Starting phenix.real_space_refine on Thu Sep 18 07:09:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j0z_61063/09_2025/9j0z_61063.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j0z_61063/09_2025/9j0z_61063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j0z_61063/09_2025/9j0z_61063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j0z_61063/09_2025/9j0z_61063.map" model { file = "/net/cci-nas-00/data/ceres_data/9j0z_61063/09_2025/9j0z_61063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j0z_61063/09_2025/9j0z_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-2.0-5805/lib/python3.9/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, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.71, per 1000 atoms: 0.25 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: 1.22 Conformation dependent library (CDL) restraints added in 640.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.51 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: 2.36 Time building geometry restraints manager: 1.63 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: 7.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.480 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.226 15222 Z= 0.790 Angle : 1.415 24.710 20611 Z= 0.855 Chirality : 0.083 0.632 2271 Planarity : 0.008 0.082 2550 Dihedral : 14.846 77.223 5523 Min Nonbonded Distance : 1.304 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.25 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 covalent geometry : bond 0.01634 (15221) covalent geometry : angle 1.41548 (20611) hydrogen bonds : bond 0.24169 ( 583) hydrogen bonds : angle 9.72745 ( 1575) Misc. bond : bond 0.22643 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.572 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: 0.7804 time to fit residues: 112.0262 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 : 0.594 ------------------------------------------------------------------------------- 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: 0.9990 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... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 342 GLN A 354 HIS A 418 ASN A 476 HIS A 487 ASN B 62 ASN B 186 GLN B 397 GLN B 416 GLN B 476 HIS ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS C 62 ASN C 186 GLN C 230 ASN C 362 GLN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 342 GLN D 465 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.209765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110923 restraints weight = 19192.870| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.25 r_work: 0.3191 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15222 Z= 0.140 Angle : 0.665 11.294 20611 Z= 0.359 Chirality : 0.044 0.173 2271 Planarity : 0.005 0.069 2550 Dihedral : 7.125 36.122 2001 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 1.73 % Allowed : 13.25 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.67 (0.18), residues: 1763 helix: -2.75 (0.14), residues: 964 sheet: -2.49 (0.45), residues: 96 loop : -1.65 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 179 TYR 0.024 0.002 TYR A 355 PHE 0.017 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 covalent geometry : bond 0.00296 (15221) covalent geometry : angle 0.66487 (20611) hydrogen bonds : bond 0.04642 ( 583) hydrogen bonds : angle 5.87417 ( 1575) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7082 (tmt170) cc_final: 0.6608 (ttt90) REVERT: A 155 ASP cc_start: 0.8223 (t70) cc_final: 0.7758 (t0) REVERT: A 323 MET cc_start: 0.7035 (mmt) cc_final: 0.6582 (ptt) REVERT: B 56 TYR cc_start: 0.6234 (m-10) cc_final: 0.6029 (p90) REVERT: B 63 ARG cc_start: 0.8122 (mtm180) cc_final: 0.7112 (ptt-90) REVERT: B 70 MET cc_start: 0.7611 (mtp) cc_final: 0.6880 (mmt) REVERT: B 155 ASP cc_start: 0.8435 (t70) cc_final: 0.8096 (t0) REVERT: B 189 GLU cc_start: 0.8116 (pp20) cc_final: 0.7848 (pp20) REVERT: B 301 TYR cc_start: 0.7782 (t80) cc_final: 0.7475 (t80) REVERT: B 477 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6866 (tp) REVERT: C 70 MET cc_start: 0.8693 (mmp) cc_final: 0.8480 (mpp) REVERT: C 127 ARG cc_start: 0.7478 (ttt180) cc_final: 0.6745 (ttp80) REVERT: C 134 ARG cc_start: 0.9039 (mtp180) cc_final: 0.8773 (mtp180) REVERT: C 200 ARG cc_start: 0.6004 (mtt-85) cc_final: 0.5801 (ptt-90) REVERT: C 282 