Starting phenix.real_space_refine on Fri Jul 3 15:49:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j0z_61063/07_2026/9j0z_61063.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j0z_61063/07_2026/9j0z_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_61063/07_2026/9j0z_61063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j0z_61063/07_2026/9j0z_61063.map" model { file = "/net/cci-nas-00/data/ceres_data/9j0z_61063/07_2026/9j0z_61063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j0z_61063/07_2026/9j0z_61063.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 0 Ad-hoc single atom residues: {' K': 3} Chain breaks: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 3.35, per 1000 atoms: 0.23 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: 1.07 Conformation dependent library (CDL) restraints added in 612.8 milliseconds 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: 0.33 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: 2.64 Time building geometry restraints manager: 1.47 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: 8.780 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.280 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.012 0.001 ARG D 497 TYR 0.036 0.004 TYR A 210 PHE 0.027 0.004 PHE D 329 TRP 0.019 0.003 TRP C 235 HIS 0.012 0.002 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.01634 / 0.77 (15221) covalent geometry : angle 1.41548 / 0.85 (20611) hydrogen bonds : bond 0.24169 / 15.82 ( 583) hydrogen bonds : angle 9.72745 / 6.74 ( 1575) Misc. bond : bond 0.22643 / 11.92 ( 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 : 0.741 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: 0.7598 (pp20) REVERT: B 285 MET cc_start: 0.8890 (mtt) cc_final: 0.8665 (mtt) REVERT: C 61 LYS cc_start: 0.8737 (mppt) cc_final: 0.8423 (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 145 LEU cc_start: 0.8225 (pt) cc_final: 0.7756 (mm) REVERT: D 147 ASP cc_start: 0.8233 (t0) cc_final: 0.7917 (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: 0.7130 time to fit residues: 102.7457 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 : 0.545 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 305 ASN D 342 GLN D 465 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.209272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.110394 restraints weight = 19210.011| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.24 r_work: 0.3192 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15222 Z= 0.143 Angle : 0.673 11.073 20611 Z= 0.364 Chirality : 0.045 0.192 2271 Planarity : 0.005 0.069 2550 Dihedral : 7.206 36.055 2001 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 1.49 % Allowed : 13.25 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.18), residues: 1763 helix: -2.79 (0.14), residues: 961 sheet: -2.14 (0.47), residues: 86 loop : -1.58 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 179 TYR 0.025 0.002 TYR A 355 PHE 0.018 0.001 PHE B 454 TRP 0.015 0.001 TRP C 255 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (15221) covalent geometry : angle 0.67292 / 0.36 (20611) hydrogen bonds : bond 0.04843 / 3.05 ( 583) hydrogen bonds : angle 5.97090 / 4.15 ( 1575) Misc. bond : bond 0.00004 / 0.00 ( 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 150 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7111 (tmt170) cc_final: 0.6645 (ttt90) REVERT: A 155 ASP cc_start: 0.8235 (t70) cc_final: 0.7717 (t0) REVERT: A 323 MET cc_start: 0.7016 (mmt) cc_final: 0.6574 (ptt) REVERT: B 56 TYR cc_start: 0.6268 (m-10) cc_final: 0.6019 (p90) REVERT: B 63 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7116 (ptt-90) REVERT: B 70 MET cc_start: 0.7629 (mtp) cc_final: 0.6931 (mmt) REVERT: B 155 ASP cc_start: 0.8445 (t70) cc_final: 0.8105 (t0) REVERT: B 189 GLU cc_start: 0.8121 (pp20) cc_final: 0.7851 (pp20) REVERT: B 301 TYR cc_start: 0.7801 (t80) cc_final: 0.7496 (t80) REVERT: B 477 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6870 (tp) REVERT: C 70 MET cc_start: 0.8684 (mmp) cc_final: 0.8473 (mpp) REVERT: C 127 ARG cc_start: 0.7441 (ttt180) cc_final: 0.6734 (ttp80) REVERT: C 200 ARG cc_start: 0.6056 (mtt-85) cc_final: 0.5805 (ptt-90) REVERT: C 282 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8188 (mp) REVERT: C 301 TYR cc_start: 0.7921 (t80) cc_final: 0.7585 (t80) REVERT: C 504 MET cc_start: -0.2352 (mtt) cc_final: -0.3043 (pmm) REVERT: D 63 ARG cc_start: 0.7850 (mtm110) cc_final: 0.6921 (ptp-110) REVERT: D 69 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7916 (mt-10) REVERT: D 95 GLU cc_start: 0.8146 (tp30) cc_final: 0.7889 (mm-30) REVERT: D 147 ASP cc_start: 0.8389 (t0) cc_final: 0.8033 (t0) REVERT: D 193 ARG cc_start: 0.6781 (mtm180) cc_final: 0.6309 (ttp-110) REVERT: D 323 MET cc_start: 0.7039 (mmm) cc_final: 0.6578 (mmm) outliers start: 24 outliers final: 3 residues processed: 144 average time/residue: 0.5809 time to fit residues: 91.9693 Evaluate side-chains 115 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 477 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 104 optimal weight: 0.9980 chunk 162 optimal weight: 20.0000 chunk 44 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 126 optimal weight: 9.9990 chunk 138 optimal weight: 0.4980 chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 342 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.209967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.111717 restraints weight = 19396.879| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.23 r_work: 0.3159 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15222 Z= 0.130 Angle : 0.618 13.231 20611 Z= 0.328 Chirality : 0.044 0.199 2271 Planarity : 0.004 0.051 2550 Dihedral : 6.416 26.842 1999 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.81 % Favored : 93.14 % Rotamer: Outliers : 2.35 % Allowed : 15.79 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.19), residues: 1763 helix: -2.00 (0.15), residues: 977 sheet: -2.09 (0.47), residues: 96 loop : -1.14 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 187 TYR 0.029 0.001 TYR A 355 PHE 0.016 0.001 PHE B 454 TRP 0.012 0.001 TRP C 255 HIS 0.006 0.001 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (15221) covalent geometry : angle 0.61771 / 0.33 (20611) hydrogen bonds : bond 0.04210 / 2.66 ( 583) hydrogen bonds : angle 5.24080 / 3.64 ( 1575) Misc. bond : bond 0.00033 / 0.02 ( 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 163 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7090 (tmt170) cc_final: 0.6691 (ttt90) REVERT: A 155 ASP cc_start: 0.8280 (t70) cc_final: 0.7831 (t0) REVERT: A 189 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7807 (mm-30) REVERT: A 200 ARG cc_start: 0.7124 (tpm170) cc_final: 0.6835 (tpt90) REVERT: A 323 MET cc_start: 0.6980 (mmt) cc_final: 0.6540 (ptt) REVERT: B 56 TYR cc_start: 0.5849 (m-10) cc_final: 0.5426 (p90) REVERT: B 63 ARG cc_start: 0.8111 (mtm180) cc_final: 0.7119 (ptt-90) REVERT: B 70 MET cc_start: 0.7485 (mtp) cc_final: 0.7102 (mmt) REVERT: B 155 ASP cc_start: 0.8461 (t70) cc_final: 0.8135 (t0) REVERT: B 183 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6856 (pp20) REVERT: B 189 GLU cc_start: 0.8094 (pp20) cc_final: 0.7829 (pp20) REVERT: B 197 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7284 (tp) REVERT: B 477 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6941 (tp) REVERT: C 61 LYS cc_start: 0.8650 (mppt) cc_final: 0.8423 (pttp) REVERT: C 70 MET cc_start: 0.8638 (mmp) cc_final: 0.8406 (mpp) REVERT: C 127 ARG cc_start: 0.7433 (ttt180) cc_final: 0.6686 (ttp80) REVERT: C 134 ARG cc_start: 0.9011 (mtp180) cc_final: 0.8683 (mtp180) REVERT: C 301 TYR cc_start: 0.7867 (t80) cc_final: 0.7472 (t80) REVERT: C 330 MET cc_start: 0.5103 (ptt) cc_final: 0.4612 (ppp) REVERT: C 504 MET cc_start: -0.2389 (mtt) cc_final: -0.3002 (pmm) REVERT: D 63 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7015 (ptp-110) REVERT: D 69 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7825 (mt-10) REVERT: D 95 GLU cc_start: 0.8134 (tp30) cc_final: 0.7862 (mm-30) REVERT: D 145 LEU cc_start: 0.7817 (pt) cc_final: 0.7483 (mm) REVERT: D 147 ASP cc_start: 0.8379 (t0) cc_final: 0.7995 (t0) REVERT: D 193 ARG cc_start: 0.6736 (mtm180) cc_final: 0.6263 (ttp-110) REVERT: D 323 MET cc_start: 0.6919 (mmm) cc_final: 0.6524 (mmm) outliers start: 38 outliers final: 10 residues processed: 154 average time/residue: 0.4943 time to fit residues: 84.3683 Evaluate side-chains 127 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 201 ILE 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 B residue 197 