Starting phenix.real_space_refine on Fri May 16 21:46:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j0z_61063/05_2025/9j0z_61063.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j0z_61063/05_2025/9j0z_61063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j0z_61063/05_2025/9j0z_61063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j0z_61063/05_2025/9j0z_61063.map" model { file = "/net/cci-nas-00/data/ceres_data/9j0z_61063/05_2025/9j0z_61063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j0z_61063/05_2025/9j0z_61063.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 76 5.16 5 C 9768 2.51 5 N 2437 2.21 5 O 2543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14828 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3708 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 13, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3709 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 13, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3698 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 13, 'TRANS': 430} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3709 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 13, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.46, per 1000 atoms: 0.71 Number of scatterers: 14828 At special positions: 0 Unit cell: (121.16, 129.548, 120.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 76 16.00 O 2543 8.00 N 2437 7.00 C 9768 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.8 seconds 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 15 sheets defined 53.0% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 74 through 90 removed outlier: 3.850A pdb=" N SER A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix removed outlier: 3.748A pdb=" N PHE A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.564A pdb=" N GLN A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.725A pdb=" N LEU A 114 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.520A pdb=" N ALA A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.850A pdb=" N ILE A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 169 through 176 removed outlier: 3.807A pdb=" N ILE A 173 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 176 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 206 through 222 removed outlier: 4.323A pdb=" N THR A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 253 through 270 removed outlier: 3.521A pdb=" N ALA A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.598A pdb=" N VAL A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.844A pdb=" N MET A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 363 removed outlier: 4.642A pdb=" N LEU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.821A pdb=" N ILE A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Proline residue: A 379 - end of helix Processing helix chain 'A' and resid 391 through 402 removed outlier: 3.968A pdb=" N ILE A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 removed outlier: 4.031A pdb=" N ILE A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS A 461 " --> pdb=" O ILE A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 456 through 461' Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 492 through 505 removed outlier: 4.418A pdb=" N THR A 498 " --> pdb=" O HIS A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.797A pdb=" N SER B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 97 through 103 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.738A pdb=" N ALA B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.728A pdb=" N CYS B 151 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 164 through 176 removed outlier: 4.078A pdb=" N LEU B 170 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 171 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.519A pdb=" N THR B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.900A pdb=" N GLU B 231 " --> pdb=" O PRO B 228 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR B 233 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 253 through 270 Processing helix chain 'B' and resid 281 through 311 removed outlier: 3.586A pdb=" N MET B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 324 Processing helix chain 'B' and resid 336 through 351 Processing helix chain 'B' and resid 356 through 360 removed outlier: 4.156A pdb=" N VAL B 359 " --> pdb=" O THR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.611A pdb=" N LEU B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 removed outlier: 3.918A pdb=" N TYR B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 399 removed outlier: 3.548A pdb=" N ILE B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 492 removed outlier: 5.455A pdb=" N LEU B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 504 Processing helix chain 'C' and resid 74 through 82 removed outlier: 3.520A pdb=" N TYR C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.543A pdb=" N PHE C 89 " --> pdb=" O MET C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 108 removed outlier: 3.775A pdb=" N GLN C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 107 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.934A pdb=" N TYR C 169 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 170 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 171 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP C 172 " --> pdb=" O TYR C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 198 through 222 removed outlier: 3.533A pdb=" N LEU C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 234 Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.517A pdb=" N ILE C 252 " --> pdb=" O PHE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 removed outlier: 3.565A pdb=" N ALA C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N THR C 268 " --> pdb=" O PHE C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 