Starting phenix.real_space_refine on Thu Nov 14 16:39:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg0_29990/11_2024/8gg0_29990.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg0_29990/11_2024/8gg0_29990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg0_29990/11_2024/8gg0_29990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg0_29990/11_2024/8gg0_29990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg0_29990/11_2024/8gg0_29990.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gg0_29990/11_2024/8gg0_29990.cif" } resolution = 2.9 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= -0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 4316 2.51 5 N 1155 2.21 5 O 1226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6745 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2427 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 347 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2171 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 20 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 5} Link IDs: {None: 5} Time building chain proxies: 4.98, per 1000 atoms: 0.74 Number of scatterers: 6745 At special positions: 0 Unit cell: (83.2992, 134.493, 98.0501, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 3 15.00 O 1226 8.00 N 1155 7.00 C 4316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 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: 1.73 Conformation dependent library (CDL) restraints added in 1.0 seconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 48.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.774A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.807A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.716A pdb=" N ILE A 235 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.553A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.743A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.968A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 24 removed outlier: 3.542A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.563A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.641A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 33 through 61 removed outlier: 3.507A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 removed outlier: 3.777A pdb=" N GLN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 65' Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.081A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 101 through 137 removed outlier: 4.337A pdb=" N TRP R 105 " --> pdb=" O PHE R 101 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.675A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 removed outlier: 3.513A pdb=" N GLU R 187 " --> pdb=" O ASN R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 237 removed outlier: 3.679A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.542A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.748A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.015A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 removed outlier: 3.820A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 321 No H-bonds generated for 'chain 'R' and resid 319 through 321' Processing helix chain 'R' and resid 322 through 327 Processing helix chain 'R' and resid 329 through 339 removed outlier: 3.906A pdb=" N ALA R 335 " --> pdb=" O ASP R 331 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN R 337 " --> pdb=" O ARG R 333 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.216A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.691A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.052A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.119A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.832A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.857A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.637A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.905A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1075 1.32 - 1.44: 1936 1.44 - 1.57: 3806 1.57 - 1.69: 6 1.69 - 1.81: 62 Bond restraints: 6885 Sorted by residual: bond pdb=" C ILE R 233 " pdb=" O ILE R 233 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.17e-02 7.31e+03 