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 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 103 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 118 optimal weight: 20.0000 chunk 167 optimal weight: 0.0870 chunk 41 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.207698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.108820 restraints weight = 19194.086| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.20 r_work: 0.3138 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15222 Z= 0.227 Angle : 0.648 16.550 20611 Z= 0.339 Chirality : 0.046 0.202 2271 Planarity : 0.004 0.054 2550 Dihedral : 6.276 27.149 1999 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.32 % Favored : 92.63 % Rotamer: Outliers : 2.85 % Allowed : 16.66 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.20), residues: 1763 helix: -1.77 (0.16), residues: 980 sheet: -1.59 (0.51), residues: 86 loop : -0.96 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 187 TYR 0.028 0.002 TYR A 355 PHE 0.017 0.001 PHE B 454 TRP 0.017 0.002 TRP B 68 HIS 0.004 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (15221) covalent geometry : angle 0.64773 / 0.34 (20611) hydrogen bonds : bond 0.04477 / 2.79 ( 583) hydrogen bonds : angle 5.10131 / 3.54 ( 1575) Misc. bond : bond 0.00044 / 0.02 ( 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 164 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7130 (tmt170) cc_final: 0.6731 (ttt90) REVERT: A 155 ASP cc_start: 0.8335 (t70) cc_final: 0.7860 (t0) REVERT: A 189 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7884 (mm-30) REVERT: A 200 ARG cc_start: 0.7400 (tpm170) cc_final: 0.7051 (tpt90) REVERT: A 323 MET cc_start: 0.6903 (mmt) cc_final: 0.6443 (ptt) REVERT: A 434 LEU cc_start: 0.4179 (OUTLIER) cc_final: 0.3757 (tp) REVERT: B 56 TYR cc_start: 0.6101 (m-10) cc_final: 0.5815 (p90) REVERT: B 63 ARG cc_start: 0.8087 (mtm180) cc_final: 0.7131 (ptt-90) REVERT: B 70 MET cc_start: 0.7805 (mtp) cc_final: 0.7492 (mmt) REVERT: B 197 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7480 (tp) REVERT: B 477 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6968 (tp) REVERT: C 127 ARG cc_start: 0.7509 (ttt180) cc_final: 0.6835 (ttp80) REVERT: C 301 TYR cc_start: 0.7909 (t80) cc_final: 0.7462 (t80) REVERT: C 504 MET cc_start: -0.2309 (mtt) cc_final: -0.2994 (pmm) REVERT: D 63 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7025 (ttm-80) REVERT: D 95 GLU cc_start: 0.8125 (tp30) cc_final: 0.7874 (mm-30) REVERT: D 145 LEU cc_start: 0.7876 (pt) cc_final: 0.7500 (mm) REVERT: D 147 ASP cc_start: 0.8390 (t0) cc_final: 0.8022 (t0) REVERT: D 193 ARG cc_start: 0.6732 (mtm180) cc_final: 0.6298 (ttp-110) REVERT: D 329 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.5741 (t80) outliers start: 46 outliers final: 16 residues processed: 149 average time/residue: 0.5678 time to fit residues: 93.7706 Evaluate side-chains 130 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 209 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 120 TYR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 197 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 D residue 175 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 295 ASP 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 148 optimal weight: 0.7980 chunk 155 optimal weight: 0.2980 chunk 122 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 chunk 174 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 66 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 ASN D 465 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.209656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.111155 restraints weight = 19228.916| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.22 r_work: 0.3143 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15222 Z= 0.138 Angle : 0.601 16.875 20611 Z= 0.313 Chirality : 0.044 0.188 2271 Planarity : 0.004 0.042 2550 Dihedral : 5.948 26.907 1999 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.58 % Favored : 93.36 % Rotamer: Outliers : 2.79 % Allowed : 18.08 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.20), residues: 1763 helix: -1.48 (0.16), residues: 988 sheet: -1.42 (0.52), residues: 86 loop : -0.79 (0.26), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 332 TYR 0.028 0.001 TYR A 355 PHE 