TYR cc_start: 0.8778 (m-80) cc_final: 0.8504 (m-80) REVERT: C 314 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7989 (tt0) outliers start: 29 outliers final: 26 residues processed: 158 average time/residue: 0.2671 time to fit residues: 60.6414 Evaluate side-chains 164 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 19 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 116 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 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 101 HIS C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118679 restraints weight = 13245.182| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.67 r_work: 0.3238 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11714 Z= 0.157 Angle : 0.548 6.628 15900 Z= 0.257 Chirality : 0.044 0.149 1770 Planarity : 0.004 0.034 2028 Dihedral : 6.015 128.171 1630 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.53 % Allowed : 17.37 % Favored : 80.10 % 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: 0.59 (0.23), residues: 1428 helix: 0.52 (0.23), residues: 582 sheet: -0.26 (0.32), residues: 256 loop : 0.87 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 79 HIS 0.019 0.001 HIS B 101 PHE 0.009 0.001 PHE C 255 TYR 0.018 0.001 TYR A 337 ARG 0.004 0.000 ARG D 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.190 Fit side-chains REVERT: A 82 MET cc_start: 0.7737 (tpt) cc_final: 0.7296 (tpt) REVERT: A 95 ARG cc_start: 0.7588 (mmt-90) cc_final: 0.7195 (mmt-90) REVERT: A 259 GLU cc_start: 0.7652 (tp30) cc_final: 0.7429 (tp30) REVERT: B 62 ARG cc_start: 0.6127 (ptt90) cc_final: 0.5869 (ptt180) REVERT: C 53 TYR cc_start: 0.8783 (m-80) cc_final: 0.8442 (m-80) REVERT: C 314 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7928 (tt0) outliers start: 31 outliers final: 27 residues processed: 158 average time/residue: 0.2553 time to fit residues: 57.1949 Evaluate side-chains 166 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 117 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.0970 chunk 98 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120787 restraints weight = 13247.540| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.64 r_work: 0.3252 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11714 Z= 0.151 Angle : 0.544 6.585 15900 Z= 0.255 Chirality : 0.043 0.152 1770 Planarity : 0.004 0.036 2028 Dihedral : 5.973 128.231 1630 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.28 % Allowed : 17.62 % Favored : 80.10 % 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: 0.71 (0.23), residues: 1428 helix: 0.62 (0.23), residues: 576 sheet: -0.24 (0.32), residues: 256 loop : 0.94 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 79 HIS 0.008 0.001 HIS B 101 PHE 0.008 0.001 PHE C 255 TYR 0.017 0.001 TYR A 337 ARG 0.004 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5700.52 seconds wall clock time: 104 minutes 16.32 seconds (6256.32 seconds total)