Starting phenix.real_space_refine on Wed Mar 12 23:45:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gag_29898/03_2025/8gag_29898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gag_29898/03_2025/8gag_29898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gag_29898/03_2025/8gag_29898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gag_29898/03_2025/8gag_29898.map" model { file = "/net/cci-nas-00/data/ceres_data/8gag_29898/03_2025/8gag_29898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gag_29898/03_2025/8gag_29898.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.071 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 S 61 5.16 5 C 5416 2.51 5 N 1454 2.21 5 O 1535 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8469 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1659 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2573 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2018 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "S" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'YVF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.57, per 1000 atoms: 0.66 Number of scatterers: 8469 At special positions: 0 Unit cell: (87.7663, 122.702, 126.111, 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 61 16.00 F 3 9.00 O 1535 8.00 N 1454 7.00 C 5416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.0 seconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 38.0% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 removed outlier: 3.916A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 28 through 31 Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.777A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.602A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.841A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.639A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 301 through 309 removed outlier: 4.285A pdb=" N CYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.108A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 4.406A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 4.230A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.911A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.724A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'R' and resid 112 through 139 removed outlier: 4.154A pdb=" N ALA R 120 " --> pdb=" O GLN R 116 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU R 122 " --> pdb=" O ALA R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 179 removed outlier: 4.044A pdb=" N ILE R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL R 168 " --> pdb=" O LEU R 164 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE R 170 " --> pdb=" O GLY R 166 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE R 175 " --> pdb=" O VAL R 171 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP R 176 " --> pdb=" O TYR R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 220 removed outlier: 4.313A pdb=" N SER R 199 " --> pdb=" O GLY R 195 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE R 200 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL R 204 " --> pdb=" O PHE R 200 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE R 212 " --> pdb=" O PHE R 208 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP R 213 " --> pdb=" O LEU R 209 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 228 removed outlier: 3.507A pdb=" N VAL R 228 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 246 removed outlier: 3.693A pdb=" N VAL R 234 " --> pdb=" O ARG R 230 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 253 removed outlier: 3.967A pdb=" N LEU R 252 " --> pdb=" O ALA R 248 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU R 253 " --> pdb=" O VAL R 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 248 through 253' Processing helix chain 'R' and resid 274 through 312 removed outlier: 4.246A pdb=" N ILE R 280 " --> pdb=" O LEU R 276 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY R 281 " --> pdb=" O MET R 277 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL R 282 " --> pdb=" O PHE R 278 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET R 295 " --> pdb=" O VAL R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 356 removed outlier: 4.442A pdb=" N THR R 344 " --> pdb=" O ARG R 340 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL R 346 " --> pdb=" O ALA R 342 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE R 353 " --> pdb=" O LEU R 349 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS R 355 " --> pdb=" O VAL R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 369 removed outlier: 3.706A pdb=" N VAL R 364 " --> pdb=" O LEU R 360 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL R 367 " --> pdb=" O MET R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 372 through 383 removed outlier: 3.555A pdb=" N LYS R 376 " --> pdb=" O ASN R 372 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE R 381 " --> pdb=" O THR R 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 397 removed outlier: 3.780A pdb=" N VAL R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN R 393 " --> pdb=" O ASN R 389 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 401 through 411 removed outlier: 3.659A