Starting phenix.real_space_refine on Tue Jul 29 06:19:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tqo_41510/07_2025/8tqo_41510.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tqo_41510/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tqo_41510/07_2025/8tqo_41510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tqo_41510/07_2025/8tqo_41510.map" model { file = "/net/cci-nas-00/data/ceres_data/8tqo_41510/07_2025/8tqo_41510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tqo_41510/07_2025/8tqo_41510.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLU:plan': 2, 'ASN:plan1': 1, '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: 7.64, per 1000 atoms: 0.69 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: 2.82 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.45 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: 4.21 Time building geometry restraints manager: 3.35 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: 1.200 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.230 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 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 TRP 0.019 0.001 TRP D 51 HIS 0.011 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.021 0.001 TYR D 337 ARG 0.015 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.21072 ( 382) hydrogen bonds : angle 6.23045 ( 1086) covalent geometry : bond 0.00204 (11323) covalent geometry : angle 0.54010 (15364) *********************** 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 : 1.258 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: 0.2160 time to fit residues: 35.4859 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 : 1.247 ------------------------------------------------------------------------------- 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 119 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 0.3980 chunk 128 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 274 HIS E 347 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.078791 restraints weight = 18205.484| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.36 r_work: 0.2887 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11323 Z= 0.210 Angle : 0.607 7.440 15364 Z= 0.316 Chirality : 0.048 0.169 1822 Planarity : 0.005 0.080 1963 Dihedral : 4.381 38.671 1555 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.33 % Allowed : 25.83 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1417 helix: 1.36 (0.25), residues: 478 sheet: -0.75 (0.36), residues: 199 loop : -0.76 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 97 HIS 0.009 0.001 HIS I 350 PHE 0.015 0.002 PHE A 215 TYR 0.027 0.002 TYR I 231 ARG 0.008 0.001 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 382) hydrogen bonds : angle 4.43454 ( 1086) covalent geometry : bond 0.00512 (11323) covalent geometry : angle 0.60668 (15364) *********************** 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 156 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.9075 (tp30) cc_final: 0.8506 (tp30) REVERT: I 8 MET cc_start: 0.8693 (mmt) cc_final: 0.8245 (mmt) REVERT: I 132 MET cc_start: 0.8184 (mtm) cc_final: 0.7687 (mtm) REVERT: I 321 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8530 (tp30) REVERT: I 424 CYS cc_start: 0.8007 (t) cc_final: 0.7753 (m) REVERT: D 180 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: D 242 ASN cc_start: 0.8433 (m110) cc_final: 0.8168 (p0) REVERT: D 292 GLU cc_start: 0.8274 (tp30) cc_final: 0.7687 (mt-10) outliers start: 41 outliers final: 26 residues processed: 148 average time/residue: 0.2336 time to fit residues: 50.0213 Evaluate side-chains 132 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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 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 110 THR Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain D residue 11 LEU 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 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 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 20 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079891 restraints weight = 18421.517| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.40 r_work: 0.2904 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11323 Z= 0.115 Angle : 0.518 7.108 15364 Z= 0.269 Chirality : 0.044 0.151 1822 Planarity : 0.004 0.101 1963 Dihedral : 4.194 37.610 1552 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.41 % Allowed : 25.91 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1417 helix: 1.56 (0.25), residues: 485 sheet: -0.63 (0.37), residues: 192 loop : -0.68 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 111 HIS 0.008 0.001 HIS I 350 PHE 0.016 0.001 PHE D 285 TYR 0.011 0.001 TYR I 319 ARG 0.005 0.000 ARG I 194 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 382) hydrogen bonds : angle 4.12936 ( 1086) covalent geometry : bond 0.00267 (11323) covalent geometry : angle 0.51849 (15364) *********************** 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: 42 poor density : 110 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.9051 (tp30) cc_final: 0.8424 (tp30) REVERT: A 170 LEU cc_start: 0.7844 (tp) cc_final: 0.7571 (tp) REVERT: I 8 MET cc_start: 0.8639 (mmt) cc_final: 0.8263 (mmt) REVERT: I 132 MET cc_start: 0.8163 (mtm) cc_final: 0.7848 (mtm) REVERT: I 161 ASP cc_start: 0.7896 (t70) cc_final: 0.7523 (t0) REVERT: I 166 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7630 (mtp180) REVERT: I 321 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8469 (tp30) REVERT: I 373 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8140 (m) REVERT: I 424 CYS cc_start: 0.8079 (t) cc_final: 0.7825 (m) REVERT: D 180 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8707 (tm-30) REVERT: D 286 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.6527 (p90) REVERT: D 345 HIS cc_start: 0.6984 (t-90) cc_final: 0.6748 (t-170) outliers start: 42 outliers final: 23 residues processed: 145 average time/residue: 0.2322 time to fit residues: 49.4819 Evaluate side-chains 127 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 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 261 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 166 ARG 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 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 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 286 HIS