312 Processing helix chain 'C' and resid 315 through 318 Processing helix chain 'C' and resid 319 through 331 removed outlier: 3.963A pdb=" N ASP C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.638A pdb=" N THR C 356 " --> pdb=" O ASP C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 368 through 376 removed outlier: 3.816A pdb=" N LEU C 376 " --> pdb=" O ILE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 382 Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 483 through 492 removed outlier: 3.573A pdb=" N ASN C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 501 Processing helix chain 'D' and resid 74 through 82 removed outlier: 3.735A pdb=" N SER D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.880A pdb=" N PHE D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 114 removed outlier: 3.521A pdb=" N ALA D 107 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 166 through 177 removed outlier: 3.734A pdb=" N TRP D 172 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 176 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 185 Processing helix chain 'D' and resid 206 through 224 removed outlier: 3.702A pdb=" N THR D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR D 224 " --> pdb=" O TYR D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 234 Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 281 through 312 removed outlier: 3.859A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 300 " --> pdb=" O MET D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 321 removed outlier: 3.685A pdb=" N ASP D 321 " --> pdb=" O GLU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 334 removed outlier: 3.605A pdb=" N ARG D 332 " --> pdb=" O SER D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 345 removed outlier: 3.609A pdb=" N GLN D 342 " --> pdb=" O ASP D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 365 through 383 Proline residue: D 379 - end of helix removed outlier: 4.130A pdb=" N LYS D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 483 through 492 removed outlier: 4.634A pdb=" N LEU D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 removed outlier: 3.636A pdb=" N GLY D 496 " --> pdb=" O TYR D 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 removed outlier: 3.840A pdb=" N PHE A 425 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 432 through 434 Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 121 removed outlier: 4.291A pdb=" N TYR B 120 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 402 through 404 Processing sheet with id=AA7, first strand: chain 'B' and resid 431 through 434 Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.539A pdb=" N TYR C 120 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AB1, first strand: chain 'C' and resid 403 through 407 Processing sheet with id=AB2, first strand: chain 'C' and resid 412 through 414 removed outlier: 6.904A pdb=" N VAL C 469 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 430 " --> pdb=" O CYS C 472 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR C 446 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 121 removed outlier: 3.558A pdb=" N TYR D 120 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 240 through 241 Processing sheet with id=AB5, first strand: chain 'D' and resid 403 through 407 removed outlier: 3.647A pdb=" N PHE D 407 " --> pdb=" O CYS D 475 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 446 through 448 removed outlier: 6.248A pdb=" N LEU D 430 " --> pdb=" O CYS D 472 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1575 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: 4.66 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2251 1.29 - 1.42: 4469 1.42 - 1.55: 8378 1.55 - 1.69: 3 1.69 - 1.82: 120 Bond restraints: 15221 Sorted by residual: bond pdb=" CA GLU A 165 " pdb=" C GLU A 165 " ideal model delta sigma weight residual 1.528 1.402 0.125 1.35e-02 5.49e+03 8.62e+01 bond pdb=" CA LYS A 159 " pdb=" C LYS A 159 " ideal model delta sigma weight residual 1.522 1.415 0.107 1.40e-02 5.10e+03 5.87e+01 bond pdb=" CA ARG A 168 " pdb=" C ARG A 168 " ideal model delta sigma weight residual 1.523 1.431 0.092 1.28e-02 6.10e+03 5.18e+01 bond pdb=" CA HIS A 164 " pdb=" C HIS A 164 " ideal model delta sigma weight residual 1.523 1.432 0.091 1.28e-02 6.10e+03 5.05e+01 bond pdb=" CA GLU C 189 " pdb=" C GLU C 189 " ideal model delta sigma weight residual 1.524 1.438 0.086 1.26e-02 6.30e+03 4.68e+01 ... (remaining 15216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 20373 4.94 - 9.88: 207 9.88 - 14.83: 24 14.83 - 19.77: 4 19.77 - 24.71: 3 Bond angle restraints: 20611 Sorted by residual: angle pdb=" N VAL A 167 " pdb=" CA VAL A 167 " pdb=" C VAL A 167 " ideal model delta sigma weight residual 112.90 94.22 18.68 9.60e-01 1.09e+00 3.79e+02 angle pdb=" N GLU B 208 " pdb=" CA GLU B 208 " pdb=" C GLU B 208 " ideal model delta sigma weight residual 110.48 85.77 24.71 1.48e+00 4.57e-01 2.79e+02 angle pdb=" N GLU A 165 " pdb=" CA GLU A 165 " pdb=" C GLU A 165 " ideal model delta sigma weight residual 110.36 86.44 23.92 1.55e+00 4.16e-01 2.38e+02 angle pdb=" N ASN C 195 " pdb=" CA ASN C 195 " pdb=" C ASN C 195 " ideal model delta sigma weight residual 110.24 127.37 -17.13 1.30e+00 5.92e-01 1.74e+02 angle pdb=" N TYR C 196 " pdb=" CA TYR C 196 " pdb=" C TYR C 196 " ideal model delta sigma weight residual 112.97 100.16 12.81 1.06e+00 8.90e-01 1.46e+02 ... (remaining 20606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.44: 7552 15.44 - 30.89: 1058 30.89 - 46.33: 245 46.33 - 61.78: 41 61.78 - 77.22: 9 Dihedral angle restraints: 8905 sinusoidal: 3636 harmonic: 5269 Sorted by residual: dihedral pdb=" C SER A 161 " pdb=" N SER A 161 " pdb=" CA SER A 161 " pdb=" CB SER A 161 " ideal model delta harmonic sigma weight residual -122.60 -104.18 -18.42 0 2.50e+00 1.60e-01 5.43e+01 dihedral pdb=" CA PHE C 485 " pdb=" C PHE C 485 " pdb=" N SER C 486 " pdb=" CA SER C 486 " ideal model delta harmonic sigma weight residual 180.00 150.24 29.76 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA PHE C 264 " pdb=" C PHE C 264 " pdb=" N ALA C 265 " pdb=" CA ALA C 265 " ideal model delta harmonic sigma weight residual 180.00 153.81 26.19 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 8902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 2053 0.126 - 0.253: 190 0.253 - 0.379: 22 0.379 - 0.505: 4 0.505 - 0.632: 2 Chirality restraints: 2271 Sorted by residual: chirality pdb=" CA LYS A 163 " pdb=" N LYS A 163 " pdb=" C LYS A 163 " pdb=" CB LYS A 163 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.97e+00 chirality pdb=" CA GLU A 165 " pdb=" N GLU A 165 " pdb=" C GLU A 165 " pdb=" CB GLU A 165 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.03e+00 chirality pdb=" CA THR C 199 " pdb=" N THR C 199 " pdb=" C THR C 199 " pdb=" CB THR C 199 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.50 2.00e-01 2.50e+01 6.17e+00 ... (remaining 2268 not shown) Planarity restraints: 2550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 194 " 0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C ILE C 194 " -0.085 2.00e-02 2.50e+03 pdb=" O ILE C 194 " 0.032 2.00e-02 2.50e+03 pdb=" N ASN C 195 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 378 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO B 379 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 379 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 379 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 374 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLN D 374 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN D 374 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU D 375 " 0.019 2.00e-02 2.50e+03 ... (remaining 2547 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.07: 7 2.07 - 2.84: 5129 2.84 - 3.61: 23276 3.61 - 4.37: 44606 4.37 - 5.14: 74897 Nonbonded interactions: 147915 Sorted by model distance: nonbonded pdb=" CE2 TYR C 355 " pdb=" CG2 THR C 358 " model vdw 1.304 3.760 nonbonded pdb=" CD2 TYR C 355 " pdb=" OG1 THR C 358 " model vdw 1.359 3.340 nonbonded pdb=" N GLU A 165 " pdb=" O GLU A 165 " model vdw 1.891 2.496 nonbonded pdb=" O GLY D 449 " pdb=" OG1 THR D 452 " model vdw 1.997 3.040 nonbonded pdb=" CE2 TYR C 355 " pdb=" CB THR C 358 " model vdw 2.003 3.770 ... (remaining 147910 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 52 through 505) selection = (chain 'B' and (resid 52 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 129 through 132 or (resid 133 an \ d (name N or name CA or name C or name O or name CB or name OG1)) or resid 134 t \ hrough 505)) selection = chain 'C' selection = (chain 'D' and (resid 52 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 129 through 132 or (resid 133 an \ d (name N or name CA or name C or name O or name CB or name OG1)) or resid 134 t \ hrough 505)) } 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: 8.400 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.670 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.016 0.226 15222 Z= 0.790 Angle : 1.415 24.710 20611 Z= 0.855 Chirality : 0.083 0.632 2271 Planarity : 0.008 0.082 2550 Dihedral : 14.846 77.223 5523 Min Nonbonded Distance : 1.304 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.25 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.16), residues: 1763 helix: -3.97 (0.10), residues: 958 sheet: -2.25 (0.41), residues: 110 loop : -2.63 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 235 HIS 0.012 0.002 HIS D 143 PHE 0.027 0.004 PHE D 329 TYR 0.036 0.004 TYR A 210 ARG 0.012 0.001 ARG D 497 Details of bonding type rmsd hydrogen bonds : bond 0.24169 ( 583) hydrogen bonds : angle 9.72745 ( 1575) covalent geometry : bond 0.01634 (15221) covalent geometry : angle 1.41548 (20611) Misc. bond : bond 0.22643 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7330 (tmt170) cc_final: 0.7003 (tpt90) REVERT: A 155 ASP cc_start: 0.8302 (t70) cc_final: 0.7747 (t0) REVERT: A 200 ARG cc_start: 0.7714 (tpm170) cc_final: 0.7434 (tpt90) REVERT: A 323 MET cc_start: 0.7051 (mmt) cc_final: 0.6500 (ptt) REVERT: B 56 TYR cc_start: 0.6293 (m-80) cc_final: 0.6040 (m-80) REVERT: B 63 ARG cc_start: 0.7979 (mtm180) cc_final: 0.7350 (ptt-90) REVERT: B 65 TYR cc_start: 0.8456 (t80) cc_final: 0.8220 (t80) REVERT: B 70 MET cc_start: 0.7655 (mtp) cc_final: 0.7292 (mmm) REVERT: B 183 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7368 (mp0) REVERT: B 189 GLU cc_start: 0.7949 (pp20) cc_final: 0.7601 (pp20) REVERT: B 285 MET cc_start: 0.8890 (mtt) cc_final: 0.8664 (mtt) REVERT: C 61 LYS cc_start: 0.8737 (mppt) cc_final: 0.8396 (mppt) REVERT: C 127 ARG cc_start: 0.7211 (ttt180) cc_final: 0.6858 (ttp80) REVERT: C 200 ARG cc_start: 0.6671 (mtt-85) cc_final: 0.6447 (pmt170) REVERT: C 231 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7124 (mt-10) REVERT: C 504 MET cc_start: -0.2074 (mtt) cc_final: -0.2869 (pmm) REVERT: D 63 ARG cc_start: 0.7636 (mtm110) cc_final: 0.6900 (ptp-110) REVERT: D 95 GLU cc_start: 0.7758 (tp30) cc_final: 0.7550 (mm-30) REVERT: D 126 TYR cc_start: 0.8455 (m-80) cc_final: 0.8078 (m-80) REVERT: D 145 LEU cc_start: 0.8225 (pt) cc_final: 0.7756 (mm) REVERT: D 147 ASP cc_start: 0.8233 (t0) cc_final: 0.7916 (t0) REVERT: D 193 ARG cc_start: 0.6728 (mtm180) cc_final: 0.6408 (ttp-110) REVERT: D 200 ARG cc_start: 0.7480 (mtm180) cc_final: 0.6988 (ttm-80) REVERT: D 323 MET cc_start: 0.7172 (mmm) cc_final: 0.6733 (mpm) REVERT: D 374 GLN cc_start: 0.7991 (tp40) cc_final: 0.7580 (mm-40) outliers start: 0 outliers final: 1 residues processed: 133 average time/residue: 1.5550 time to fit residues: 224.5351 Evaluate side-chains 105 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.5980 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 342 GLN A 354 HIS A 418 ASN A 