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8135 (mp) REVERT: C 301 TYR cc_start: 0.7922 (t80) cc_final: 0.7544 (t80) REVERT: C 504 MET cc_start: -0.2299 (mtt) cc_final: -0.3039 (pmm) REVERT: D 63 ARG cc_start: 0.7852 (mtm110) cc_final: 0.6928 (ptp-110) REVERT: D 69 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7909 (mt-10) REVERT: D 95 GLU cc_start: 0.8160 (tp30) cc_final: 0.7911 (mm-30) REVERT: D 147 ASP cc_start: 0.8371 (t0) cc_final: 0.8013 (t0) REVERT: D 193 ARG cc_start: 0.6745 (mtm180) cc_final: 0.6287 (ttp-110) REVERT: D 323 MET cc_start: 0.7059 (mmm) cc_final: 0.6581 (mmm) outliers start: 28 outliers final: 4 residues processed: 150 average time/residue: 0.6621 time to fit residues: 109.1068 Evaluate side-chains 114 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 469 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: 5.9990 chunk 44 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 126 optimal weight: 30.0000 chunk 138 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN ** 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 = 0.4601 r_free = 0.4601 target = 0.208122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108261 restraints weight = 19360.289| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.25 r_work: 0.3144 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15222 Z= 0.186 Angle : 0.652 14.489 20611 Z= 0.345 Chirality : 0.046 0.186 2271 Planarity : 0.004 0.052 2550 Dihedral : 6.570 26.932 1999 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.03 % Favored : 92.91 % Rotamer: Outliers : 2.41 % Allowed : 15.42 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.19), residues: 1763 helix: -2.14 (0.15), residues: 976 sheet: -2.15 (0.47), residues: 96 loop : -1.18 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 187 TYR 0.028 0.002 TYR A 355 PHE 0.017 0.001 PHE B 454 TRP 0.015 0.001 TRP D 255 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00429 (15221) covalent geometry : angle 0.65215 (20611) hydrogen bonds : bond 0.04574 ( 583) hydrogen bonds : angle 5.36190 ( 1575) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7067 (tmt170) cc_final: 0.6663 (ttt90) REVERT: A 155 ASP cc_start: 0.8305 (t70) cc_final: 0.7834 (t0) REVERT: A 189 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7897 (mm-30) REVERT: A 323 MET cc_start: 0.6979 (mmt) cc_final: 0.6544 (ptt) REVERT: B 56 TYR cc_start: 0.5960 (m-10) cc_final: 0.5521 (p90) REVERT: B 63 ARG cc_start: 0.8124 (mtm180) cc_final: 0.7156 (ptt-90) REVERT: B 70 MET cc_start: 0.7698 (mtp) cc_final: 0.7036 (mmt) REVERT: B 155 ASP cc_start: 0.8526 (t70) cc_final: 0.8207 (t0) REVERT: B 189 GLU cc_start: 0.8101 (pp20) cc_final: 0.7840 (pp20) REVERT: B 197 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7367 (tp) REVERT: B 477 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6933 (tp) REVERT: C 61 LYS cc_start: 0.8672 (mppt) cc_final: 0.8455 (pttp) REVERT: C 70 MET cc_start: 0.8656 (mmp) cc_final: 0.8397 (mpp) REVERT: C 127 ARG cc_start: 0.7498 (ttt180) cc_final: 0.6824 (ttp80) REVERT: C 200 ARG cc_start: 0.6062 (mtt-85) cc_final: 0.5779 (ptt-90) REVERT: C 282 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8209 (mp) REVERT: C 301 TYR cc_start: 0.7932 (t80) cc_final: 0.7533 (t80) REVERT: C 330 MET cc_start: 0.5037 (ptt) cc_final: 0.4613 (ppp) REVERT: C 504 MET cc_start: -0.2329 (mtt) cc_final: -0.2965 (pmm) REVERT: D 63 ARG cc_start: 0.7863 (mtm110) cc_final: 0.7078 (ptp-110) REVERT: D 95 GLU cc_start: 0.8144 (tp30) cc_final: 0.7886 (mm-30) REVERT: D 147 ASP cc_start: 0.8393 (t0) cc_final: 0.8033 (t0) REVERT: D 193 ARG cc_start: 0.6682 (mtm180) cc_final: 0.6257 (ttp-110) REVERT: D 323 MET cc_start: 0.6917 (mmm) cc_final: 0.6508 (mmm) outliers start: 39 outliers final: 12 residues processed: 145 average time/residue: 0.6405 time to fit residues: 102.3212 Evaluate side-chains 123 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 167 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 396 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.208184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.108775 restraints weight = 19287.389| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.49 r_work: 0.3140 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15222 Z= 0.188 Angle : 0.626 17.123 20611 Z= 0.328 Chirality : 0.045 0.160 2271 Planarity : 0.004 