Starting phenix.real_space_refine on Sat Aug 23 09:11:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tqo_41510/08_2025/8tqo_41510.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tqo_41510/08_2025/8tqo_41510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tqo_41510/08_2025/8tqo_41510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tqo_41510/08_2025/8tqo_41510.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tqo_41510/08_2025/8tqo_41510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tqo_41510/08_2025/8tqo_41510.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.007 sd= 0.080 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 7047 2.51 5 N 1959 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11122 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3200 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "I" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2716 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2734 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 332} Time building chain proxies: 2.38, per 1000 atoms: 0.21 Number of scatterers: 11122 At special positions: 0 Unit cell: (131.095, 96.025, 129.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2052 8.00 N 1959 7.00 C 7047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 397.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 37.2% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.705A pdb=" N TYR A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.648A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.636A pdb=" N ASP A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.806A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.515A pdb=" N ASN A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'I' and resid 24 through 27 Processing helix chain 'I' and resid 36 through 44 Processing helix chain 'I' and resid 85 through 93 Processing helix chain 'I' and resid 114 through 124 removed outlier: 3.784A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.688A pdb=" N LYS I 189 " --> pdb=" O SER I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 218 removed outlier: 4.154A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP I 213 " --> pdb=" O LYS I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 235 Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix removed outlier: 3.911A pdb=" N ALA I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 4.216A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 128 through 146 removed outlier: 4.070A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.592A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.709A pdb=" N GLU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 337 through 344 removed outlier: 3.990A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 240 removed outlier: 3.568A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.006A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix removed outlier: 3.504A pdb=" N CYS E 266 " --> pdb=" O PHE E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 Processing helix chain 'E' and resid 314 through 325 removed outlier: 4.056A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 319 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 351 removed outlier: 3.878A pdb=" N THR E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 379 removed outlier: 3.986A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 419 through 430 removed outlier: 3.762A pdb=" N LEU E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 429 " --> pdb=" O LEU E 425 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS E 430 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.647A pdb=" N LYS E 442 " --> pdb=" O GLU E 439 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 443 " --> pdb=" O THR E 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 439 through 443' Processing helix chain 'E' and resid 459 through 463 Processing helix chain 'E' and resid 511 through 517 removed outlier: 3.957A pdb=" N VAL E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.611A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS A 247 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 184 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE A 249 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR A 182 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE A 251 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL A 180 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLN A 286 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 181 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 212 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP A 206 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 204 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 216 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE I 169 " --> pdb=" O GLY I 159 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP I 161 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU I 167 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 225 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 338 removed outlier: 3.666A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.526A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 