1.29e+01 bond pdb=" C LYS R 232 " pdb=" O LYS R 232 " ideal model delta sigma weight residual 1.237 1.204 0.033 1.17e-02 7.31e+03 7.73e+00 bond pdb=" C LEU R 230 " pdb=" N GLN R 231 " ideal model delta sigma weight residual 1.335 1.301 0.034 1.31e-02 5.83e+03 6.78e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" CA LYS R 235 " pdb=" C LYS R 235 " ideal model delta sigma weight residual 1.524 1.494 0.031 1.24e-02 6.50e+03 6.06e+00 ... (remaining 6880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 9192 1.35 - 2.69: 154 2.69 - 4.04: 32 4.04 - 5.38: 15 5.38 - 6.73: 6 Bond angle restraints: 9399 Sorted by residual: angle pdb=" N SER R 236 " pdb=" CA SER R 236 " pdb=" C SER R 236 " ideal model delta sigma weight residual 111.28 118.01 -6.73 1.09e+00 8.42e-01 3.81e+01 angle pdb=" N LYS R 232 " pdb=" CA LYS R 232 " pdb=" C LYS R 232 " ideal model delta sigma weight residual 111.28 117.90 -6.62 1.09e+00 8.42e-01 3.69e+01 angle pdb=" O LEU R 230 " pdb=" C LEU R 230 " pdb=" N GLN R 231 " ideal model delta sigma weight residual 122.12 116.45 5.67 1.06e+00 8.90e-01 2.86e+01 angle pdb=" CA LEU R 230 " pdb=" C LEU R 230 " pdb=" N GLN R 231 " ideal model delta sigma weight residual 117.30 123.05 -5.75 1.16e+00 7.43e-01 2.46e+01 angle pdb=" N ASP R 234 " pdb=" CA ASP R 234 " pdb=" C ASP R 234 " ideal model delta sigma weight residual 113.28 117.92 -4.64 1.22e+00 6.72e-01 1.45e+01 ... (remaining 9394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.29: 3885 28.29 - 56.58: 110 56.58 - 84.87: 11 84.87 - 113.17: 1 113.17 - 141.46: 1 Dihedral angle restraints: 4008 sinusoidal: 1393 harmonic: 2615 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -36.86 141.46 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual -56.21 -159.06 102.85 1 2.00e+01 2.50e-03 2.93e+01 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 4005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 724 0.034 - 0.068: 278 0.068 - 0.103: 83 0.103 - 0.137: 24 0.137 - 0.171: 3 Chirality restraints: 1112 Sorted by residual: chirality pdb=" CA LYS R 232 " pdb=" N LYS R 232 " pdb=" C LYS R 232 " pdb=" CB LYS R 232 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CA ASP R 234 " pdb=" N ASP R 234 " pdb=" C ASP R 234 " pdb=" CB ASP R 234 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 1109 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C ILE R 205 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 230 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C LEU R 230 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU R 230 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN R 231 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 281 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C THR R 281 " 0.020 2.00e-02 2.50e+03 pdb=" O THR R 281 " -0.008 2.00e-02 2.50e+03 pdb=" N PHE R 282 " -0.007 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 856 2.75 - 3.29: 6107 3.29 - 3.83: 10610 3.83 - 4.36: 12314 4.36 - 4.90: 22571 Nonbonded interactions: 52458 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.215 3.040 nonbonded pdb=" O TYR R 132 " pdb=" OG1 THR R 136 " model vdw 2.296 3.040 nonbonded pdb=" OD2 ASP A 343 " pdb=" NH2 ARG R 239 " model vdw 2.334 3.120 nonbonded pdb=" O SER R 137 " pdb=" OG SER R 137 " model vdw 2.343 3.040 nonbonded pdb=" OD1 ASN A 239 " pdb=" NZ LYS B 57 " model vdw 2.348 3.120 ... (remaining 52453 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.500 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.990 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6885 Z= 0.209 Angle : 0.512 6.731 9399 Z= 0.297 Chirality : 0.041 0.171 1112 Planarity : 0.003 0.028 1177 Dihedral : 13.395 141.458 2307 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 881 helix: 1.23 (0.26), residues: 388 sheet: 0.42 (0.41), residues: 160 loop : -0.63 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.015 0.001 PHE B 234 TYR 0.010 0.001 TYR A 339 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.720 Fit side-chains REVERT: B 153 ASP cc_start: 0.7488 (t70) cc_final: 0.7211 (t70) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 1.1255 time to fit residues: 103.8485 Evaluate