Chi-restraints excluded: chain D residue 308 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 117 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 80 optimal weight: 30.0000 chunk 61 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN D 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.112047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.077986 restraints weight = 18190.503| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.35 r_work: 0.2877 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11323 Z= 0.145 Angle : 0.537 8.153 15364 Z= 0.276 Chirality : 0.045 0.154 1822 Planarity : 0.004 0.095 1963 Dihedral : 4.211 38.811 1552 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.71 % Allowed : 25.02 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1417 helix: 1.62 (0.25), residues: 479 sheet: -0.46 (0.38), residues: 186 loop : -0.68 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 97 HIS 0.008 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.016 0.001 TYR E 214 ARG 0.006 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 382) hydrogen bonds : angle 3.97922 ( 1086) covalent geometry : bond 0.00354 (11323) covalent geometry : angle 0.53659 (15364) *********************** 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 157 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 99 time to evaluate : 1.259 Fit side-chains REVERT: A 104 GLU cc_start: 0.9052 (tp30) cc_final: 0.8592 (tp30) REVERT: A 264 PHE cc_start: 0.8072 (m-80) cc_final: 0.7474 (t80) REVERT: I 4 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7069 (mt0) REVERT: I 161 ASP cc_start: 0.8106 (t70) cc_final: 0.7711 (t0) REVERT: I 166 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.6996 (tpt90) REVERT: I 321 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8489 (tp30) REVERT: I 373 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.8175 (m) REVERT: I 424 CYS cc_start: 0.8056 (t) cc_final: 0.7802 (m) REVERT: D 180 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8717 (tm-30) REVERT: E 386 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7845 (pp) outliers start: 58 outliers final: 40 residues processed: 148 average time/residue: 0.2304 time to fit residues: 49.3653 Evaluate side-chains 140 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 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 4 GLN 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 166 ARG 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 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 11 LEU 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 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 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 386 LEU 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 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 78 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 137 optimal weight: 0.0970 chunk 128 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.076864 restraints weight = 18170.804| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.33 r_work: 0.2859 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11323 Z= 0.159 Angle : 0.542 7.956 15364 Z= 0.277 Chirality : 0.045 0.153 1822 Planarity : 0.004 0.108 1963 Dihedral : 4.277 38.271 1552 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.36 % Allowed : 24.21 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1417 helix: 1.54 (0.25), residues: 484 sheet: -0.43 (0.38), residues: 186 loop : -0.67 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 97 HIS 0.006 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.018 0.001 TYR E 214 ARG 0.006 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 382) hydrogen bonds : angle 3.94700 ( 1086) covalent geometry : bond 0.00395 (11323) covalent geometry : angle 0.54200 (15364) *********************** 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 166 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 100 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.9055 (tp30) cc_final: 0.8590 (tp30) REVERT: A 264 PHE cc_start: 0.8194 (m-80) cc_final: 0.7575 (t80) REVERT: A 299 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.6725 (ttt90) REVERT: I 4 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7044 (mt0) REVERT: I 51 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8671 (p) REVERT: I 161 ASP cc_start: 0.8134 (t70) cc_final: 0.7726 (t0) REVERT: I 166 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.6987 (tpt90) REVERT: I 321 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8496 (tp30) REVERT: I 373 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.8166 (m) REVERT: I 424 CYS cc_start: 0.8087 (t) cc_final: 0.7763 (m) REVERT: D 180 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8770 (tm-30) outliers start: 66 outliers final: 43 residues processed: 158 average time/residue: 0.2251 time to fit residues: 51.3678 Evaluate side-chains 143 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 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 261 THR Chi-restraints excluded: chain A residue 299 ARG 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 A residue 390 VAL Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 166 ARG 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 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 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 308 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 137 optimal weight: 0.0770 chunk 83 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN 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 = 0.112810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.078733 restraints weight = 18125.220| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.35 r_work: 0.2888 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11323 Z= 0.105 Angle : 0.520 8.002 15364 Z= 0.267 Chirality : 0.044 0.182 1822 Planarity : 0.004 0.111 1963 Dihedral : 4.166 39.759 1552 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.98 % Allowed : 25.