Starting phenix.real_space_refine on Sat Nov 16 16:12:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjo_50507/11_2024/9fjo_50507.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjo_50507/11_2024/9fjo_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjo_50507/11_2024/9fjo_50507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjo_50507/11_2024/9fjo_50507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjo_50507/11_2024/9fjo_50507.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjo_50507/11_2024/9fjo_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.66, per 1000 atoms: 0.67 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: 3.34 Conformation dependent library (CDL) restraints added in 1.5 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: 1.96 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: 4.35 Time building geometry restraints manager: 3.75 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: 0.00 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: 14.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.080 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.170 ------------------------------------------------------------------------------- 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 : 1.245 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: 0.2473 time to fit residues: 50.0297 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 : 2.360 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 1.494 Fit side-chains REVERT: A 95 ARG cc_start: 0.7538 (mmt-90) cc_final: 0.7112 (mmt-90) REVERT: A 259 GLU cc_start: 0.7600 (tp30) cc_final: 0.7394 (tp30) REVERT: B 100 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7182 (mp0) outliers start: 22 outliers final: 13 residues processed: 156 average time/residue: 0.3174 time to fit residues: 70.8118 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 : 1.658 ------------------------------------------------------------------------------- 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 71 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11714 Z= 0.258 Angle : 0.590 7.264 15900 Z= 0.281 Chirality : 0.046 0.165 1770 Planarity : 0.004 0.037 2028 Dihedral : 5.994 91.325 1632 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.28 % Allowed : 16.31 % Favored : 81.40 % 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: 0.29 (0.23), residues: 1428 helix: 0.19 (0.22), residues: 576 sheet: -0.38 (0.33), residues: 250 loop : 0.76 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.002 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 171 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.392 Fit side-chains REVERT: A 82 MET cc_start: 0.7849 (tpt) cc_final: 0.7492 (tpt) REVERT: A 95 ARG cc_start: 0.7577 (mmt-90) cc_final: 0.7324 (mmt-90) REVERT: A 259 GLU cc_start: 0.7672 (tp30) cc_final: 0.7442 (tp30) REVERT: B 100 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: C 89 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8685 (m) REVERT: C 314 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8012 (tt0) outliers start: 28 outliers final: 19 residues processed: 162 average time/residue: 0.2607 time to fit residues: 59.9734 Evaluate side-chains 160 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 89 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 222 ASP 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 127 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1544 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= 0.391 Angle : 0.645 7.217 15900 Z= 0.311 Chirality : 0.049 0.183 1770 Planarity : 0.005 0.036 2028 Dihedral : 6.313 100.776 1632 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.85 % Allowed : 16.31 % Favored : 80.83 % 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: -0.07 (0.22), residues: 1428 helix: -0.09 (0.22), residues: 580 sheet: -0.53 (0.32), residues: 252 loop : 0.52 (0.26), residues: 596 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 0.013 0.002 PHE C 255 TYR 0.010 0.001 TYR D 218 ARG 0.003 0.000 ARG A 335 *********************** 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 170 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.378 Fit side-chains REVERT: A 82 MET cc_start: 0.7906 (tpt) cc_final: 0.7227 (tpt) REVERT: A 259 GLU cc_start: 0.7750 (tp30) cc_final: 0.7500 (tp30) REVERT: B 100 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: C 53 TYR cc_start: 0.8795 (m-80) cc_final: 0.8530 (m-80) REVERT: C 314 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8022 (tt0) outliers start: 35 outliers final: 27 residues processed: 161 average time/residue: 0.2452 time to fit residues: 56.4134 Evaluate side-chains 159 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 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 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 116 ARG 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 77 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 102 optimal weight: 0.0980 chunk 56 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11714 Z= 0.476 Angle : 0.691 7.695 15900 Z= 0.336 Chirality : 0.051 0.196 1770 Planarity : 