476 HIS A 487 ASN B 62 ASN B 186 GLN B 397 GLN B 416 GLN B 476 HIS ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS C 62 ASN C 186 GLN C 230 ASN C 362 GLN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 342 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.209045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.109900 restraints weight = 19258.456| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.25 r_work: 0.3172 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15222 Z= 0.157 Angle : 0.671 11.314 20611 Z= 0.363 Chirality : 0.045 0.183 2271 Planarity : 0.005 0.067 2550 Dihedral : 7.149 36.790 2001 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.15 % Favored : 92.80 % Rotamer: Outliers : 1.92 % Allowed : 13.00 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.18), residues: 1763 helix: -2.75 (0.14), residues: 964 sheet: -2.13 (0.47), residues: 86 loop : -1.68 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 255 HIS 0.004 0.001 HIS A 476 PHE 0.018 0.001 PHE B 454 TYR 0.024 0.002 TYR A 355 ARG 0.005 0.001 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 583) hydrogen bonds : angle 5.88912 ( 1575) covalent geometry : bond 0.00345 (15221) covalent geometry : angle 0.67091 (20611) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.672 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7077 (tmt170) cc_final: 0.6593 (ttt90) REVERT: A 155 ASP cc_start: 0.8234 (t70) cc_final: 0.7711 (t0) REVERT: A 323 MET cc_start: 0.7009 (mmt) cc_final: 0.6578 (ptt) REVERT: B 56 TYR cc_start: 0.6255 (m-10) cc_final: 0.6052 (p90) REVERT: B 63 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7123 (ptt-90) REVERT: B 65 TYR cc_start: 0.7967 (t80) cc_final: 0.7682 (t80) REVERT: B 70 MET cc_start: 0.7622 (mtp) cc_final: 0.6921 (mmt) REVERT: B 155 ASP cc_start: 0.8444 (t70) cc_final: 0.8099 (t0) REVERT: B 189 GLU cc_start: 0.8130 (pp20) cc_final: 0.7859 (pp20) REVERT: B 301 TYR cc_start: 0.7791 (t80) cc_final: 0.7487 (t80) REVERT: B 477 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6850 (tp) REVERT: C 70 MET cc_start: 0.8687 (mmp) cc_final: 0.8469 (mpp) REVERT: C 127 ARG cc_start: 0.7403 (ttt180) cc_final: 0.6723 (ttp80) REVERT: C 200 ARG cc_start: 0.6068 (mtt-85) cc_final: 0.5808 (ptt-90) REVERT: C 282 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8188 (mp) REVERT: C 301 TYR cc_start: 0.7949 (t80) cc_final: 0.7547 (t80) REVERT: C 504 MET cc_start: -0.2361 (mtt) cc_final: -0.3023 (pmm) REVERT: D 63 ARG cc_start: 0.7858 (mtm110) cc_final: 0.6928 (ptp-110) REVERT: D 69 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7994 (mt-10) REVERT: D 95 GLU cc_start: 0.8170 (tp30) cc_final: 0.7930 (mm-30) REVERT: D 147 ASP cc_start: 0.8378 (t0) cc_final: 0.8019 (t0) REVERT: D 193 ARG cc_start: 0.6763 (mtm180) cc_final: 0.6307 (ttp-110) REVERT: D 323 MET cc_start: 0.7030 (mmm) cc_final: 0.6568 (mpm) outliers start: 31 outliers final: 6 residues processed: 150 average time/residue: 1.2291 time to fit residues: 204.0211 Evaluate side-chains 113 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 175 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 112 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 168 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.208315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.108666 restraints weight = 19229.069| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.22 r_work: 0.3151 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15222 Z= 0.181 Angle : 0.646 14.467 20611 Z= 0.341 Chirality : 0.045 0.178 2271 Planarity : 0.004 0.051 2550 Dihedral : 6.533 26.887 1999 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.09 % Favored : 92.85 % Rotamer: Outliers : 2.54 % Allowed : 15.29 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.19), residues: 1763 helix: -2.10 (0.15), residues: 983 sheet: -2.13 (0.48), residues: 96 loop : -1.19 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 255 HIS 0.005 0.001 HIS D 59 PHE 0.017 0.001 PHE B 454 TYR 0.029 0.002 TYR A 355 ARG 0.008 0.000 ARG D 187 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 583) hydrogen bonds : angle 5.33883 ( 1575) covalent geometry : bond 0.00416 (15221) covalent geometry : angle 0.64640 (20611) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7068 (tmt170) cc_final: 0.6672 (ttt90) REVERT: A 155 ASP cc_start: 0.8309 (t70) cc_final: 0.7815 (t0) REVERT: A 189 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7901 (mm-30) REVERT: B 56 TYR cc_start: 0.5957 (m-10) cc_final: 0.5525 (p90) REVERT: B 63 ARG cc_start: 0.8122 (mtm180) cc_final: 0.7153 (ptt-90) REVERT: B 70 MET cc_start: 0.7691 (mtp) cc_final: 0.7344 (mmt) REVERT: B 155 ASP cc_start: 0.8553 (t70) cc_final: 0.8238 (t0) REVERT: B 189 GLU cc_start: 0.8089 (pp20) cc_final: 0.7832 (pp20) REVERT: B 477 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6936 (tp) REVERT: C 61 LYS cc_start: 0.8679 (mppt) cc_final: 0.8460 (pttp) REVERT: C 70 MET cc_start: 0.8662 (mmp) cc_final: 0.8404 (mpp) REVERT: C 127 ARG cc_start: 0.7510 (ttt180) cc_final: 0.6833 (ttp80) REVERT: C 200 ARG cc_start: 0.6110 (mtt-85) cc_final: 0.5788 (ptt-90) REVERT: C 282 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8214 (mp) REVERT: C 301 TYR cc_start: 0.7931 (t80) cc_final: 0.7526 (t80) REVERT: C 330 MET cc_start: 0.5150 (ptt) cc_final: 0.4744 (ppp) REVERT: C 504 MET cc_start: -0.2301 (mtt) cc_final: -0.2955 (pmm) REVERT: D 63 ARG cc_start: 0.7841 (mtm110) cc_final: 0.7057 (ptp-110) REVERT: D 95 GLU cc_start: 0.8138 (tp30) cc_final: 0.7880 (mm-30) REVERT: D 147 ASP cc_start: 0.8388 (t0) cc_final: 0.8024 (t0) REVERT: D 193 ARG cc_start: 0.6679 (mtm180) cc_final: 0.6249 (ttp-110) REVERT: D 323 MET cc_start: 0.6941 (mmm) cc_final: 0.6541 (mmm) outliers start: 41 outliers final: 15 residues processed: 145 average time/residue: 1.1598 time to fit residues: 187.3475 Evaluate side-chains 126 