side-chains 74 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 175 GLN R 241 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 6885 Z= 0.184 Angle : 0.495 5.793 9399 Z= 0.265 Chirality : 0.041 0.129 1112 Planarity : 0.003 0.029 1177 Dihedral : 8.232 141.285 985 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.52 % Allowed : 6.82 % Favored : 91.67 % 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: 1.02 (0.28), residues: 881 helix: 1.78 (0.27), residues: 390 sheet: 0.47 (0.42), residues: 159 loop : -0.51 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.790 Fit side-chains REVERT: A 29 GLN cc_start: 0.7591 (tp40) cc_final: 0.7321 (mm-40) REVERT: B 111 TYR cc_start: 0.8747 (m-80) cc_final: 0.8510 (m-80) REVERT: B 153 ASP cc_start: 0.7500 (t70) cc_final: 0.7068 (t70) REVERT: R 65 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8172 (mm110) REVERT: R 82 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.5972 (tpp) outliers start: 10 outliers final: 4 residues processed: 90 average time/residue: 1.2001 time to fit residues: 114.0420 Evaluate side-chains 81 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 184 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 67 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 236 GLN B 175 GLN R 51 ASN R 241 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6885 Z= 0.146 Angle : 0.455 5.787 9399 Z= 0.243 Chirality : 0.040 0.130 1112 Planarity : 0.003 0.028 1177 Dihedral : 8.081 140.722 985 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.52 % Allowed : 10.00 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.29), residues: 881 helix: 2.04 (0.27), residues: 392 sheet: 0.59 (0.41), residues: 159 loop : -0.47 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS R 178 PHE 0.011 0.001 PHE A 212 TYR 0.011 0.001 TYR A 339 ARG 0.001 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.778 Fit side-chains REVERT: A 29 GLN cc_start: 0.7537 (tp40) cc_final: 0.7261 (mm-40) REVERT: A 338 LYS cc_start: 0.6482 (mtmt) cc_final: 0.6280 (mtmt) REVERT: B 111 TYR cc_start: 0.8750 (m-80) cc_final: 0.8512 (m-80) REVERT: B 153 ASP cc_start: 0.7363 (t70) cc_final: 0.6867 (t70) REVERT: R 82 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.5922 (tpp) outliers start: 10 outliers final: 4 residues processed: 85 average time/residue: 1.2668 time to fit residues: 113.7526 Evaluate side-chains 84 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.2980 chunk 42 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.0170 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 236 GLN B 175 GLN R 51 ASN R 65 GLN R 241 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6885 Z= 0.148 Angle : 0.453 5.809 9399 Z= 0.242 Chirality : 0.040 0.133 1112 Planarity : 0.003 0.030 1177 Dihedral : 8.027 140.325 985 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.06 % Allowed : 13.33 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 881 helix: 2.17 (0.27), residues: 392 sheet: 0.66 (0.41), residues: 159 loop : -0.46 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.765 Fit side-chains REVERT: A 29 GLN cc_start: 0.7572 (tp40) cc_final: 0.7306 (mm-40) REVERT: A 222 PHE cc_start: 0.7439 (m-80) cc_final: 0.7210 (m-80) REVERT: B 111 TYR cc_start: 0.8734 (m-80) cc_final: 0.8518 (m-80) REVERT: B 153 ASP cc_start: 0.7355 (t70) cc_final: 0.6822 (t70) REVERT: B 262 MET cc_start: 0.8702 (ttp) cc_final: 0.8395 (ttm) REVERT: R 82 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.5999 (tpp) outliers start: 7 outliers final: 4 residues processed: 85 average time/residue: 1.2005 time to fit residues: 107.9841 Evaluate side-chains 84 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 236 GLN B 175 GLN R 51 ASN R 241 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6885 Z= 0.187 Angle : 0.476 5.844 9399 Z= 0.254 Chirality : 0.041 0.141 1112 Planarity : 0.003 0.032 1177 Dihedral : 8.097 140.678 985 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.42 % Allowed : 12.73 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.29), residues: 881 helix: 2.15 (0.27), residues: 391 sheet: 0.68 (0.40), residues: 164 loop : -0.47 