424 " --> pdb=" O LEU A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 6.459A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'I' and resid 76 through 77 removed outlier: 6.426A pdb=" N ALA I 5 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N HIS I 203 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU I 131 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU I 204 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA I 129 " --> pdb=" O LEU I 204 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU I 128 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N HIS I 303 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N MET I 130 " --> pdb=" O HIS I 303 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N MET I 305 " --> pdb=" O MET I 130 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET I 132 " --> pdb=" O MET I 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 29 through 30 Processing sheet with id=AA9, first strand: chain 'I' and resid 353 through 354 removed outlier: 4.031A pdb=" N VAL I 354 " --> pdb=" O ILE I 370 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER I 369 " --> pdb=" O ILE I 387 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR I 386 " --> pdb=" O ILE I 404 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASN I 403 " --> pdb=" O ILE I 421 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP I 420 " --> pdb=" O LYS I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'I' and resid 391 through 392 removed outlier: 6.647A pdb=" N LEU I 391 " --> pdb=" O ILE I 409 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL I 408 " --> pdb=" O ILE I 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 414 through 415 removed outlier: 7.350A pdb=" N VAL I 414 " --> pdb=" O ILE I 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 323 through 325 removed outlier: 6.846A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR D 167 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.403A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 362 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR E 336 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY E 404 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 407 through 408 removed outlier: 3.604A pdb=" N VAL E 414 " --> pdb=" O THR E 492 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1086 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: 1.59 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3705 1.34 - 1.46: 2234 1.46 - 1.58: 5289 1.58 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 11323 Sorted by residual: bond pdb=" CB GLU D 135 " pdb=" CG GLU D 135 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CG ARG A 145 " pdb=" CD ARG A 145 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB GLU E 469 " pdb=" CG GLU E 469 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" C PHE D 278 " pdb=" N PRO D 279 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.89e-01 bond pdb=" C VAL I 326 " pdb=" N PRO I 327 " ideal model delta sigma weight residual 1.334 1.347 -0.013 1.51e-02 4.39e+03 7.50e-01 ... (remaining 11318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 15060 1.63 - 3.26: 249 3.26 - 4.88: 38 4.88 - 6.51: 14 6.51 - 8.14: 3 Bond angle restraints: 15364 Sorted by residual: angle pdb=" N VAL D 312 " pdb=" CA VAL D 312 " pdb=" C VAL D 312 " ideal model delta sigma weight residual 112.96 109.83 3.13 1.00e+00 1.00e+00 9.82e+00 angle pdb=" C GLU I 44 " pdb=" N ARG I 45 " pdb=" CA ARG I 45 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.67e+00 angle pdb=" CB GLU D 135 " pdb=" CG GLU D 135 " pdb=" CD GLU D 135 " ideal model delta sigma weight residual 112.60 117.21 -4.61 1.70e+00 3.46e-01 7.36e+00 angle pdb=" CA SER A 60 " pdb=" C SER A 60 " pdb=" N LYS A 61 " ideal model delta sigma weight residual 116.84 121.41 -4.57 1.71e+00 3.42e-01 7.14e+00 angle pdb=" C LEU I 351 " pdb=" N VAL I 352 " pdb=" CA VAL I 352 " ideal model delta sigma weight residual 121.97 126.76 -4.79 1.80e+00 3.09e-01 7.08e+00 ... (remaining 15359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5906 17.82 - 35.64: 761 35.64 - 53.45: 196 53.45 - 71.27: 28 71.27 - 89.09: 10 Dihedral angle restraints: 6901 sinusoidal: 2715 harmonic: 4186 Sorted by residual: dihedral pdb=" CA PHE A 57 " pdb=" C PHE A 57 " pdb=" N PRO A 58 " pdb=" CA PRO A 58 " ideal model delta harmonic sigma weight residual 180.00 140.19 39.81 0 5.00e+00 4.00e-02 6.34e+01 dihedral pdb=" CA ARG I 45 " pdb=" C ARG I 45 " pdb=" N VAL I 46 " pdb=" CA VAL I 46 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP A 147 " pdb=" CB ASP A 147 " pdb=" CG ASP A 147 " pdb=" OD1 ASP A 147 " ideal model delta sinusoidal sigma weight residual -30.00 -89.98 59.98 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 6898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1245 0.035 - 0.070: 362 0.070 - 0.106: 157 0.106 - 0.141: 55 0.141 - 0.176: 3 Chirality restraints: 1822 Sorted by residual: chirality pdb=" CB VAL I 54 " pdb=" CA VAL I 54 " pdb=" CG1 VAL I 54 " pdb=" CG2 VAL I 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CB ILE I 346 " pdb=" CA ILE I 346 " pdb=" CG1 ILE I 346 " pdb=" CG2 ILE I 346 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA ILE