pdb=" N ARG R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS R 406 " --> pdb=" O LYS R 402 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG R 409 " --> pdb=" O ARG R 405 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.798A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.758A pdb=" N SER S 55 " --> pdb=" O SER S 52 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 52 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.578A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.616A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38 removed outlier: 3.959A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 223 removed outlier: 3.502A pdb=" N ILE A 265 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 266 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.988A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.055A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.077A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.796A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.819A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 284 through 285 removed outlier: 3.863A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 8 removed outlier: 4.017A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.954A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.509A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR S 203 " --> pdb=" O SER S 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER S 192 " --> pdb=" O THR S 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.596A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.596A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 987 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: 2.20 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1337 1.31 - 1.44: 2420 1.44 - 1.57: 4799 1.57 - 1.70: 2 1.70 - 1.83: 87 Bond restraints: 8645 Sorted by residual: bond pdb=" C06 YVF R 501 " pdb=" C07 YVF R 501 " ideal model delta sigma weight residual 1.420 1.527 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C05 YVF R 501 " pdb=" S09 YVF R 501 " ideal model delta sigma weight residual 1.722 1.616 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C12 YVF R 501 " pdb=" N11 YVF R 501 " ideal model delta sigma weight residual 1.345 1.450 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C08 YVF R 501 " pdb=" S09 YVF R 501 " ideal model delta sigma weight residual 1.710 1.616 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C03 YVF R 501 " pdb=" O02 YVF R 501 " ideal model delta sigma weight residual 1.318 1.399 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 8640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 11307 1.86 - 3.71: 349 3.71 - 5.57: 61 5.57 - 7.43: 12 7.43 - 9.28: 6 Bond angle restraints: 11735 Sorted by residual: angle pdb=" C05 YVF R 501 " pdb=" S09 YVF R 501 " pdb=" C08 YVF R 501 " ideal model delta sigma weight residual 92.16 101.44 -9.28 3.00e+00 1.11e-01 9.58e+00 angle pdb=" C SER A 293 " pdb=" N ASN A 294 " pdb=" CA ASN A 294 " ideal model delta sigma weight residual 124.82 130.08 -5.26 1.78e+00 3.16e-01 8.74e+00 angle pdb=" CA TYR S 178 " pdb=" CB TYR S 178 " pdb=" CG TYR S 178 " ideal model delta sigma weight residual 113.90 119.12 -5.22 1.80e+00 3.09e-01 8.42e+00 angle pdb=" CA ASP B 247 " pdb=" CB ASP B 247 " pdb=" CG ASP B 247 " ideal model delta sigma weight residual 112.60 115.47 -2.87 1.00e+00 1.00e+00 8.25e+00 angle pdb=" CA LYS S 43 " pdb=" CB LYS S 43 " pdb=" CG LYS S 43 " ideal model delta sigma weight residual 114.10 119.52 -5.42 2.00e+00 2.50e-01 7.36e+00 ... (remaining 11730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4487 17.93 - 35.86: 496 35.86 - 53.79: 95 53.79 - 71.72: 12 71.72 - 89.65: 10 Dihedral angle restraints: 5100 sinusoidal: 1884 harmonic: 3216 Sorted by residual: dihedral pdb=" CA MET B 325 " pdb=" C MET B 325 " pdb=" N ALA B 326 " pdb=" CA ALA B 326 " ideal model delta harmonic sigma weight residual -180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLY S 26 " pdb=" C GLY S 26 " pdb=" N PHE S 27 " pdb=" CA PHE S 27 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1051 0.052 - 0.105: 246 0.105 - 0.157: 59 0.157 - 0.209: 3 0.209 - 0.262: 1 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CA ASP S 109 " pdb=" N ASP S 109 " pdb=" C ASP S 109 " pdb=" CB ASP S 109 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1357 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 47 " 0.023 2.00e-02 2.50e+03 1.72e-02 7.41e+00 pdb=" CG TRP S 47 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP S 47 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP S 47 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP S 47 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP S 47 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP S 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 47 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 47 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP S 47 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO C 49 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 180 " 0.013 2.00e-02 2.50e+03 1.60e-02 4.49e+00 pdb=" CG PHE R 180 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE R 180 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE R 180 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE R 180 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 180 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 180 " 0.001 2.00e-02 2.50e+03 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 194 2.69 - 3.24: 8182 3.24 - 3.79: 12256 3.79 - 4.35: 16124 4.35 - 4.90: 27132 Nonbonded interactions: 63888 Sorted by model distance: nonbonded pdb=" O ILE S 100 " pdb=" OG SER S 105 " model vdw 2.132 3.040 nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.137 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.168 3.040 nonbonded pdb=" ND1 HIS R 302 " pdb=" OD2 ASP R 338 " model vdw 2.178 3.120 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.183 3.040 ... (remaining 63883 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: 2.270 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.730 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 8645 Z= 0.341 Angle : 0.811 9.284 11735 Z= 0.432 Chirality : 0.048 0.262 1360 Planarity : 0.005 0.058 1471 Dihedral : 15.819 89.648 3019 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.24), residues: 1088 helix: -0.95 (0.26), residues: 355 sheet: -1.28 (0.32), residues: 253 loop : -1.14 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP S 47 HIS 0.012 0.002 HIS B 311 PHE 0.037 0.003 PHE R 180 TYR 0.026 0.003 TYR S 223 ARG 0.007 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.913 Fit side-chains REVERT: R 343 LYS cc_start: 0.7367 (ttpt) cc_final: 0.7163 (ttpp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2195 time to fit residues: 31.7716 Evaluate side-chains 96 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN R 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.195864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.158799 restraints weight = 9912.402| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 3.17 r_work: 0.3715 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8645 Z= 0.199 Angle : 0.655 6.974 11735 Z= 0.344 Chirality : 0.044 0.177 1360 Planarity : 0.004 0.035 1471 Dihedral : 6.283 70.745 1226 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.68 % Allowed : 12.33 % Favored : 86.99 % 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: -1.06 (0.25), residues: 1088 helix: -0.19 (0.28), residues: 361 sheet: -0.81 (0.32), residues: 251 loop : -0.89 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP S 47 HIS 0.005 0.001 HIS B 311 PHE 0.016 0.002 PHE R 237 TYR 0.021 0.002 TYR S 223 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.815 Fit side-chains REVERT: A 247 MET cc_start: 0.6446 (mtp) cc_final: 0.6218 (mtm) REVERT: S 93 MET cc_start: 0.7513 (mmm) cc_final: 0.6919 (mpp) REVERT: S 218 MET cc_start: 0.7048 (ttp) cc_final: 0.6782 (ttp) REVERT: S 225 LEU cc_start: 0.4562 (mt) cc_final: 0.4344 (mt) outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 0.2058 time to fit residues: 30.2849 Evaluate side-chains 93 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain R residue 354 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 66 optimal weight: 0.0770 chunk 31 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 32 GLN R 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.195428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.156175 restraints weight = 9994.100| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.23 r_work: 0.3690 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8645 Z= 0.188 Angle : 0.596 6.581 11735 Z= 0.315 Chirality : 0.043 0.171 1360 Planarity : 0.004 0.037 1471 Dihedral : 5.923 65.763 1226 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.14 % Allowed : 15.07 % 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: -0.80 (0.25), residues: 1088 helix: 0.09 (0.28), residues: 363 sheet: -0.71 (0.32), residues: 255 loop : -0.76 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP S 47 HIS 0.005 0.001 HIS B 311 PHE 0.016 0.001 PHE R 237 TYR 0.018 0.002 TYR S 223 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.887 Fit side-chains REVERT: A 247 MET cc_start: 0.6383 (mtp) cc_final: 0.6158 (mtm) REVERT: S 93 MET cc_start: 0.7416 (mmm) cc_final: 0.6937 (mpp) outliers start: 10 outliers final: 8 residues processed: 99 average time/residue: 0.2004 time to fit residues: 27.7519 Evaluate side-chains 97 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.0060 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 44 GLN R 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.194113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.154530 restraints weight = 9921.539| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.23 r_work: 0.3719 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.003 0.030 8645 Z= 0.192 Angle : 0.580 7.257 11735 Z= 0.308 Chirality : 0.042 0.168 1360 Planarity : 0.004 0.035 1471 Dihedral : 5.742 60.093 1226 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.94 % Allowed : 17.24 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.26), residues: 1088 helix: 0.16 (0.29), residues: 366 sheet: -0.74 (0.31), residues: 258 loop : -0.53 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP S 47 HIS 0.005 0.001 HIS B 311 PHE 0.016 0.001 PHE R 237 TYR 0.019 0.002 TYR S 50 