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 79 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 125 optimal weight: 20.0000 chunk 154 optimal weight: 0.4980 chunk 119 optimal weight: 0.0070 chunk 91 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.210427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111890 restraints weight = 19231.603| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.24 r_work: 0.3197 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15222 Z= 0.126 Angle : 0.592 16.891 20611 Z= 0.309 Chirality : 0.043 0.156 2271 Planarity : 0.004 0.048 2550 Dihedral : 6.040 27.538 1999 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 2.41 % Allowed : 16.84 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.20), residues: 1763 helix: -1.64 (0.16), residues: 990 sheet: -1.54 (0.51), residues: 86 loop : -0.94 (0.26), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 255 HIS 0.003 0.001 HIS B 213 PHE 0.016 0.001 PHE B 454 TYR 0.029 0.001 TYR A 355 ARG 0.004 0.000 ARG D 187 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 583) hydrogen bonds : angle 4.90737 ( 1575) covalent geometry : bond 0.00280 (15221) covalent geometry : angle 0.59167 (20611) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7101 (tmt170) cc_final: 0.6707 (ttt90) REVERT: A 137 PHE cc_start: 0.8283 (m-80) cc_final: 0.8057 (m-10) REVERT: A 155 ASP cc_start: 0.8297 (t70) cc_final: 0.7840 (t0) REVERT: A 189 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7904 (mm-30) REVERT: A 434 LEU cc_start: 0.4492 (OUTLIER) cc_final: 0.4053 (tp) REVERT: B 56 TYR cc_start: 0.5796 (m-10) cc_final: 0.5460 (p90) REVERT: B 63 ARG cc_start: 0.7964 (mtm180) cc_final: 0.6934 (ptt-90) REVERT: B 70 MET cc_start: 0.7504 (mtp) cc_final: 0.6863 (mmp) REVERT: B 155 ASP cc_start: 0.8513 (t70) cc_final: 0.8204 (t0) REVERT: B 183 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6880 (pp20) REVERT: B 189 GLU cc_start: 0.8092 (pp20) cc_final: 0.7691 (pp20) REVERT: B 190 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7975 (mmtm) REVERT: B 477 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6960 (tp) REVERT: C 69 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8276 (mm-30) REVERT: C 70 MET cc_start: 0.8644 (mmp) cc_final: 0.8399 (mpp) REVERT: C 127 ARG cc_start: 0.7542 (ttt180) cc_final: 0.6882 (ttp80) REVERT: C 301 TYR cc_start: 0.7839 (t80) cc_final: 0.7376 (t80) REVERT: C 504 MET cc_start: -0.2383 (mtt) cc_final: -0.3010 (pmm) REVERT: D 63 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7014 (ttm-80) REVERT: D 95 GLU cc_start: 0.8164 (tp30) cc_final: 0.7906 (mm-30) REVERT: D 147 ASP cc_start: 0.8405 (t0) cc_final: 0.8022 (t0) REVERT: D 193 ARG cc_start: 0.6708 (mtm180) cc_final: 0.6236 (ttp-110) REVERT: D 323 MET cc_start: 0.6959 (mmm) cc_final: 0.6579 (mmm) REVERT: D 329 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.5805 (t80) outliers start: 39 outliers final: 11 residues processed: 153 average time/residue: 1.2149 time to fit residues: 206.8055 Evaluate side-chains 131 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 165 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 153 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 278 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.209203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.109945 restraints weight = 19232.780| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.23 r_work: 0.3170 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15222 Z= 0.158 Angle : 0.604 17.078 20611 Z= 0.315 Chirality : 0.045 0.235 2271 Planarity : 0.004 0.045 2550 Dihedral : 5.861 27.171 1999 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.98 % Favored : 92.97 % Rotamer: Outliers : 2.72 % Allowed : 18.08 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.20), residues: 1763 helix: -1.37 (0.16), residues: 980 sheet: -1.40 (0.52), residues: 86 loop : -0.84 (0.26), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 68 HIS 0.006 0.001 HIS B 346 PHE 0.017 0.001 PHE B 454 TYR 0.028 0.001 TYR A 355 ARG 0.003 0.000 ARG C 200 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 583) hydrogen bonds : angle 4.76774 ( 1575) covalent geometry : bond 0.00363 (15221) covalent geometry : angle 0.60395 (20611) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7148 (tmt170) cc_final: 0.6780 (ttt90) REVERT: A 137 PHE cc_start: 0.8193 (m-80) cc_final: 0.7989 (m-10) REVERT: A 189 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7957 (mm-30) REVERT: A 434 LEU cc_start: 0.4685 (OUTLIER) cc_final: 0.4306 (tp) REVERT: B 56 TYR cc_start: 0.5839 (m-10) cc_final: 0.5502 (p90) REVERT: B 63 ARG cc_start: 0.7929 (mtm180) cc_final: 0.6920 (ptt-90) REVERT: B 70 MET cc_start: 0.7588 (mtp) cc_final: 0.6985 (mmp) REVERT: B 155 ASP cc_start: 0.8541 (t70) cc_final: 0.8233 (t0) REVERT: B 189 GLU cc_start: 0.8101 (pp20) cc_final: 0.7681 (pp20) REVERT: B 190 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7983 (mmtm) REVERT: B 301 TYR cc_start: 0.7812 (t80) cc_final: 0.7153 (m-80) REVERT: B 477 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6964 (tp) REVERT: C 127 ARG cc_start: 0.7491 (ttt180) cc_final: 0.6856 (ttp80) REVERT: C 189 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7346 (mm-30) REVERT: C 301 TYR cc_start: 0.8020 (t80) cc_final: 0.7488 (t80) REVERT: C 330 MET cc_start: 0.5230 (OUTLIER) cc_final: 0.4827 (ppp) REVERT: C 504 MET cc_start: -0.2427 (mtt) cc_final: -0.3006 (pmm) REVERT: D 63 ARG cc_start: 0.7810 (mtm110) cc_final: 0.6990 (ttm-80) REVERT: D 95 GLU cc_start: 0.8086 (tp30) cc_final: 0.7834 (mm-30) REVERT: D 147 ASP cc_start: 0.8413 (t0) cc_final: 0.8039 (t0) REVERT: D 193 ARG cc_start: 0.6635 (mtm180) cc_final: 0.6192 (ttp-110) REVERT: D 323 MET cc_start: 0.6989 (mmm) cc_final: 0.6499 (mmp) REVERT: D 329 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.5784 (t80) outliers start: 44 outliers final: 