I 404 " pdb=" N ILE I 404 " pdb=" C ILE I 404 " pdb=" CB ILE I 404 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 1819 not shown) Planarity restraints: 1963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 57 " 0.077 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO A 58 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 395 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO E 396 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 396 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 396 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " 0.105 9.50e-02 1.11e+02 4.78e-02 2.13e+00 pdb=" NE ARG A 145 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " -0.001 2.00e-02 2.50e+03 ... (remaining 1960 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 803 2.74 - 3.28: 10959 3.28 - 3.82: 18019 3.82 - 4.36: 20823 4.36 - 4.90: 37285 Nonbonded interactions: 87889 Sorted by model distance: nonbonded pdb=" O PRO A 69 " pdb=" OH TYR A 306 " model vdw 2.202 3.040 nonbonded pdb=" OG SER I 402 " pdb=" O ALA I 419 " model vdw 2.214 3.040 nonbonded pdb=" N GLU E 469 " pdb=" OE1 GLU E 469 " model vdw 2.247 3.120 nonbonded pdb=" OG SER I 127 " pdb=" OH TYR I 210 " model vdw 2.253 3.040 nonbonded pdb=" O LEU D 265 " pdb=" OG1 THR D 322 " model vdw 2.254 3.040 ... (remaining 87884 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: 1.000 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.060 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11323 Z= 0.101 Angle : 0.540 8.139 15364 Z= 0.282 Chirality : 0.043 0.176 1822 Planarity : 0.005 0.119 1963 Dihedral : 16.855 89.091 4179 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.16 % Allowed : 28.68 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.23), residues: 1417 helix: 1.64 (0.26), residues: 456 sheet: -0.39 (0.38), residues: 193 loop : -0.72 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 145 TYR 0.021 0.001 TYR D 337 PHE 0.012 0.001 PHE D 177 TRP 0.019 0.001 TRP D 51 HIS 0.011 0.001 HIS I 350 Details of bonding type rmsd covalent geometry : bond 0.00204 (11323) covalent geometry : angle 0.54010 (15364) hydrogen bonds : bond 0.21072 ( 382) hydrogen bonds : angle 6.23045 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.474 Fit side-chains REVERT: A 305 MET cc_start: 0.8541 (mmm) cc_final: 0.8318 (tpp) REVERT: I 424 CYS cc_start: 0.8171 (t) cc_final: 0.7903 (m) REVERT: D 20 GLU cc_start: 0.8183 (mp0) cc_final: 0.7938 (mp0) REVERT: D 292 GLU cc_start: 0.8418 (tp30) cc_final: 0.8124 (mt-10) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.1000 time to fit residues: 16.1676 Evaluate side-chains 106 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0060 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.0070 overall best weight: 1.2018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** I 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 286 HIS E 347 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.084481 restraints weight = 18114.458| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.39 r_work: 0.2988 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11323 Z= 0.136 Angle : 0.528 6.618 15364 Z= 0.275 Chirality : 0.045 0.160 1822 Planarity : 0.004 0.080 1963 Dihedral : 3.997 36.293 1555 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.19 % Allowed : 26.16 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.23), residues: 1417 helix: 1.50 (0.25), residues: 479 sheet: -0.67 (0.35), residues: 205 loop : -0.67 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 194 TYR 0.024 0.001 TYR I 231 PHE 0.013 0.001 PHE D 177 TRP 0.007 0.001 TRP A 97 HIS 0.008 0.001 HIS I 350 Details of bonding type rmsd covalent geometry : bond 0.00304 (11323) covalent geometry : angle 0.52808 (15364) hydrogen bonds : bond 0.03739 ( 382) hydrogen bonds : angle 4.47415 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.9045 (tp30) cc_final: 0.8829 (tp30) REVERT: A 264 PHE cc_start: 0.7672 (m-80) cc_final: 0.7151 (t80) REVERT: A 392 ASP cc_start: 0.7510 (t0) cc_final: 0.7258 (t0) REVERT: I 321 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8549 (tp30) REVERT: I 391 LEU cc_start: 0.8664 (tp) cc_final: 0.8450 (tt) REVERT: I 424 CYS cc_start: 0.8025 (t) cc_final: 0.7796 (m) REVERT: D 180 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8631 (tm-30) REVERT: D 217 MET cc_start: 0.8460 (ptt) cc_final: 0.8234 (ptt) REVERT: D 292 GLU cc_start: 0.8199 (tp30) cc_final: 0.7650 (mt-10) outliers start: 27 outliers final: 19 residues processed: 140 average time/residue: 0.0971 time to fit residues: 19.7794 Evaluate side-chains 125 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 7 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 114 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.117098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.083016 restraints weight = 18314.774| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.42 r_work: 0.2961 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11323 Z= 0.113 Angle : 0.505 6.879 15364 Z= 0.261 Chirality : 0.044 0.153 1822 Planarity : 0.004 0.100 1963 Dihedral : 3.952 36.941 1552 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.09 % Allowed : 26.16 