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1417 helix: 1.71 (0.25), residues: 479 sheet: -0.43 (0.37), residues: 196 loop : -0.59 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 97 HIS 0.009 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.021 0.001 TYR E 214 ARG 0.009 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 382) hydrogen bonds : angle 3.81258 ( 1086) covalent geometry : bond 0.00246 (11323) covalent geometry : angle 0.52026 (15364) *********************** 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 147 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 98 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.9038 (tp30) cc_final: 0.8590 (tp30) REVERT: A 264 PHE cc_start: 0.8120 (m-80) cc_final: 0.7546 (t80) REVERT: I 161 ASP cc_start: 0.8084 (t70) cc_final: 0.7659 (t0) REVERT: I 166 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7682 (mtp180) REVERT: I 321 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8506 (tp30) REVERT: I 373 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8136 (m) REVERT: I 424 CYS cc_start: 0.8113 (t) cc_final: 0.7806 (m) REVERT: D 81 MET cc_start: 0.6958 (mmm) cc_final: 0.6704 (mmm) REVERT: D 180 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8761 (tm-30) outliers start: 49 outliers final: 37 residues processed: 142 average time/residue: 0.2323 time to fit residues: 47.6679 Evaluate side-chains 134 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 94 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 166 ARG 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 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 218 THR Chi-restraints excluded: chain D residue 242 ASN 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 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 492 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 106 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 32 optimal weight: 0.0670 chunk 135 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN D 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.074629 restraints weight = 18736.042| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.38 r_work: 0.2812 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11323 Z= 0.226 Angle : 0.603 8.833 15364 Z= 0.309 Chirality : 0.047 0.162 1822 Planarity : 0.005 0.120 1963 Dihedral : 4.411 39.881 1552 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.04 % Allowed : 25.35 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1417 helix: 1.55 (0.25), residues: 481 sheet: -0.39 (0.38), residues: 191 loop : -0.73 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 97 HIS 0.008 0.001 HIS I 350 PHE 0.014 0.002 PHE A 56 TYR 0.016 0.002 TYR A 128 ARG 0.007 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 382) hydrogen bonds : angle 4.00631 ( 1086) covalent geometry : bond 0.00564 (11323) covalent geometry : angle 0.60303 (15364) *********************** 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 158 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 96 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.9002 (tp30) cc_final: 0.8528 (tp30) REVERT: A 299 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.6711 (ttt90) REVERT: I 161 ASP cc_start: 0.8263 (t70) cc_final: 0.7848 (t0) REVERT: I 166 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7070 (tpt90) REVERT: I 321 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8575 (tp30) REVERT: I 373 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8239 (m) REVERT: I 424 CYS cc_start: 0.8166 (t) cc_final: 0.7727 (m) REVERT: D 156 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7856 (mm) REVERT: D 180 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8677 (tm-30) outliers start: 62 outliers final: 45 residues processed: 151 average time/residue: 0.2181 time to fit residues: 48.1533 Evaluate side-chains 142 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 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 299 ARG Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 SER 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 166 ARG 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 396 VAL 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 156 LEU 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 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 308 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 38 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 140 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.077520 restraints weight = 18268.125| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.36 r_work: 0.2867 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11323 Z= 0.104 Angle : 0.531 8.660 15364 Z= 0.273 Chirality : 0.044 0.156 1822 Planarity : 0.005 0.121 1963 Dihedral : 4.262 40.242 1552 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.98 % Allowed : 26.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1417 helix: 1.74 (0.25), residues: 479 sheet: -0.44 (0.37), residues: 196 loop : -0.59 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 97 HIS 0.007 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.011 0.001 TYR E 385 ARG 0.008 0.000 ARG I 372 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 382) hydrogen bonds : angle 3.85798 ( 1086) covalent geometry : bond 0.00240 (11323) covalent geometry : angle 0.53115 (15364) *********************** 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 150 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 101 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8992 (tp30) cc_final: 0.8581 (tp30) REVERT: A 264 PHE cc_start: 0.8299 (m-80) cc_final: 0.7687 (t80) REVERT: I 161 ASP cc_start: 0.8121 (t70) cc_final: 0.7734 (t0) REVERT: I 166 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7002 (tpt90) REVERT: I 321 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8497 (tp30) REVERT: I 373 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8160 (m) REVERT: I 424 CYS cc_start: 0.8164 (t) cc_final: 0.7782 (m) REVERT: D 179 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7419 (mtmt) outliers start: 49 outliers final: 39 residues processed: 146 average time/residue: 0.2320 time to fit residues: 49.3008 Evaluate side-chains 137 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 180 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 377 SER 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 166 ARG 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 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 179 LYS 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 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 18 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.076430 restraints weight = 18353.708| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.37 r_work: 0.2841 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11323 Z= 0.146 Angle : 0.557 8.864 15364 Z= 0.284 Chirality : 0.045 0.162 1822 Planarity : 0.005 0.124 1963 Dihedral : 4.278 40.195 1552 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.14 % Allowed : 26.