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR A 339 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.706 Fit side-chains REVERT: A 29 GLN cc_start: 0.7558 (tp40) cc_final: 0.7286 (mm-40) REVERT: A 368 ASP cc_start: 0.7661 (m-30) cc_final: 0.7332 (m-30) REVERT: B 153 ASP cc_start: 0.7445 (t70) cc_final: 0.6888 (t70) REVERT: B 234 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: B 262 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8409 (ttm) REVERT: R 82 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.5956 (tpp) outliers start: 16 outliers final: 6 residues processed: 86 average time/residue: 1.2366 time to fit residues: 112.2512 Evaluate side-chains 85 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6885 Z= 0.148 Angle : 0.454 5.808 9399 Z= 0.242 Chirality : 0.040 0.142 1112 Planarity : 0.003 0.031 1177 Dihedral : 8.006 140.347 985 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.67 % Allowed : 14.55 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.29), residues: 881 helix: 2.24 (0.27), residues: 391 sheet: 0.73 (0.40), residues: 164 loop : -0.44 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS R 178 PHE 0.014 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.565 Fit side-chains REVERT: A 29 GLN cc_start: 0.7563 (tp40) cc_final: 0.7289 (mm-40) REVERT: B 111 TYR cc_start: 0.8754 (m-80) cc_final: 0.8524 (m-80) REVERT: B 153 ASP cc_start: 0.7454 (t70) cc_final: 0.6893 (t70) REVERT: B 234 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: B 262 MET cc_start: 0.8710 (ttp) cc_final: 0.8434 (ttm) REVERT: R 52 VAL cc_start: 0.7300 (t) cc_final: 0.7052 (m) REVERT: R 82 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.5888 (tpp) REVERT: R 235 LYS cc_start: 0.7565 (tttm) cc_final: 0.7273 (tmtt) outliers start: 11 outliers final: 5 residues processed: 88 average time/residue: 0.8140 time to fit residues: 75.7873 Evaluate side-chains 88 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 175 GLN B 237 ASN R 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6885 Z= 0.164 Angle : 0.466 5.831 9399 Z= 0.249 Chirality : 0.041 0.154 1112 Planarity : 0.003 0.032 1177 Dihedral : 8.007 140.311 985 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.52 % Allowed : 15.30 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.29), residues: 881 helix: 2.24 (0.27), residues: 391 sheet: 0.73 (0.40), residues: 164 loop : -0.46 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.009 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.011 0.001 TYR A 339 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.761 Fit side-chains REVERT: A 29 GLN cc_start: 0.7554 (tp40) cc_final: 0.7311 (mm-40) REVERT: A 368 ASP cc_start: 0.7624 (m-30) cc_final: 0.7286 (m-30) REVERT: B 153 ASP cc_start: 0.7511 (t70) cc_final: 0.6902 (t70) REVERT: B 262 MET cc_start: 0.8661 (ttp) cc_final: 0.8368 (ttm) REVERT: R 82 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.5891 (tpp) REVERT: R 235 LYS cc_start: 0.7576 (tttm) cc_final: 0.7298 (tmtt) outliers start: 10 outliers final: 5 residues processed: 83 average time/residue: 1.1997 time to fit residues: 105.3407 Evaluate side-chains 85 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 175 GLN R 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6885 Z= 0.156 Angle : 0.460 5.818 9399 Z= 0.245 Chirality : 0.041 0.153 1112 Planarity : 0.003 0.031 1177 Dihedral : 7.955 140.070 985 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.52 % Allowed : 15.45 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.29), residues: 881 helix: 2.25 (0.27), residues: 392 sheet: 0.69 (0.40), residues: 164 loop : -0.42 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.009 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.760 Fit side-chains REVERT: A 29 GLN cc_start: 0.7580 (tp40) cc_final: 0.7303 (mm-40) REVERT: A 330 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: A 368 ASP cc_start: 0.7613 (m-30) cc_final: 0.7336 (m-30) REVERT: B 16 ASN cc_start: 0.6980 (m-40) cc_final: 0.6402 (m110) REVERT: B 111 TYR cc_start: 0.8779 (m-80) cc_final: 0.8552 (m-80) REVERT: B 153 ASP cc_start: 0.7499 (t70) cc_final: 0.6851 (t70) REVERT: B 