0.016 0.001 PHE B 454 TRP 0.013 0.001 TRP B 68 HIS 0.004 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (15221) covalent geometry : angle 0.60092 / 0.31 (20611) hydrogen bonds : bond 0.03984 / 2.50 ( 583) hydrogen bonds : angle 4.80374 / 3.33 ( 1575) Misc. bond : bond 0.00041 / 0.02 ( 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 168 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7087 (tmt170) cc_final: 0.6700 (ttt90) REVERT: A 137 PHE cc_start: 0.8205 (m-80) cc_final: 0.7991 (m-10) REVERT: A 155 ASP cc_start: 0.8314 (t70) cc_final: 0.7815 (t0) REVERT: A 189 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7868 (mm-30) REVERT: A 200 ARG cc_start: 0.7271 (tpm170) cc_final: 0.6890 (tpt90) REVERT: A 323 MET cc_start: 0.6893 (mmt) cc_final: 0.6505 (ptt) REVERT: B 56 TYR cc_start: 0.5822 (m-10) cc_final: 0.5484 (p90) REVERT: B 63 ARG cc_start: 0.7931 (mtm180) cc_final: 0.6958 (ptt-90) REVERT: B 70 MET cc_start: 0.7707 (mtp) cc_final: 0.7061 (mmp) REVERT: B 155 ASP cc_start: 0.8515 (t70) cc_final: 0.8213 (t0) REVERT: B 183 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6873 (pp20) REVERT: B 189 GLU cc_start: 0.8267 (pp20) cc_final: 0.7760 (pp20) REVERT: B 190 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7946 (mmtm) REVERT: B 317 GLU cc_start: 0.6755 (pp20) cc_final: 0.6214 (tm-30) REVERT: B 321 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: B 477 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6985 (tp) REVERT: C 127 ARG cc_start: 0.7484 (ttt180) cc_final: 0.6823 (ttp80) REVERT: C 231 GLU cc_start: 0.7534 (tt0) cc_final: 0.7327 (tt0) REVERT: C 301 TYR cc_start: 0.7934 (t80) cc_final: 0.7336 (t80) REVERT: C 330 MET cc_start: 0.5157 (OUTLIER) cc_final: 0.4683 (ppp) REVERT: C 504 MET cc_start: -0.2352 (mtt) cc_final: -0.2947 (pmm) REVERT: D 63 ARG cc_start: 0.7823 (mtm110) cc_final: 0.6979 (ttm-80) REVERT: D 95 GLU cc_start: 0.8126 (tp30) cc_final: 0.7815 (tm-30) REVERT: D 145 LEU cc_start: 0.7862 (pt) cc_final: 0.7586 (mm) REVERT: D 147 ASP cc_start: 0.8371 (t0) cc_final: 0.7983 (t0) REVERT: D 193 ARG cc_start: 0.6614 (mtm180) cc_final: 0.6169 (ttp-110) REVERT: D 323 MET cc_start: 0.6206 (mmm) cc_final: 0.5923 (mmt) REVERT: D 329 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.5831 (t80) outliers start: 45 outliers final: 10 residues processed: 158 average time/residue: 0.5399 time to fit residues: 94.6341 Evaluate side-chains 133 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 77 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 136 optimal weight: 0.0050 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.209997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.111761 restraints weight = 19143.547| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.22 r_work: 0.3147 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15222 Z= 0.135 Angle : 0.595 17.349 20611 Z= 0.308 Chirality : 0.044 0.187 2271 Planarity : 0.004 0.046 2550 Dihedral : 5.738 26.850 1999 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.48 % Rotamer: Outliers : 2.66 % Allowed : 18.58 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.20), residues: 1763 helix: -1.25 (0.16), residues: 984 sheet: -1.29 (0.53), residues: 86 loop : -0.68 (0.26), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 168 TYR 0.028 0.001 TYR A 355 PHE 0.016 0.001 PHE B 454 TRP 0.014 0.001 TRP B 68 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (15221) covalent geometry : angle 0.59516 / 0.31 (20611) hydrogen bonds : bond 0.03891 / 2.43 ( 583) hydrogen bonds : angle 4.66240 / 3.23 ( 1575) Misc. bond : bond 0.00038 / 0.02 ( 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 170 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7104 (tmt170) cc_final: 0.6734 (ttt90) REVERT: A 137 PHE cc_start: 0.8133 (m-80) cc_final: 0.7914 (m-10) REVERT: A 155 ASP cc_start: 0.8244 (t70) cc_final: 0.7788 (t0) REVERT: A 189 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7875 (mm-30) REVERT: A 200 ARG cc_start: 0.7295 (tpm170) cc_final: 0.6898 (tpt90) REVERT: A 434 LEU cc_start: 0.4580 (OUTLIER) cc_final: 0.4300 (tp) REVERT: B 56 TYR cc_start: 0.5763 (m-10) cc_final: 0.5478 (p90) REVERT: B 63 ARG cc_start: 0.7839 (mtm180) cc_final: 0.6828 (ptt-90) REVERT: B 65 TYR cc_start: 0.7490 (t80) cc_final: 0.7255 (t80) REVERT: B 70 MET cc_start: 0.7612 (mtp) cc_final: 0.6986 (mmp) REVERT: B 155 ASP cc_start: 0.8496 (t70) cc_final: 0.8194 (t0) REVERT: B 183 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6818 (pp20) REVERT: B 189 GLU cc_start: 0.8292 (pp20) cc_final: 0.7925 (pp20) REVERT: B 301 TYR cc_start: 0.7743 (t80) cc_final: 0.7097 (m-80) REVERT: B 317 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6322 (tm-30) REVERT: B 321 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: B 477 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7048 (tp) REVERT: C 127 ARG cc_start: 0.7458 (ttt180) cc_final: 0.6817 (ttp80) REVERT: C 200 ARG cc_start: 0.5297 (tpt170) cc_final: 0.4789 (tpt170) REVERT: C 301 TYR cc_start: 0.7968 (t80) cc_final: 0.7337 (t80) REVERT: C 330 MET cc_start: 0.5159 (OUTLIER) cc_final: 0.4697 (ppp) REVERT: C 504 MET cc_start: -0.2326 (mtt) cc_final: -0.2945 (pmm) REVERT: D 63 ARG cc_start: 0.7781 (mtm110) cc_final: 0.6958 (ttm-80) REVERT: D 95 GLU cc_start: 0.8066 (tp30) cc_final: 0.7782 (tm-30) REVERT: D 145 LEU cc_start: 0.7940 (pt) cc_final: 0.7628 (mm) REVERT: D 147 ASP cc_start: 0.8365 (t0) cc_final: 0.8017 (t0) REVERT: D 193 ARG cc_start: 0.6599 (mtm180) cc_final: 0.6167 (ttp-110) REVERT: D 323 MET cc_start: 0.6451 (mmm) cc_final: 0.6029 (mmt) REVERT: D 329 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.5829 (t80) outliers start: 43 outliers final: 16 residues processed: 159 average time/residue: 0.4994 time to fit residues: 88.2537 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 : 0.418 ------------------------------------------------------------------------------- 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 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 317 GLU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 280 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 123 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 133 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 126 optimal weight: 0.5980 chunk 154 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.210575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112505 restraints weight = 19172.989| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.24 r_work: 0.3160 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15222 Z= 0.126 Angle : 0.582 17.482 20611 Z= 0.302 Chirality : 0.044 0.161 2271 Planarity : 0.004 0.042 2550 Dihedral : 5.578 26.641 1999 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.96 % Favored : 93.99 % Rotamer: Outliers : 2.48 % Allowed : 18.95 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.21), residues: 1763 helix: -1.08 (0.17), residues: 984 sheet: -1.12 (0.53), residues: 91 loop : -0.57 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 138 TYR 0.028 0.001 TYR A 355 PHE 0.016 0.001 PHE B 454 TRP 0.014 0.001 TRP B 68 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (15221) covalent geometry : angle 0.58232 / 0.30 (20611) hydrogen bonds : bond 0.03777 / 2.35 ( 583) hydrogen bonds : angle 4.56728 / 3.16 ( 1575) Misc. bond : bond 0.00042 / 0.02 ( 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 163 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8064 (m-10) cc_final: 0.7524 (m-90) REVERT: A 96 ARG cc_start: 0.7107 (tmt170) cc_final: 0.6743 (ttt90) REVERT: A 137 PHE cc_start: 0.8073 (m-80) cc_final: 0.7855 (m-10) REVERT: A 155 ASP cc_start: 0.8228 (t70) cc_final: 0.7780 (t0) REVERT: A 189 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7825 (mm-30) REVERT: A 200 ARG cc_start: 0.7156 (tpm170) cc_final: 0.6849 (tpt90) REVERT: A 323 MET cc_start: 0.6911 (mmt) cc_final: 0.6499 (ptt) REVERT: A 434 LEU cc_start: 0.4633 (OUTLIER) cc_final: 0.4367 (tp) REVERT: B 56 TYR cc_start: 0.5722 (m-10) cc_final: 0.5498 (p90) REVERT: B 63 ARG cc_start: 0.7822 (mtm180) cc_final: 0.6826 (ptt-90) REVERT: B 70 MET cc_start: 0.7601 (mtp) cc_final: 0.7047 (mmp) REVERT: B 155 ASP cc_start: 0.8481 (t70) cc_final: 0.8184 (t0) REVERT: B 183 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6816 (pp20) REVERT: B 189 GLU cc_start: 0.8178 (pp20) cc_final: 0.7888 (pp20) REVERT: B 301 TYR cc_start: 0.7704 (t80) cc_final: 0.7074 (m-80) REVERT: B 477 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6978 (tp) REVERT: C 127 ARG cc_start: 0.7484 (ttt180) cc_final: 0.6837 (ttp80) REVERT: C 200 ARG cc_start: 0.5335 (tpt170) cc_final: 0.4869 (tpt170) REVERT: C 301 TYR cc_start: 0.7974 (t80) cc_final: 0.7420 (t80) REVERT: C 504 MET cc_start: -0.2336 (mtt) cc_final: -0.2879 (pmm) REVERT: D 63 ARG cc_start: 0.7805 (mtm110) cc_final: 0.6983 (ttm-80) REVERT: D 95 GLU cc_start: 0.8061 (tp30) cc_final: 0.7785 (tm-30) REVERT: D 145 LEU cc_start: 0.7928 (pt) cc_final: 0.7642 (mm) REVERT: D 147 ASP cc_start: 0.8324 (t0) cc_final: 0.7986 (t0) REVERT: D 193 ARG cc_start: 0.6584 (mtm180) cc_final: 0.6146 (ttp-110) REVERT: D 319 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.6129 (t80) REVERT: D 323 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6073 (mmp) REVERT: D 329 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.5876 (t80) REVERT: D 360 MET cc_start: 0.6592 (mpt) cc_final: 0.6140 (ptm) outliers start: 40 outliers final: 19 residues processed: 154 average time/residue: 0.4892 time to fit residues: 83.4255 Evaluate side-chains 138 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 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 109 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 280 VAL 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 319 PHE Chi-restraints excluded: chain D residue 323 MET 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 37 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 278 HIS ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.202144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102636 restraints weight = 20191.952| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.15 r_work: 0.3110 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.105 15222 Z= 0.579 Angle : 0.858 16.581 20611 Z= 0.443 Chirality : 0.060 0.236 2271 Planarity : 0.006 0.071 2550 Dihedral : 6.398 27.714 1999 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.46 % Rotamer: Outliers : 3.03 % Allowed : 19.20 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.20), residues: 1763 helix: -1.68 (0.15), residues: 975 sheet: -0.96 (0.56), residues: 82 loop : -1.04 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 138 TYR 0.030 0.003 TYR B 196 PHE 0.023 0.003 PHE C 264 TRP 0.042 0.003 TRP B 68 HIS 0.010 0.002 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.01380 / 0.58 (15221) covalent geometry : angle 0.85765 / 0.44 (20611) hydrogen bonds : bond 0.05427 / 3.38 ( 583) hydrogen bonds : angle 5.19113 / 3.59 ( 1575) Misc. bond : bond 0.00086 / 0.05 ( 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 154 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 105 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7173 (tmt170) cc_final: 0.6712 (ttt90) REVERT: A 155 ASP cc_start: 0.8453 (t70) cc_final: 0.7906 (t0) REVERT: A 189 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7837 (mm-30) REVERT: A 323 MET cc_start: 0.6896 (mmt) cc_final: 0.6416 (ptt) REVERT: A 434 LEU cc_start: 0.4444 (OUTLIER) cc_final: 0.4135 (tp) REVERT: A 489 LEU cc_start: 0.1789 (OUTLIER) cc_final: 0.1589 (mp) REVERT: B 63 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7009 (ptt-90) REVERT: B 70 MET cc_start: 0.8192 (mtp) cc_final: 0.7832 (mmm) REVERT: B 183 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7286 (mp0) REVERT: B 189 GLU cc_start: 0.8291 (pp20) cc_final: 0.8013 (pp20) REVERT: B 200 ARG cc_start: 0.7466 (mtp85) cc_final: 0.6625 (tpt-90) REVERT: B 477 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6886 (tp) REVERT: C 127 ARG cc_start: 0.7557 (ttt180) cc_final: 0.6867 (ttp80) REVERT: C 504 MET cc_start: -0.2031 (mtt) cc_final: -0.2881 (pmm) REVERT: D 63 ARG cc_start: 0.7846 (mtm110) cc_final: 0.7148 (ttm-80) REVERT: D 95 GLU cc_start: 0.8104 (tp30) cc_final: 0.7875 (mm-30) REVERT: D 145 LEU cc_start: 0.7914 (pt) cc_final: 0.7576 (mm) REVERT: D 147 ASP cc_start: 0.8277 (t0) cc_final: 0.8030 (t0) REVERT: D 193 ARG cc_start: 0.6707 (mtm180) cc_final: 0.6351 (ttp-110) REVERT: D 319 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.6205 (t80) REVERT: D 323 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.6054 (mmt) REVERT: D 329 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.5711 (t80) outliers start: 49 outliers final: 25 residues processed: 145 average time/residue: 0.4753 time to fit residues: 76.7421 Evaluate side-chains 131 