17 residues processed: 156 average time/residue: 1.1941 time to fit residues: 207.0376 Evaluate side-chains 139 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 476 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.207493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.107143 restraints weight = 19171.929| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.23 r_work: 0.3128 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15222 Z= 0.239 Angle : 0.639 17.030 20611 Z= 0.333 Chirality : 0.047 0.185 2271 Planarity : 0.004 0.047 2550 Dihedral : 5.926 26.907 1999 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.26 % Favored : 92.68 % Rotamer: Outliers : 3.28 % Allowed : 17.89 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.20), residues: 1763 helix: -1.35 (0.16), residues: 974 sheet: -1.32 (0.53), residues: 86 loop : -0.80 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 68 HIS 0.005 0.001 HIS B 143 PHE 0.017 0.002 PHE B 454 TYR 0.027 0.002 TYR A 355 ARG 0.003 0.000 ARG D 138 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 583) hydrogen bonds : angle 4.80765 ( 1575) covalent geometry : bond 0.00566 (15221) covalent geometry : angle 0.63864 (20611) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7143 (tmt170) cc_final: 0.6759 (ttt90) REVERT: A 137 PHE cc_start: 0.8248 (m-80) cc_final: 0.8004 (m-10) REVERT: A 155 ASP cc_start: 0.8280 (t70) cc_final: 0.7781 (t0) REVERT: A 189 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7884 (mm-30) REVERT: A 434 LEU cc_start: 0.4663 (OUTLIER) cc_final: 0.4307 (tp) REVERT: B 56 TYR cc_start: 0.6110 (m-10) cc_final: 0.5871 (p90) REVERT: B 63 ARG cc_start: 0.7933 (mtm180) cc_final: 0.6951 (ptt-90) REVERT: B 70 MET cc_start: 0.7749 (mtp) cc_final: 0.7112 (mmp) REVERT: B 189 GLU cc_start: 0.8191 (pp20) cc_final: 0.7949 (pp20) REVERT: B 321 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: B 477 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6987 (tp) REVERT: C 127 ARG cc_start: 0.7501 (ttt180) cc_final: 0.6845 (ttp80) REVERT: C 134 ARG cc_start: 0.8996 (mtp180) cc_final: 0.8763 (mtp180) REVERT: C 189 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7423 (mm-30) REVERT: C 231 GLU cc_start: 0.7919 (tt0) cc_final: 0.7707 (tt0) REVERT: C 282 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8338 (mp) REVERT: C 301 TYR cc_start: 0.8026 (t80) cc_final: 0.7567 (t80) REVERT: C 330 MET cc_start: 0.5168 (OUTLIER) cc_final: 0.4748 (ppp) REVERT: C 504 MET cc_start: -0.2255 (mtt) cc_final: -0.2889 (pmm) REVERT: D 63 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7007 (ttm-80) REVERT: D 95 GLU cc_start: 0.8083 (tp30) cc_final: 0.7841 (mm-30) REVERT: D 147 ASP cc_start: 0.8399 (t0) cc_final: 0.8019 (t0) REVERT: D 193 ARG cc_start: 0.6638 (mtm180) cc_final: 0.6191 (ttp-110) REVERT: D 329 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.5717 (t80) REVERT: D 347 VAL cc_start: 0.7123 (OUTLIER) cc_final: 0.6906 (m) outliers start: 53 outliers final: 23 residues processed: 159 average time/residue: 1.1608 time to fit residues: 205.5044 Evaluate side-chains 141 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 149 optimal weight: 0.0070 chunk 117 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 174 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 167 optimal weight: 0.0570 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 133 optimal weight: 0.0570 chunk 138 optimal weight: 0.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN D 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.211559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.113275 restraints weight = 19316.233| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.24 r_work: 0.3179 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15222 Z= 0.103 Angle : 0.578 17.122 20611 Z= 0.298 Chirality : 0.043 0.159 2271 Planarity : 0.003 0.042 2550 Dihedral : 5.584 26.767 1999 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.90 % Favored : 94.04 % Rotamer: Outliers : 2.04 % Allowed : 19.94 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1763 helix: -1.06 (0.17), residues: 981 sheet: -1.38 (0.51), residues: 96 loop : -0.61 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 255 HIS 0.003 0.001 HIS B 354 PHE 0.023 0.001 PHE D 319 TYR 0.028 0.001 TYR A 355 ARG 0.005 0.000 ARG C 187 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 583) hydrogen bonds : angle 4.54244 ( 1575) covalent geometry : bond 0.00223 (15221) covalent geometry : angle 0.57761 (20611) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7082 (tmt170) cc_final: 0.6723 (ttt90) REVERT: A 137 PHE cc_start: 0.8139 (m-80) cc_final: 0.7910 (m-10) REVERT: A 155 ASP cc_start: 0.8203 (t70) cc_final: 0.7759 (t0) REVERT: A 189 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7897 (mm-30) REVERT: A 330 MET cc_start: 0.2975 (OUTLIER) cc_final: 0.2178 (ptp) REVERT: A 434 LEU cc_start: 0.4634 (OUTLIER) cc_final: 0.4352 (tp) REVERT: B 56 TYR cc_start: 0.5420 (m-10) cc_final: 0.5114 (p90) REVERT: B 63 ARG cc_start: 0.7821 (mtm180) cc_final: 0.6839 (ptt-90) REVERT: B 70 MET cc_start: 0.7461 (mtp) cc_final: 0.6923 (mmp) REVERT: B 155 ASP cc_start: 0.8458 (t70) cc_final: 0.8172 (t0) REVERT: B 189 GLU cc_start: 0.8170 (pp20) cc_final: 0.7894 (pp20) REVERT: B 301 TYR cc_start: 0.7697 (t80) cc_final: 0.7087 (m-80) REVERT: B 477 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6973 (tp) REVERT: C 127 ARG cc_start: 0.7476 (ttt180) cc_final: 0.6823 (ttp80) REVERT: C 200 ARG cc_start: 0.5351 (tpt170) cc_final: 0.4892 (tpt170) REVERT: C 301 TYR cc_start: 0.7992 (t80) cc_final: 0.7455 (t80) REVERT: C 330 MET cc_start: 0.5136 (OUTLIER) cc_final: 0.4807 (ppp) REVERT: C 504 MET cc_start: -0.2309 (mtt) cc_final: -0.2877 (pmm) REVERT: D 63 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7015 (ttm-80) REVERT: D 95 GLU cc_start: 0.8072 (tp30) cc_final: 0.7786 (tm-30) REVERT: D 147 ASP cc_start: 0.8407 (t0) cc_final: 0.8057 (t0) REVERT: D 193 ARG cc_start: 0.6567 (mtm180) cc_final: 0.6138 (ttp-110) REVERT: D 323 MET cc_start: 0.6293 (mmt) cc_final: 0.5924 (mpm) REVERT: D 329 PHE cc_start: 0.6469 (OUTLIER) cc_final: 0.5850 (t80) REVERT: D 360 MET cc_start: 0.6591 (mpt) cc_final: 0.6174 (ptm) outliers start: 33 outliers final: 13 residues processed: 147 average time/residue: 1.2164 time to fit residues: 198.1220 Evaluate side-chains 133 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 0 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 19 optimal weight: 0.0000 chunk 26 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 4 optimal weight: 0.1980 chunk 172 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 HIS D 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.208660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108280 restraints weight = 19195.392| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.24 r_work: 0.3145 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15222 Z= 0.199 Angle : 0.623 16.962 20611 Z= 0.322 Chirality : 0.046 0.171 2271 Planarity : 0.004 0.046 2550 Dihedral : 5.634 26.869 1999 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.86 % Favored : 93.08 % Rotamer: Outliers : 2.60 % Allowed : 19.44 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.21), residues: 1763 helix: -1.07 (0.17), residues: 981 sheet: -1.33 (0.51), residues: 96 loop : -0.55 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 68 HIS 0.008 0.001 HIS B 476 PHE 0.025 0.002 PHE A 485 TYR 0.029 0.002 TYR B 196 ARG 0.005 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 583) hydrogen bonds : angle 4.60381 ( 1575) covalent geometry : bond 0.00469 (15221) covalent geometry : angle 0.62285 (20611) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7117 (tmt170) cc_final: 0.6758 (ttt90) REVERT: A 137 PHE cc_start: 0.8160 (m-80) cc_final: 0.7945 (m-10) REVERT: A 189 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7906 (mm-30) REVERT: A 330 MET cc_start: 0.2962 (OUTLIER) cc_final: 0.2170 (ptp) REVERT: A 434 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4364 (tp) REVERT: B 56 TYR cc_start: 0.5863 (m-10) cc_final: 0.5623 (p90) REVERT: B 63 ARG cc_start: 0.7868 (mtm180) cc_final: 0.6909 (ptt-90) REVERT: B 70 MET cc_start: 0.7716 (mtp) cc_final: 0.7124 (mmp) REVERT: B 189 GLU cc_start: 0.8205 (pp20) cc_final: 0.7993 (pp20) REVERT: B 301 TYR cc_start: 0.7756 (t80) cc_final: 0.7095 (m-80) REVERT: B 477 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6835 (tp) REVERT: C 127 ARG cc_start: 0.7519 (ttt180) cc_final: 0.6837 (ttp80) REVERT: C 134 ARG cc_start: 0.8993 (mtp180) cc_final: 0.8736 (mtp180) REVERT: C 200 ARG cc_start: 0.5607 (tpt170) cc_final: 0.5207 (tpt170) REVERT: C 282 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8323 (mp) REVERT: C 301 TYR cc_start: 0.8002 (t80) cc_final: 0.7521 (t80) REVERT: C 330 MET cc_start: 0.5184 (OUTLIER) cc_final: 0.4727 (ppp) REVERT: C 504 MET cc_start: -0.2124 (mtt) cc_final: -0.2789 (pmm) REVERT: D 63 ARG cc_start: 0.7808 (mtm110) cc_final: 0.7021 (ttm-80) REVERT: D 95 GLU cc_start: 0.8061 (tp30) cc_final: 0.7815 (mm-30) REVERT: D 147 ASP cc_start: 0.8380 (t0) cc_final: 0.8064 (t0) REVERT: D 193 ARG cc_start: 0.6618 (mtm180) cc_final: 0.6175 (ttp-110) REVERT: D 323 MET cc_start: 0.6440 (mmm) cc_final: 0.6043 (mmt) REVERT: D 329 PHE cc_start: 0.6456 (OUTLIER) cc_final: 0.5821 (t80) outliers start: 42 outliers final: 19 residues processed: 151 average time/residue: 1.1393 time to fit residues: 192.2826 Evaluate side-chains 138 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 TYR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 161 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 55 optimal weight: 0.0370 chunk 80 optimal weight: 30.0000 chunk 1 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 HIS C 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.209284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109345 restraints weight = 19114.001| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.24 r_work: 0.3157 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15222 Z= 0.166 Angle : 0.612 17.018 20611 Z= 0.314 Chirality : 0.045 0.168 2271 Planarity : 0.004 0.043 2550 Dihedral : 5.574 26.301 1999 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 1.80 % Allowed : 20.62 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.21), residues: 1763 helix: -1.01 (0.17), residues: 983 sheet: -1.28 (0.52), residues: 96 loop : -0.54 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 68 HIS 0.007 0.001 HIS B 354 PHE 0.018 0.001 PHE D 319 TYR 0.027 0.001 TYR A 355 ARG 0.004 0.000 ARG C 187 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 583) hydrogen bonds : angle 4.53936 ( 1575) covalent geometry : bond 0.00387 (15221) covalent geometry : angle 0.61189 (20611) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7173 (tmt170) cc_final: 0.6812 (ttt90) REVERT: A 137 PHE cc_start: 0.8166 (m-80) cc_final: 0.7948 (m-10) REVERT: A 189 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7894 (mm-30) REVERT: A 330 MET cc_start: 0.2958 (OUTLIER) cc_final: 0.2179 (ptp) REVERT: A 434 LEU cc_start: 0.4638 (OUTLIER) cc_final: 0.4392 (tp) REVERT: B 63 ARG cc_start: 0.7800 (mtm180) cc_final: 0.6872 (ptt-90) REVERT: B 70 MET cc_start: 0.7748 (mtp) cc_final: 0.7145 (mmp) REVERT: B 189 GLU cc_start: 0.8169 (pp20) cc_final: 0.7963 (pp20) REVERT: B 296 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8247 (mtp) REVERT: B 301 TYR cc_start: 0.7730 (t80) cc_final: 0.7093 (m-80) REVERT: B 411 GLU cc_start: 0.4547 (OUTLIER) cc_final: 0.4148 (mp0) REVERT: B 477 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6636 (tp) REVERT: C 127 ARG cc_start: 0.7540 (ttt180) cc_final: 0.6862 (ttp80) REVERT: C 134 ARG cc_start: 0.9022 (mtp180) cc_final: 0.8763 (mtp180) REVERT: C 200 ARG cc_start: 0.5464 (tpt170) cc_final: 0.5123 (tpt170) REVERT: C 281 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7595 (t0) REVERT: C 282 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8190 (mp) REVERT: C 301 TYR cc_start: 0.8009 (t80) cc_final: 0.7560 (t80) REVERT: C 330 MET cc_start: 0.5172 (OUTLIER) cc_final: 0.4717 (ppp) REVERT: C 504 MET cc_start: -0.2070 (mtt) cc_final: -0.2764 (pmm) REVERT: D 63 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7017 (ttm-80) REVERT: D 95 GLU cc_start: 0.8061 (tp30) cc_final: 0.7819 (mm-30) REVERT: D 147 ASP cc_start: 0.8312 (t0) cc_final: 0.7982 (t0) REVERT: D 193 ARG cc_start: 0.6605 (mtm180) cc_final: 0.6166 (ttp-110) REVERT: D 323 MET cc_start: 0.6384 (mmm) cc_final: 0.5857 (mpm) REVERT: D 329 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.5581 (t80) REVERT: D 360 MET cc_start: 0.6512 (mpt) cc_final: 0.6047 (ptm) outliers start: 29 outliers final: 14 residues processed: 137 average time/residue: 1.2283 time to fit residues: 186.6813 Evaluate side-chains 136 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 151 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 136 optimal weight: 0.0050 chunk 8 optimal weight: 0.3980 chunk 70 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 154 optimal weight: 0.0670 chunk 15 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.3732 ------------------------------------------------------------------------------- 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 = 0.4630 r_free = 0.4630 target = 0.211463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.113198 restraints weight = 19294.481| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.25 r_work: 0.3172 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15222 Z= 0.109 Angle : 0.590 16.946 20611 Z= 0.301 Chirality : 0.043 0.162 2271 Planarity : 0.003 0.047 2550 Dihedral : 5.369 26.251 1999 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 1.61 % Allowed : 20.80 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.21), residues: 1763 helix: -0.82 (0.17), residues: 990 sheet: -1.21 (0.52), residues: 96 loop : -0.44 (0.27), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 68 HIS 0.007 0.001 HIS B 354 PHE 0.018 0.001 PHE D 319 TYR 0.028 0.001 TYR B 196 ARG 0.004 0.000 ARG C 187 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 583) hydrogen bonds : angle 4.40607 ( 1575) covalent geometry : bond 0.00242 (15221) covalent geometry : angle 0.58993 (20611) Misc. bond : bond 0.00042 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8070 (m-10) cc_final: 0.7691 (m-90) REVERT: A 96 ARG cc_start: 0.7061 (tmt170) cc_final: 0.6751 (ttt90) REVERT: A 137 PHE cc_start: 0.8039 (m-80) cc_final: 0.7830 (m-10) REVERT: A 189 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7846 (mm-30) REVERT: A 330 MET cc_start: 0.2991 (OUTLIER) cc_final: 0.2311 (ptp) REVERT: A 331 ASN cc_start: 0.7057 (OUTLIER) cc_final: 0.6772 (m-40) REVERT: A 434 LEU cc_start: 0.4730 (OUTLIER) cc_final: 0.4484 (tp) REVERT: B 56 TYR cc_start: 0.5726 (OUTLIER) cc_final: 0.5503 (p90) REVERT: B 63 ARG cc_start: 0.7728 (mtm180) cc_final: 0.6791 (ptt-90) REVERT: B 70 MET cc_start: 0.7635 (mtp) cc_final: 0.7068 (mmp) REVERT: B 137 PHE cc_start: 0.6520 (m-80) cc_final: 0.6228 (m-80) REVERT: B 155 ASP cc_start: 0.8500 (t70) cc_final: 0.8221 (t0) REVERT: B 189 GLU cc_start: 0.8171 (pp20) cc_final: 0.7960 (pp20) REVERT: B 301 TYR cc_start: 0.7679 (t80) cc_final: 0.7098 (m-80) REVERT: B 477 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6587 (tp) REVERT: C 127 ARG cc_start: 0.7531 (ttt180) cc_final: 0.6827 (ttp80) REVERT: C 134 ARG cc_start: 0.9004 (mtp180) cc_final: 0.8751 (mtp180) REVERT: C 200 ARG cc_start: 0.5267 (tpt170) cc_final: 0.4894 (tpt170) REVERT: C 301 TYR cc_start: 0.7966 (t80) cc_final: 0.7442 (t80) REVERT: C 330 MET cc_start: 0.5075 (OUTLIER) cc_final: 0.4631 (ppp) REVERT: C 504 MET cc_start: -0.2088 (mtt) cc_final: -0.2741 (pmm) REVERT: D 63 ARG cc_start: 0.7753 (mtm110) cc_final: 0.6964 (ttm-80) REVERT: D 95 GLU cc_start: 0.8065 (tp30) cc_final: 0.7793 (tm-30) REVERT: D 147 ASP cc_start: 0.8287 (t0) cc_final: 0.7950 (t0) REVERT: D 193 ARG cc_start: 0.6626 (mtm180) cc_final: 0.6205 (ttp-110) REVERT: D 323 MET cc_start: 0.6458 (mmm) cc_final: 0.5961 (mpm) REVERT: D 329 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.5651 (t80) REVERT: D 360 MET cc_start: 0.6695 (mpt) cc_final: 0.6271 (ptm) outliers start: 26 outliers final: 12 residues processed: 136 average time/residue: 1.2453 time to fit residues: 187.7727 Evaluate side-chains 132 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 170 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 0.0770 chunk 91 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.208946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.108989 restraints weight = 19280.512| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.24 r_work: 0.3154 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15222 Z= 0.192 Angle : 0.633 16.523 20611 Z= 0.321 Chirality : 0.046 0.175 2271 Planarity : 0.004 0.043 2550 Dihedral : 5.462 26.693 1999 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.64 % Favored : 93.31 % Rotamer: Outliers : 1.98 % Allowed : 20.68 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1763 helix: -0.80 (0.17), residues: 972 sheet: -1.21 (0.52), residues: 96 loop : -0.47 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 68 HIS 0.004 0.001 HIS B 354 PHE 0.017 0.001 PHE D 319 TYR 0.031 0.002 TYR B 196 ARG 0.005 0.000 ARG C 187 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 583) hydrogen bonds : angle 4.49627 ( 1575) covalent geometry : bond 0.00456 (15221) covalent geometry : angle 0.63343 (20611) Misc. bond : bond 0.00049 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17697.78 seconds wall clock time: 304 minutes 36.32 seconds (18276.32 seconds total)