262 MET cc_start: 0.8650 (ttp) cc_final: 0.8365 (ttm) REVERT: R 52 VAL cc_start: 0.7286 (t) cc_final: 0.7056 (m) REVERT: R 82 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.5883 (tpp) REVERT: R 235 LYS cc_start: 0.7589 (tttm) cc_final: 0.7325 (tmtt) outliers start: 10 outliers final: 5 residues processed: 90 average time/residue: 1.1667 time to fit residues: 110.9775 Evaluate side-chains 89 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 175 GLN R 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6885 Z= 0.153 Angle : 0.459 5.809 9399 Z= 0.244 Chirality : 0.041 0.160 1112 Planarity : 0.003 0.031 1177 Dihedral : 7.880 139.761 985 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.67 % Allowed : 15.61 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.29), residues: 881 helix: 2.26 (0.27), residues: 392 sheet: 0.66 (0.40), residues: 164 loop : -0.41 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.001 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.682 Fit side-chains REVERT: A 29 GLN cc_start: 0.7578 (tp40) cc_final: 0.7305 (mm-40) REVERT: A 368 ASP cc_start: 0.7694 (m-30) cc_final: 0.7336 (m-30) REVERT: B 16 ASN cc_start: 0.6978 (m-40) cc_final: 0.6396 (m110) REVERT: B 111 TYR cc_start: 0.8766 (m-80) cc_final: 0.8544 (m-80) REVERT: B 153 ASP cc_start: 0.7473 (t70) cc_final: 0.6845 (t70) REVERT: B 262 MET cc_start: 0.8655 (ttp) cc_final: 0.8402 (ttm) REVERT: R 52 VAL cc_start: 0.7282 (t) cc_final: 0.7039 (m) REVERT: R 82 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5863 (tpp) REVERT: R 235 LYS cc_start: 0.7579 (tttm) cc_final: 0.7322 (tmtt) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 1.2372 time to fit residues: 112.9406 Evaluate side-chains 88 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 0.0670 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 0.0270 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 175 GLN R 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6885 Z= 0.118 Angle : 0.429 5.761 9399 Z= 0.228 Chirality : 0.040 0.163 1112 Planarity : 0.003 0.029 1177 Dihedral : 7.602 138.069 985 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.21 % Allowed : 16.06 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.29), residues: 881 helix: 2.48 (0.27), residues: 388 sheet: 0.71 (0.41), residues: 160 loop : -0.33 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.001 0.000 ARG R 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.710 Fit side-chains REVERT: A 29 GLN cc_start: 0.7582 (tp40) cc_final: 0.7307 (mm-40) REVERT: A 368 ASP cc_start: 0.7639 (m-30) cc_final: 0.7312 (m-30) REVERT: B 16 ASN cc_start: 0.6965 (m-40) cc_final: 0.6383 (m110) REVERT: B 111 TYR cc_start: 0.8702 (m-80) cc_final: 0.8494 (m-80) REVERT: B 153 ASP cc_start: 0.7352 (t70) cc_final: 0.7030 (t70) REVERT: R 52 VAL cc_start: 0.7345 (t) cc_final: 0.7108 (m) REVERT: R 82 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6016 (tpp) REVERT: R 130 ASP cc_start: 0.8239 (t70) cc_final: 0.7997 (t0) REVERT: R 235 LYS cc_start: 0.7532 (tttm) cc_final: 0.7313 (tmtt) outliers start: 8 outliers final: 5 residues processed: 89 average time/residue: 1.1747 time to fit residues: 110.5799 Evaluate side-chains 84 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 0.0010 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 175 GLN R 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112296 restraints weight = 8706.917| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.17 r_work: 0.3179 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6885 Z= 0.119 Angle : 0.430 5.794 9399 Z= 0.229 Chirality : 0.040 0.159 1112 Planarity : 0.003 0.030 1177 Dihedral : 7.394 137.182 985 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.91 % Allowed : 16.97 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.29), residues: 881 helix: 2.58 (0.27), residues: 388 sheet: 0.74 (0.41), residues: 160 loop : -0.31 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.008 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.001 0.000 ARG R 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.19 seconds wall clock time: 52 minutes 46.39 seconds (3166.39 seconds total)