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 204 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 330 MET Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 489 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 321 ASP 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 280 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain D residue 157 ILE 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 297 VAL Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 323 MET 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 80 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 157 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 67 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 161 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.207741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108334 restraints weight = 19250.288| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.26 r_work: 0.3149 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15222 Z= 0.174 Angle : 0.642 16.628 20611 Z= 0.332 Chirality : 0.046 0.162 2271 Planarity : 0.004 0.044 2550 Dihedral : 5.985 26.423 1999 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.30 % Favored : 93.65 % Rotamer: Outliers : 2.17 % Allowed : 20.43 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.20), residues: 1763 helix: -1.30 (0.16), residues: 969 sheet: -1.16 (0.54), residues: 91 loop : -0.74 (0.26), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.028 0.002 TYR B 196 PHE 0.017 0.001 PHE B 454 TRP 0.018 0.001 TRP B 68 HIS 0.006 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (15221) covalent geometry : angle 0.64195 / 0.33 (20611) hydrogen bonds : bond 0.04199 / 2.61 ( 583) hydrogen bonds : angle 4.78806 / 3.31 ( 1575) Misc. bond : bond 0.00040 / 0.02 ( 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 146 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8295 (tm) REVERT: A 96 ARG cc_start: 0.7137 (tmt170) cc_final: 0.6759 (ttt90) REVERT: A 155 ASP cc_start: 0.8353 (t70) cc_final: 0.7853 (t0) REVERT: A 189 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7841 (mm-30) REVERT: A 323 MET cc_start: 0.6919 (mmt) cc_final: 0.6502 (ptt) REVERT: A 434 LEU cc_start: 0.4613 (OUTLIER) cc_final: 0.4353 (tp) REVERT: B 63 ARG cc_start: 0.7800 (mtm180) cc_final: 0.6919 (ptt-90) REVERT: B 70 MET cc_start: 0.7944 (mtp) cc_final: 0.7604 (mmt) REVERT: B 183 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7104 (mp0) REVERT: B 189 GLU cc_start: 0.8291 (pp20) cc_final: 0.7986 (pp20) REVERT: B 477 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6669 (tp) REVERT: C 127 ARG cc_start: 0.7525 (ttt180) cc_final: 0.6818 (ttp80) REVERT: C 134 ARG cc_start: 0.8983 (mtp180) cc_final: 0.8707 (mtp180) REVERT: C 301 TYR cc_start: 0.8097 (t80) cc_final: 0.7740 (t80) REVERT: C 504 MET cc_start: -0.2064 (mtt) cc_final: -0.2766 (pmm) REVERT: D 95 GLU cc_start: 0.8130 (tp30) cc_final: 0.7888 (mm-30) REVERT: D 145 LEU cc_start: 0.7967 (pt) cc_final: 0.7597 (mm) REVERT: D 147 ASP cc_start: 0.8235 (t0) cc_final: 0.7945 (t0) REVERT: D 193 ARG cc_start: 0.6744 (mtm180) cc_final: 0.6286 (ttp-110) REVERT: D 319 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.5798 (t80) REVERT: D 323 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5932 (mpm) REVERT: D 329 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.5726 (t80) REVERT: D 360 MET cc_start: 0.6497 (mpt) cc_final: 0.6003 (ptm) outliers start: 35 outliers final: 17 residues processed: 139 average time/residue: 0.4896 time to fit residues: 75.7634 Evaluate side-chains 129 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 267 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 73 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 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 280 VAL 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 319 PHE Chi-restraints excluded: chain D residue 323 MET 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 109 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.209606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.111203 restraints weight = 19232.139| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.25 r_work: 0.3185 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15222 Z= 0.135 Angle : 0.604 16.548 20611 Z= 0.312 Chirality : 0.044 0.166 2271 Planarity : 0.004 0.046 2550 Dihedral : 5.636 26.955 1999 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.64 % Favored : 93.31 % Rotamer: Outliers : 1.73 % Allowed : 20.