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1417 helix: 1.69 (0.25), residues: 480 sheet: -0.45 (0.37), residues: 196 loop : -0.58 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 97 HIS 0.009 0.001 HIS I 350 PHE 0.043 0.002 PHE A 57 TYR 0.015 0.001 TYR I 319 ARG 0.008 0.000 ARG I 372 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 382) hydrogen bonds : angle 3.86680 ( 1086) covalent geometry : bond 0.00361 (11323) covalent geometry : angle 0.55675 (15364) *********************** 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 149 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 98 time to evaluate : 1.328 Fit side-chains REVERT: A 104 GLU cc_start: 0.8984 (tp30) cc_final: 0.8561 (tp30) REVERT: A 264 PHE cc_start: 0.8370 (m-80) cc_final: 0.7730 (t80) REVERT: I 161 ASP cc_start: 0.8172 (t70) cc_final: 0.7792 (t0) REVERT: I 166 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7016 (tpt90) REVERT: I 321 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8465 (tp30) REVERT: I 373 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8185 (m) REVERT: I 424 CYS cc_start: 0.8143 (t) cc_final: 0.7687 (m) REVERT: D 13 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8106 (pp20) REVERT: D 20 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: D 179 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7448 (mtmt) outliers start: 51 outliers final: 43 residues processed: 141 average time/residue: 0.2280 time to fit residues: 47.2447 Evaluate side-chains 141 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 94 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 180 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 377 SER 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 166 ARG Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 224 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 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 179 LYS 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 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 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 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 123 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 85 optimal weight: 0.3980 chunk 65 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN E 238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.077940 restraints weight = 18305.680| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.35 r_work: 0.2870 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11323 Z= 0.106 Angle : 0.547 8.663 15364 Z= 0.279 Chirality : 0.044 0.152 1822 Planarity : 0.005 0.126 1963 Dihedral : 4.227 41.663 1552 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.82 % Allowed : 26.73 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1417 helix: 1.75 (0.25), residues: 479 sheet: -0.27 (0.38), residues: 188 loop : -0.54 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 97 HIS 0.011 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.010 0.001 TYR E 385 ARG 0.008 0.000 ARG I 372 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 382) hydrogen bonds : angle 3.83781 ( 1086) covalent geometry : bond 0.00247 (11323) covalent geometry : angle 0.54731 (15364) ********************** 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 144 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 1.473 Fit side-chains REVERT: A 104 GLU cc_start: 0.8977 (tp30) cc_final: 0.8566 (tp30) REVERT: A 264 PHE cc_start: 0.8321 (m-80) cc_final: 0.7707 (t80) REVERT: I 161 ASP cc_start: 0.8152 (t70) cc_final: 0.7784 (t0) REVERT: I 166 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7009 (tpt90) REVERT: I 321 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8472 (tp30) REVERT: I 373 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8196 (t) REVERT: I 424 CYS cc_start: 0.8201 (t) cc_final: 0.7735 (m) REVERT: D 13 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8116 (pp20) REVERT: D 20 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: D 217 MET cc_start: 0.8136 (ptt) cc_final: 0.7873 (ptt) outliers start: 47 outliers final: 41 residues processed: 140 average time/residue: 0.2363 time to fit residues: 47.8446 Evaluate side-chains 141 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 180 VAL Chi-restraints excluded: chain A residue 230 LEU 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 377 SER 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 166 ARG Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 224 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 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 30 SER 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 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 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 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 140 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 4 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.1302 ------------------------------------------------------------------------------- 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 = 0.111937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.077642 restraints weight = 18070.434| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.34 r_work: 0.2869 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 11323 Z= 0.161 Angle : 0.817 59.194 15364 Z= 0.463 Chirality : 0.045 0.285 1822 Planarity : 0.005 0.127 1963 Dihedral : 4.263 41.723 1552 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.82 % Allowed : 26.56 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1417 helix: 1.74 (0.25), residues: 479 sheet: -0.27 (0.38), residues: 188 loop : -0.56 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 97 HIS 0.010 0.001 HIS I 350 PHE 0.029 0.001 PHE A 57 TYR 0.010 0.001 TYR A 128 ARG 0.009 0.000 ARG I 372 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 382) hydrogen bonds : angle 3.83648 ( 1086) covalent geometry : bond 0.00372 (11323) covalent geometry : angle 0.81668 (15364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5378.89 seconds wall clock time: 93 minutes 10.77 seconds (5590.77 seconds total)