0.005 0.038 2028 Dihedral : 6.685 109.452 1632 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.75 % Allowed : 15.74 % 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: -0.42 (0.22), residues: 1428 helix: -0.35 (0.22), residues: 580 sheet: -0.72 (0.31), residues: 270 loop : 0.34 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.006 0.002 HIS D 87 PHE 0.014 0.002 PHE C 255 TYR 0.022 0.002 TYR A 337 ARG 0.004 0.001 ARG B 95 *********************** 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 180 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 1.325 Fit side-chains REVERT: A 95 ARG cc_start: 0.7663 (mmt-90) cc_final: 0.7214 (mmt-90) REVERT: A 259 GLU cc_start: 0.7872 (tp30) cc_final: 0.7634 (tp30) REVERT: B 100 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: B 349 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6711 (mp) REVERT: C 53 TYR cc_start: 0.8793 (m-80) cc_final: 0.8396 (m-80) REVERT: C 314 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: D 82 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7940 (tpt) outliers start: 46 outliers final: 31 residues processed: 167 average time/residue: 0.2458 time to fit residues: 58.7340 Evaluate side-chains 167 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 250 ILE 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 47 MET 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 227 MET Chi-restraints excluded: chain C residue 289 ILE 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 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 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 123 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 132 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11714 Z= 0.169 Angle : 0.567 7.000 15900 Z= 0.269 Chirality : 0.044 0.152 1770 Planarity : 0.004 0.037 2028 Dihedral : 6.314 112.537 1632 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.53 % Allowed : 16.97 % 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: 0.14 (0.23), residues: 1428 helix: 0.19 (0.23), residues: 568 sheet: -0.54 (0.31), residues: 270 loop : 0.61 (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 C 161 PHE 0.010 0.001 PHE C 255 TYR 0.013 0.001 TYR D 362 ARG 0.003 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 170 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.197 Fit side-chains REVERT: A 82 MET cc_start: 0.7884 (tpt) cc_final: 0.7547 (tpt) REVERT: A 117 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6649 (mm-30) REVERT: A 196 ARG cc_start: 0.6956 (tpp80) cc_final: 0.6729 (tpp80) REVERT: A 259 GLU cc_start: 0.7703 (tp30) cc_final: 0.7483 (tp30) REVERT: B 62 ARG cc_start: 0.6268 (ptt90) cc_final: 0.6029 (ptt180) REVERT: B 349 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6601 (mp) REVERT: C 53 TYR cc_start: 0.8796 (m-80) cc_final: 0.8494 (m-80) REVERT: C 314 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7939 (tt0) outliers start: 31 outliers final: 20 residues processed: 164 average time/residue: 0.2485 time to fit residues: 58.1727 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 : 1.357 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11714 Z= 0.164 Angle : 0.552 7.004 15900 Z= 0.260 Chirality : 0.044 0.142 1770 Planarity : 0.004 0.034 2028 Dihedral : 6.155 117.960 1632 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.61 % Allowed : 16.97 % 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: 0.43 (0.23), residues: 1428 helix: 0.39 (0.23), residues: 570 sheet: -0.43 (0.31), residues: 262 loop : 0.81 (0.27), residues: 596 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 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 173 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.403 Fit side-chains REVERT: A 82 MET cc_start: 0.7881 (tpt) cc_final: 0.7333 (tpt) REVERT: A 95 ARG cc_start: 0.7638 (mmt-90) cc_final: 0.7412 (mmt-90) REVERT: A 117 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6695 (mm-30) REVERT: B 62 ARG cc_start: 0.6275 (ptt90) cc_final: 0.6011 (ptt180) REVERT: C 53 TYR cc_start: 0.8790 (m-80) cc_final: 0.8426 (m-80) REVERT: C 314 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7963 (tt0) outliers start: 32 outliers final: 23 residues processed: 164 average time/residue: 0.2461 time to fit residues: 57.8086 Evaluate side-chains 161 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 47 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 227 MET 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 132 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 353 GLN C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1832 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= 0.167 Angle : 0.552 6.957 15900 Z= 0.260 Chirality : 0.044 0.140 1770 Planarity : 0.004 0.033 2028 Dihedral : 6.028 121.407 1630 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.45 % Allowed : 16.88 % Favored : 80.67 % 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 (0.23), residues: 1428 helix: 0.48 (0.23), residues: 570 sheet: -0.45 (0.31), residues: 274 loop : 0.88 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 79 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE C 255 TYR 0.017 0.001 TYR A 337 ARG 0.003 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 172 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.408 Fit side-chains REVERT: A 82 MET cc_start: 0.7870 (tpt) cc_final: 0.7338 (tpt) REVERT: A 95 ARG cc_start: 0.7640 (mmt-90) cc_final: 0.7403 (mmt-90) REVERT: A 117 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6708 (mm-30) REVERT: B 62 ARG cc_start: 0.6173 (ptt90) cc_final: 0.5925 (ptt180) REVERT: C 53 TYR cc_start: 0.8785 (m-80) cc_final: 0.8421 (m-80) REVERT: C 289 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7993 (pt) REVERT: C 314 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7996 (tt0) outliers start: 30 outliers final: 24 residues processed: 163 average time/residue: 0.2520 time to fit residues: 58.4601 Evaluate side-chains 165 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 12 ASN Chi-restraints excluded: chain C residue 47 MET 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 300 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 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 B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1859 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= 0.176 Angle : 0.551 6.951 15900 Z= 0.260 Chirality : 0.044 0.142 1770 Planarity : 0.004 0.033 2028 Dihedral : 6.015 123.976 1630 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.28 % Allowed : 17.29 % 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: 0.53 (0.23), residues: 1428 helix: 0.50 (0.23), residues: 570 sheet: -0.38 (0.31), residues: 272 loop : 0.87 (0.27), residues: 586 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 0.017 0.001 TYR A 337 ARG 0.004 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 168 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.418 Fit side-chains REVERT: A 82 MET cc_start: 0.7861 (tpt) cc_final: 0.7340 (tpt) REVERT: A 95 ARG cc_start: 0.7627 (mmt-90) cc_final: 0.7381 (mmt-90) REVERT: A 117 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: B 62 ARG cc_start: 0.6148 (ptt90) cc_final: 0.5899 (ptt180) REVERT: C 53 TYR cc_start: 0.8791 (m-80) cc_final: 0.8430 (m-80) REVERT: C 289 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7991 (pt) REVERT: C 314 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7993 (tt0) outliers start: 28 outliers final: 24 residues processed: 158 average time/residue: 0.2519 time to fit residues: 56.7526 Evaluate side-chains 165 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 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 300 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11714 Z= 0.353 Angle : 0.622 7.400 15900 Z= 0.299 Chirality : 0.048 0.160 1770 Planarity : 0.004 0.037 2028 Dihedral : 6.347 136.021 1630 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.28 % Allowed : 17.29 % 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: 0.22 (0.23), residues: 1428 helix: 0.22 (0.23), residues: 562 sheet: -0.52 (0.31), residues: 268 loop : 0.69 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.006 0.001 HIS B 101 PHE 0.012 0.001 PHE C 255 TYR 0.020 0.001 TYR A 337 ARG 0.007 0.000 ARG B 95 ********************** 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 161 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.286 Fit side-chains REVERT: A 82 MET cc_start: 0.7843 (tpt) cc_final: 0.7477 (tpt) REVERT: A 95 ARG cc_start: 0.7626 (mmt-90) cc_final: 0.7215 (mmt-90) REVERT: B 100 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: C 53 TYR cc_start: 0.8801 (m-80) cc_final: 0.8376 (m-80) REVERT: C 289 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8037 (pt) REVERT: D 82 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7905 (tpt) REVERT: D 190 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8359 (mtt) outliers start: 28 outliers final: 24 residues processed: 150 average time/residue: 0.2500 time to fit residues: 53.5506 Evaluate side-chains 160 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 100 GLU 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 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 300 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 82 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 115 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS B 353 GLN C 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120225 restraints weight = 13192.820| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.62 r_work: 0.3239 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 0.031 11714 Z= 0.162 Angle : 0.552 6.752 15900 Z= 0.260 Chirality : 0.044 0.143 1770 Planarity : 0.004 0.034 2028 Dihedral : 6.159 135.985 1630 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.37 % Allowed : 17.13 % 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: 0.50 (0.23), residues: 1428 helix: 0.41 (0.23), residues: 576 sheet: -0.25 (0.32), residues: 258 loop : 0.83 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 356 HIS 0.005 0.001 HIS B 101 PHE 0.009 0.001 PHE C 255 TYR 0.016 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: 2527.43 seconds wall clock time: 47 minutes 46.12 seconds (2866.12 seconds total)