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.21), residues: 1763 helix: -0.99 (0.17), residues: 985 sheet: -1.42 (0.53), residues: 86 loop : -0.60 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 187 TYR 0.028 0.001 TYR B 196 PHE 0.015 0.001 PHE B 454 TRP 0.012 0.001 TRP C 64 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (15221) covalent geometry : angle 0.60420 / 0.31 (20611) hydrogen bonds : bond 0.03837 / 2.40 ( 583) hydrogen bonds : angle 4.59496 / 3.18 ( 1575) Misc. bond : bond 0.00052 / 0.03 ( 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 139 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8421 (mmm) cc_final: 0.8022 (tpp) REVERT: A 96 ARG cc_start: 0.7125 (tmt170) cc_final: 0.6774 (ttt90) REVERT: A 137 PHE cc_start: 0.8088 (m-80) cc_final: 0.7869 (m-10) REVERT: A 155 ASP cc_start: 0.8276 (t70) cc_final: 0.7798 (t0) REVERT: A 189 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7848 (mm-30) REVERT: A 434 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.4434 (tp) REVERT: B 63 ARG cc_start: 0.7733 (mtm180) cc_final: 0.6804 (ptt-90) REVERT: B 70 MET cc_start: 0.7668 (mtp) cc_final: 0.7036 (mmp) REVERT: B 155 ASP cc_start: 0.8553 (t70) cc_final: 0.8266 (t0) REVERT: B 189 GLU cc_start: 0.8265 (pp20) cc_final: 0.7991 (pp20) REVERT: B 301 TYR cc_start: 0.7712 (t80) cc_final: 0.7079 (m-80) REVERT: B 477 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6680 (tp) REVERT: C 127 ARG cc_start: 0.7549 (ttt180) cc_final: 0.6871 (ttp80) REVERT: C 134 ARG cc_start: 0.8966 (mtp180) cc_final: 0.8703 (mtp180) REVERT: C 301 TYR cc_start: 0.8081 (t80) cc_final: 0.7599 (t80) REVERT: C 504 MET cc_start: -0.2005 (mtt) cc_final: -0.2679 (pmm) REVERT: D 95 GLU cc_start: 0.8050 (tp30) cc_final: 0.7810 (mm-30) REVERT: D 145 LEU cc_start: 0.8024 (pt) cc_final: 0.7757 (mm) REVERT: D 147 ASP cc_start: 0.8128 (t0) cc_final: 0.7817 (t0) REVERT: D 319 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.5794 (t80) REVERT: D 323 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6001 (mpm) REVERT: D 329 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5594 (t80) REVERT: D 360 MET cc_start: 0.6547 (mpt) cc_final: 0.6111 (ptm) outliers start: 28 outliers final: 16 residues processed: 134 average time/residue: 0.5268 time to fit residues: 78.1687 Evaluate side-chains 131 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 209 VAL Chi-restraints excluded: chain A residue 267 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 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 204 LEU Chi-restraints excluded: chain C residue 280 VAL 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 319 PHE Chi-restraints excluded: chain D residue 323 MET 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 89 optimal weight: 0.0970 chunk 1 optimal weight: 0.0570 chunk 28 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 109 optimal weight: 0.9990 chunk 132 optimal weight: 0.0670 chunk 113 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.210798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.113487 restraints weight = 19127.506| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.25 r_work: 0.3216 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15222 Z= 0.116 Angle : 0.591 16.865 20611 Z= 0.304 Chirality : 0.043 0.173 2271 Planarity : 0.004 0.045 2550 Dihedral : 5.424 27.862 1999 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 1.24 % Allowed : 21.30 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.21), residues: 1763 helix: -0.77 (0.17), residues: 990 sheet: -1.76 (0.55), residues: 80 loop : -0.47 (0.26), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 187 TYR 0.028 0.001 TYR A 355 PHE 0.021 0.001 PHE D 329 TRP 0.014 0.001 TRP C 64 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (15221) covalent geometry : angle 0.59063 / 0.30 (20611) hydrogen bonds : bond 0.03716 / 2.34 ( 583) hydrogen bonds : angle 4.48478 / 3.10 ( 1575) Misc. bond : bond 0.00045 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8046.29 seconds wall clock time: 137 minutes 13.25 seconds (8233.25 seconds total)