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.23), residues: 1417 helix: 1.63 (0.25), residues: 485 sheet: -0.64 (0.35), residues: 205 loop : -0.64 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 57 TYR 0.023 0.001 TYR I 94 PHE 0.020 0.001 PHE D 285 TRP 0.006 0.001 TRP A 97 HIS 0.016 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00261 (11323) covalent geometry : angle 0.50514 (15364) hydrogen bonds : bond 0.03513 ( 382) hydrogen bonds : angle 4.14018 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.7840 (tp) cc_final: 0.7555 (tp) REVERT: A 264 PHE cc_start: 0.7707 (m-80) cc_final: 0.7187 (t80) REVERT: I 321 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8545 (tp30) REVERT: I 373 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8117 (m) REVERT: I 424 CYS cc_start: 0.8008 (t) cc_final: 0.7789 (m) REVERT: D 180 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8584 (tm-30) REVERT: D 217 MET cc_start: 0.8408 (ptt) cc_final: 0.8144 (ptt) REVERT: D 292 GLU cc_start: 0.8224 (tp30) cc_final: 0.7636 (mt-10) outliers start: 38 outliers final: 22 residues processed: 146 average time/residue: 0.0940 time to fit residues: 19.8607 Evaluate side-chains 127 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 100 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 46 optimal weight: 0.0070 chunk 102 optimal weight: 0.5980 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN D 286 HIS E 245 ASN E 274 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.080270 restraints weight = 18296.162| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.40 r_work: 0.2916 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11323 Z= 0.128 Angle : 0.521 8.872 15364 Z= 0.268 Chirality : 0.045 0.221 1822 Planarity : 0.004 0.093 1963 Dihedral : 4.057 37.579 1552 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.71 % Allowed : 24.29 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.23), residues: 1417 helix: 1.78 (0.25), residues: 472 sheet: -0.58 (0.36), residues: 199 loop : -0.58 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 57 TYR 0.017 0.001 TYR I 94 PHE 0.011 0.001 PHE D 177 TRP 0.006 0.001 TRP A 97 HIS 0.009 0.001 HIS I 350 Details of bonding type rmsd covalent geometry : bond 0.00304 (11323) covalent geometry : angle 0.52062 (15364) hydrogen bonds : bond 0.03266 ( 382) hydrogen bonds : angle 3.91915 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 104 time to evaluate : 0.427 Fit side-chains REVERT: A 104 GLU cc_start: 0.8992 (tp30) cc_final: 0.8473 (tp30) REVERT: A 170 LEU cc_start: 0.7878 (tp) cc_final: 0.7603 (tp) REVERT: A 264 PHE cc_start: 0.7880 (m-80) cc_final: 0.7358 (t80) REVERT: I 8 MET cc_start: 0.8652 (mmt) cc_final: 0.8236 (mmt) REVERT: I 132 MET cc_start: 0.8147 (mtm) cc_final: 0.7647 (mtm) REVERT: I 161 ASP cc_start: 0.7949 (t70) cc_final: 0.7491 (t0) REVERT: I 321 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8553 (tp30) REVERT: I 373 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8131 (m) REVERT: D 20 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: D 81 MET cc_start: 0.6689 (mmm) cc_final: 0.6420 (mmm) REVERT: D 180 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8682 (tm-30) outliers start: 58 outliers final: 37 residues processed: 153 average time/residue: 0.1019 time to fit residues: 22.5536 Evaluate side-chains 137 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 369 SER Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 507 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 141 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 4 GLN D 242 ASN D 286 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079791 restraints weight = 18231.523| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.39 r_work: 0.2907 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11323 Z= 0.121 Angle : 0.519 6.974 15364 Z= 0.265 Chirality : 0.044 0.152 1822 Planarity : 0.004 0.107 1963 Dihedral : 4.061 37.003 1552 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.22 % Allowed : 25.02 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.23), residues: 1417 helix: 1.65 (0.25), residues: 485 sheet: -0.51 (0.37), residues: 192 loop : -0.55 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 163 TYR 0.015 0.001 TYR I 94 PHE 0.011 0.001 PHE D 177 TRP 0.005 0.001 TRP A 97 HIS 0.009 0.001 HIS I 350 Details of bonding type rmsd covalent geometry : bond 0.00292 (11323) covalent geometry : angle 0.51868 (15364) hydrogen bonds : bond 0.03142 ( 382) hydrogen bonds : angle 3.84288 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 103 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7991 (mp) REVERT: A 104 GLU cc_start: 0.8999 (tp30) cc_final: 0.8516 (tp30) REVERT: A 264 PHE cc_start: 0.7929 (m-80) cc_final: 0.7428 (t80) REVERT: I 8 MET cc_start: 0.8595 (mmt) cc_final: 0.8251 (mmt) REVERT: I 132 MET cc_start: 0.8213 (mtm) cc_final: 0.7861 (mtm) REVERT: I 161 ASP cc_start: 0.8038 (t70) cc_final: 0.7564 (t0) REVERT: I 321 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8579 (tp30) REVERT: I 373 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8177 (m) REVERT: D 180 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8689 (tm-30) REVERT: D 278 PHE cc_start: 0.6956 (m-80) cc_final: 0.5479 (p90) outliers start: 52 outliers final: 37 residues processed: 145 average time/residue: 0.0979 time to fit residues: 20.8164 Evaluate side-chains 136 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 84 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.077970 restraints weight = 18417.453| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.39 r_work: 0.2872 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11323 Z= 0.147 Angle : 0.538 7.353 15364 Z= 0.276 Chirality : 0.045 0.152 1822 Planarity : 0.004 0.113 1963 Dihedral : 4.171 40.370 1552 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.39 % Allowed : 25.59 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.23), residues: 1417 helix: 1.72 (0.25), residues: 479 sheet: -0.41 (0.38), residues: 186 loop : -0.56 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 163 TYR 0.018 0.001 TYR E 214 PHE 0.012 0.001 PHE D 177 TRP 0.007 0.001 TRP A 97 HIS 0.007 0.001 HIS I 350 Details of bonding type rmsd covalent geometry : bond 0.00363 (11323) covalent geometry : angle 0.53758 (15364) hydrogen bonds : bond 0.03341 ( 382) hydrogen bonds : angle 3.84407 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 99 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8999 (tp30) cc_final: 0.8492 (tp30) REVERT: A 264 PHE cc_start: 0.8072 (m-80) cc_final: 0.7516 (t80) REVERT: I 161 ASP cc_start: 0.8138 (t70) cc_final: 0.7694 (t0) REVERT: I 321 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8542 (tp30) REVERT: I 373 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8261 (t) REVERT: D 180 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8744 (tm-30) outliers start: 54 outliers final: 45 residues processed: 143 average time/residue: 0.1042 time to fit residues: 21.6448 Evaluate side-chains 140 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 93 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 369 SER Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 507 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 97 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 141 optimal weight: 0.0020 chunk 68 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.110853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.076583 restraints weight = 18379.907| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.37 r_work: 0.2849 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11323 Z= 0.163 Angle : 0.553 8.144 15364 Z= 0.282 Chirality : 0.046 0.179 1822 Planarity : 0.005 0.116 1963 Dihedral : 4.280 38.733 1552 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.71 % Allowed : 25.43 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.23), residues: 1417 helix: 1.64 (0.25), residues: 482 sheet: -0.42 (0.38), residues: 191 loop : -0.59 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 163 TYR 0.013 0.001 TYR A 128 PHE 0.012 0.001 PHE D 177 TRP 0.008 0.001 TRP A 97 HIS 0.008 0.001 HIS I 350 Details of bonding type rmsd covalent geometry : bond 0.00406 (11323) covalent geometry : angle 0.55260 (15364) hydrogen bonds : bond 0.03454 ( 382) hydrogen bonds : angle 3.87736 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 96 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8136 (mp) REVERT: A 104 GLU cc_start: 0.8948 (tp30) cc_final: 0.8438 (tp30) REVERT: A 264 PHE cc_start: 0.8222 (m-80) cc_final: 0.7628 (t80) REVERT: I 161 ASP cc_start: 0.8212 (t70) cc_final: 0.7763 (t0) REVERT: I 321 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8480 (tp30) REVERT: I 373 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8218 (t) REVERT: D 180 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8790 (tm-30) outliers start: 58 outliers final: 45 residues processed: 143 average time/residue: 0.0853 time to fit residues: 18.0722 Evaluate side-chains 140 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 92 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 369 SER Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 104 optimal weight: 0.0870 chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.077668 restraints weight = 18265.129| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.36 r_work: 0.2868 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11323 Z= 0.125 Angle : 0.529 8.143 15364 Z= 0.269 Chirality : 0.044 0.166 1822 Planarity : 0.005 0.124 1963 Dihedral : 4.212 40.503 1552 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.31 % Allowed : 25.51 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.23), residues: 1417 helix: 1.72 (0.25), residues: 479 sheet: -0.38 (0.38), residues: 191 loop : -0.54 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 372 TYR 0.020 0.001 TYR E 214 PHE 0.012 0.001 PHE D 177 TRP 0.007 0.001 TRP A 97 HIS 0.007 0.001 HIS I 350 Details of bonding type rmsd covalent geometry : bond 0.00305 (11323) covalent geometry : angle 0.52862 (15364) hydrogen bonds : bond 0.03177 ( 382) hydrogen bonds : angle 3.81807 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 98 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8142 (mp) REVERT: A 104 GLU cc_start: 0.8942 (tp30) cc_final: 0.8450 (tp30) REVERT: A 264 PHE cc_start: 0.8150 (m-80) cc_final: 0.7578 (t80) REVERT: I 161 ASP cc_start: 0.8132 (t70) cc_final: 0.7710 (t0) REVERT: I 321 