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.945 Fit side-chains REVERT: A 247 MET cc_start: 0.6380 (mtp) cc_final: 0.6132 (mtt) REVERT: S 93 MET cc_start: 0.7252 (mmm) cc_final: 0.6905 (mpp) outliers start: 17 outliers final: 12 residues processed: 100 average time/residue: 0.2049 time to fit residues: 28.7704 Evaluate side-chains 98 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 102 optimal weight: 0.0470 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 HIS S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.192852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154021 restraints weight = 9869.522| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.14 r_work: 0.3689 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8645 Z= 0.211 Angle : 0.593 8.354 11735 Z= 0.313 Chirality : 0.043 0.166 1360 Planarity : 0.004 0.034 1471 Dihedral : 5.701 56.273 1226 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.94 % Allowed : 20.55 % Favored : 77.51 % 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: -0.64 (0.26), residues: 1088 helix: 0.19 (0.29), residues: 366 sheet: -0.71 (0.32), residues: 252 loop : -0.59 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP S 47 HIS 0.005 0.001 HIS B 311 PHE 0.017 0.002 PHE R 237 TYR 0.020 0.002 TYR S 50 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.911 Fit side-chains REVERT: A 247 MET cc_start: 0.6400 (mtp) cc_final: 0.6179 (mtm) REVERT: S 93 MET cc_start: 0.7291 (mmm) cc_final: 0.7078 (mpp) REVERT: S 218 MET cc_start: 0.7057 (ttp) cc_final: 0.6773 (ttp) outliers start: 17 outliers final: 14 residues processed: 102 average time/residue: 0.2000 time to fit residues: 28.7433 Evaluate side-chains 100 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain R residue 213 ASP Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN R 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.191680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.152364 restraints weight = 10085.633| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 3.32 r_work: 0.3637 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8645 Z= 0.296 Angle : 0.647 8.524 11735 Z= 0.345 Chirality : 0.045 0.167 1360 Planarity : 0.004 0.035 1471 Dihedral : 5.990 52.020 1226 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.51 % Allowed : 21.69 % Favored : 75.80 % 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: -0.86 (0.26), residues: 1088 helix: 0.03 (0.28), residues: 362 sheet: -0.96 (0.31), residues: 266 loop : -0.64 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP S 47 HIS 0.007 0.001 HIS B 311 PHE 0.021 0.002 PHE R 237 TYR 0.031 0.002 TYR S 50 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.844 Fit side-chains REVERT: A 223 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: A 247 MET cc_start: 0.6370 (mtp) cc_final: 0.6143 (mtt) REVERT: S 39 GLN cc_start: 0.6322 (tt0) cc_final: 0.6005 (mt0) REVERT: S 93 MET cc_start: 0.7277 (mmm) cc_final: 0.7061 (mpp) REVERT: S 177 ILE cc_start: 0.7273 (mm) cc_final: 0.7035 (mt) REVERT: S 218 MET cc_start: 0.7087 (ttp) cc_final: 0.6741 (ttp) outliers start: 22 outliers final: 16 residues processed: 114 average time/residue: 0.2117 time to fit residues: 33.4442 Evaluate side-chains 109 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 213 ASP Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN R 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.193972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.154851 restraints weight = 9906.096| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 3.18 r_work: 0.3694 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8645 Z= 0.189 Angle : 0.582 10.049 11735 Z= 0.308 Chirality : 0.042 0.163 1360 Planarity : 0.004 0.033 1471 Dihedral : 5.642 54.779 1226 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.74 % Allowed : 22.72 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1088 helix: 0.28 (0.29), residues: 362 sheet: -0.79 (0.32), residues: 257 loop : -0.53 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP S 47 HIS 0.004 0.001 HIS B 311 PHE 0.023 0.002 PHE B 292 TYR 0.016 0.002 TYR S 223 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.839 Fit side-chains REVERT: A 223 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7208 (m-80) REVERT: A 247 MET cc_start: 0.6380 (mtp) cc_final: 0.6159 (mtt) outliers start: 24 outliers final: 18 residues processed: 113 average time/residue: 0.1823 time to fit residues: 29.6700 Evaluate side-chains 111 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 139 CYS Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 389 ASN Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 31 optimal weight: 0.0980 chunk 88 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.196447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.156894 restraints weight = 9988.937| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.19 r_work: 0.3680 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8645 Z= 0.164 Angle : 0.582 10.851 11735 Z= 0.303 Chirality : 0.042 0.162 1360 Planarity : 0.003 0.034 1471 Dihedral : 5.480 54.528 1226 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.40 % Allowed : 23.17 % Favored : 74.43 % 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: -0.45 (0.26), residues: 1088 helix: 0.34 (0.29), residues: 368 sheet: -0.72 (0.32), residues: 249 loop : -0.39 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP S 47 HIS 0.003 0.001 HIS B 311 PHE 0.015 0.001 PHE R 237 TYR 0.016 0.001 TYR S 223 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.890 Fit side-chains REVERT: A 223 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: A 247 MET cc_start: 0.6307 (mtp) cc_final: 0.6096 (mtt) REVERT: B 333 ASP cc_start: 0.7533 (p0) cc_final: 0.7269 (p0) outliers start: 21 outliers final: 17 residues processed: 110 average time/residue: 0.2052 time to fit residues: 32.3155 Evaluate side-chains 110 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 139 CYS Chi-restraints excluded: chain R residue 279 TRP Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 389 ASN Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 103 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: R 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.196684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.158037 restraints weight = 9929.780| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.14 r_work: 0.3733 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8645 Z= 0.158 Angle : 0.559 9.745 11735 Z= 0.293 Chirality : 0.041 0.159 1360 Planarity : 0.003 0.035 1471 Dihedral : 5.332 53.089 1226 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.63 % Allowed : 22.72 % Favored : 74.66 % 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 (0.26), residues: 1088 helix: 0.47 (0.29), residues: 368 sheet: -0.65 (0.31), residues: 262 loop : -0.27 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP S 47 HIS 0.003 0.001 HIS B 311 PHE 0.014 0.001 PHE R 237 TYR 0.019 0.001 TYR S 59 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.852 Fit side-chains REVERT: A 223 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7222 (m-80) REVERT: A 247 MET cc_start: 0.6374 (mtp) cc_final: 0.6165 (mtt) REVERT: B 333 ASP cc_start: 0.7494 (p0) cc_final: 0.7170 (p0) REVERT: R 109 MET cc_start: 0.5843 (ptm) cc_final: 0.5605 (ptm) REVERT: S 218 MET cc_start: 0.6915 (ttp) cc_final: 0.6627 (mtp) outliers start: 23 outliers final: 19 residues processed: 111 average time/residue: 0.1856 time to fit residues: 29.3788 Evaluate side-chains 110 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 139 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 279 TRP Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 389 ASN Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 0.0170 chunk 73 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.196821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.158455 restraints weight = 9870.525| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.21 r_work: 0.3702 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8645 Z= 0.167 Angle : 0.567 9.876 11735 Z= 0.297 Chirality : 0.041 0.162 1360 Planarity : 0.003 0.034 1471 Dihedral : 5.322 52.570 1226 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.74 % Allowed : 22.72 % Favored : 74.54 % 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: -0.28 (0.27), residues: 1088 helix: 0.52 (0.29), residues: 368 sheet: -0.67 (0.31), residues: 266 loop : -0.28 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP S 47 HIS 0.003 0.001 HIS B 311 PHE 0.015 0.001 PHE R 237 TYR 0.014 0.001 TYR S 50 ARG 0.002 0.000 ARG R 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.983 Fit side-chains REVERT: A 223 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: A 247 MET cc_start: 0.6285 (mtp) cc_final: 0.6062 (mtt) REVERT: B 333 ASP cc_start: 0.7532 (p0) cc_final: 0.7265 (p0) REVERT: R 109 MET cc_start: 0.5825 (ptm) cc_final: 0.5602 (ptm) REVERT: S 218 MET cc_start: 0.6969 (ttp) cc_final: 0.6629 (mtp) outliers start: 24 outliers final: 22 residues processed: 112 average time/residue: 0.1877 time to fit residues: 30.5296 Evaluate side-chains 114 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 139 CYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 213 ASP Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 279 TRP Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 363 MET Chi-restraints excluded: chain R residue 389 ASN Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 147 CYS Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 2 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.190751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.150259 restraints weight = 10054.144| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.13 r_work: 0.3665 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8645 Z= 0.277 Angle : 0.649 9.998 11735 Z= 0.342 Chirality : 0.044 0.164 1360 Planarity : 0.004 0.033 1471 Dihedral : 5.757 49.409 1226 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.31 % Allowed : 22.95 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.26), residues: 1088 helix: 0.26 (0.28), residues: 365 sheet: -1.03 (0.31), residues: 273 loop : -0.51 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP S 47 HIS 0.005 0.001 HIS B 311 PHE 0.019 0.002 PHE R 237 TYR 0.026 0.002 TYR S 50 ARG 0.003 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6299.28 seconds wall clock time: 109 minutes 13.30 seconds (6553.30 seconds total)