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8480 (tp30) REVERT: I 373 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8206 (t) REVERT: D 180 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8802 (tm-30) outliers start: 53 outliers final: 42 residues processed: 141 average time/residue: 0.0902 time to fit residues: 18.8831 Evaluate side-chains 139 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 369 SER Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 507 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 117 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 0.0000 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.078344 restraints weight = 18003.352| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.34 r_work: 0.2881 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11323 Z= 0.113 Angle : 0.522 8.080 15364 Z= 0.266 Chirality : 0.044 0.166 1822 Planarity : 0.004 0.122 1963 Dihedral : 4.141 38.380 1552 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.90 % Allowed : 26.00 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.23), residues: 1417 helix: 1.80 (0.25), residues: 479 sheet: -0.16 (0.39), residues: 183 loop : -0.52 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 372 TYR 0.014 0.001 TYR I 94 PHE 0.012 0.001 PHE D 177 TRP 0.007 0.001 TRP A 97 HIS 0.009 0.001 HIS I 350 Details of bonding type rmsd covalent geometry : bond 0.00273 (11323) covalent geometry : angle 0.52207 (15364) hydrogen bonds : bond 0.03001 ( 382) hydrogen bonds : angle 3.76062 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8917 (tp30) cc_final: 0.8423 (tp30) REVERT: A 264 PHE cc_start: 0.8190 (m-80) cc_final: 0.7628 (t80) REVERT: I 161 ASP cc_start: 0.8152 (t70) cc_final: 0.7747 (t0) REVERT: I 321 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8519 (tp30) REVERT: I 373 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8104 (t) REVERT: D 13 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8108 (pp20) REVERT: D 180 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8790 (tm-30) outliers start: 48 outliers final: 43 residues processed: 141 average time/residue: 0.0952 time to fit residues: 19.6621 Evaluate side-chains 136 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 91 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 369 SER Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 48 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.112859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078620 restraints weight = 18105.122| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.36 r_work: 0.2886 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11323 Z= 0.104 Angle : 0.521 7.929 15364 Z= 0.266 Chirality : 0.044 0.160 1822 Planarity : 0.005 0.125 1963 Dihedral : 4.106 39.570 1552 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.49 % Allowed : 26.56 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.23), residues: 1417 helix: 1.91 (0.25), residues: 472 sheet: -0.27 (0.38), residues: 193 loop : -0.52 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 372 TYR 0.014 0.001 TYR I 94 PHE 0.049 0.001 PHE A 57 TRP 0.006 0.001 TRP A 97 HIS 0.011 0.001 HIS I 350 Details of bonding type rmsd covalent geometry : bond 0.00246 (11323) covalent geometry : angle 0.52126 (15364) hydrogen bonds : bond 0.02907 ( 382) hydrogen bonds : angle 3.74585 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8901 (tp30) cc_final: 0.8558 (tp30) REVERT: A 145 ARG cc_start: 0.8365 (mtm110) cc_final: 0.8083 (ptp-110) REVERT: A 264 PHE cc_start: 0.8173 (m-80) cc_final: 0.7638 (t80) REVERT: A 358 GLU cc_start: 0.7958 (tt0) cc_final: 0.7721 (tt0) REVERT: I 161 ASP cc_start: 0.8142 (t70) cc_final: 0.7746 (t0) REVERT: I 321 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8518 (tp30) REVERT: I 373 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8096 (t) outliers start: 43 outliers final: 39 residues processed: 136 average time/residue: 0.1032 time to fit residues: 20.5612 Evaluate side-chains 131 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 124 optimal weight: 0.0770 chunk 27 optimal weight: 5.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.111430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.077201 restraints weight = 18318.515| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.37 r_work: 0.2859 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11323 Z= 0.139 Angle : 0.550 8.151 15364 Z= 0.281 Chirality : 0.045 0.154 1822 Planarity : 0.005 0.117 1963 Dihedral : 4.176 39.605 1552 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.82 % Allowed : 26.48 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.23), residues: 1417 helix: 1.82 (0.25), residues: 478 sheet: -0.24 (0.38), residues: 193 loop : -0.53 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 372 TYR 0.012 0.001 TYR I 94 PHE 0.012 0.001 PHE D 177 TRP 0.007 0.001 TRP A 97 HIS 0.011 0.001 HIS I 350 Details of bonding type rmsd covalent geometry : bond 0.00342 (11323) covalent geometry : angle 0.54988 (15364) hydrogen bonds : bond 0.03215 ( 382) hydrogen bonds : angle 3.81069 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2434.07 seconds wall clock time: 42 minutes 25.95 seconds (2545.95 seconds total)