0.047 2550 Dihedral : 6.222 27.202 1999 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.74 % Rotamer: Outliers : 3.03 % Allowed : 16.53 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.20), residues: 1763 helix: -1.73 (0.16), residues: 979 sheet: -1.95 (0.49), residues: 96 loop : -1.01 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 187 TYR 0.028 0.001 TYR A 355 PHE 0.017 0.001 PHE B 454 TRP 0.015 0.001 TRP B 68 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00436 (15221) covalent geometry : angle 0.62582 (20611) hydrogen bonds : bond 0.04300 ( 583) hydrogen bonds : angle 5.03081 ( 1575) Misc. bond : bond 0.00045 ( 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 171 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7137 (tmt170) cc_final: 0.6734 (ttt90) REVERT: A 155 ASP cc_start: 0.8346 (t70) cc_final: 0.7846 (t0) REVERT: A 189 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7880 (mm-30) REVERT: A 200 ARG cc_start: 0.7410 (tpm170) cc_final: 0.7059 (tpt90) REVERT: A 323 MET cc_start: 0.6913 (mmt) cc_final: 0.6459 (ptt) REVERT: A 434 LEU cc_start: 0.4122 (OUTLIER) cc_final: 0.3720 (tp) REVERT: B 56 TYR cc_start: 0.5926 (m-10) cc_final: 0.5537 (p90) REVERT: B 63 ARG cc_start: 0.7978 (mtm180) cc_final: 0.6981 (ptt-90) REVERT: B 70 MET cc_start: 0.7710 (mtp) cc_final: 0.7392 (mmt) REVERT: B 197 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7420 (tp) REVERT: B 477 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6961 (tp) REVERT: C 69 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8339 (mm-30) REVERT: C 70 MET cc_start: 0.8654 (mmp) cc_final: 0.8398 (mpp) REVERT: C 127 ARG cc_start: 0.7501 (ttt180) cc_final: 0.6847 (ttp80) REVERT: C 282 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8227 (mp) REVERT: C 301 TYR cc_start: 0.7868 (t80) cc_final: 0.7346 (t80) REVERT: C 504 MET cc_start: -0.2248 (mtt) cc_final: -0.2968 (pmm) REVERT: D 63 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7039 (ttm-80) REVERT: D 95 GLU cc_start: 0.8119 (tp30) cc_final: 0.7866 (mm-30) REVERT: D 147 ASP cc_start: 0.8393 (t0) cc_final: 0.8009 (t0) REVERT: D 193 ARG cc_start: 0.6617 (mtm180) cc_final: 0.6195 (ttp-110) REVERT: D 329 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.5809 (t80) outliers start: 49 outliers final: 17 residues processed: 156 average time/residue: 0.6164 time to fit residues: 105.9087 Evaluate side-chains 136 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 280 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 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 378 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 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: 0.9990 chunk 155 optimal weight: 0.7980 chunk 122 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 174 optimal weight: 0.1980 chunk 30 optimal weight: 30.0000 chunk 66 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS D 465 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.209287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.111117 restraints weight = 19202.730| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.32 r_work: 0.3173 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2720 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= 0.145 Angle : 0.607 17.075 20611 Z= 0.316 Chirality : 0.044 0.203 2271 Planarity : 0.004 0.045 2550 Dihedral : 5.930 26.876 1999 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.86 % Favored : 93.08 % Rotamer: Outliers : 2.66 % Allowed : 18.45 % Favored : 78.89 % 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 aren not related in a simple way. whole: -2.05 (0.20), residues: 1763 helix: -1.47 (0.16), residues: 988 sheet: -1.45 (0.52), residues: 86 loop : -0.87 (0.26), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 121 TYR 0.028 0.001 TYR A 355 PHE 0.017 0.001 PHE B 454 TRP 0.012 0.001 TRP C 255 HIS 0.004 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00331 (15221) covalent geometry : angle 0.60706 (20611) hydrogen bonds : bond 0.04041 ( 583) hydrogen bonds : angle 4.80299 ( 1575) Misc. bond : bond 0.00042 ( 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 164 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7139 (tmt170) cc_final: 0.6753 (ttt90) REVERT: A 137 PHE cc_start: 0.8206 (m-80) cc_final: 0.7980 (m-10) REVERT: A 155 ASP cc_start: 0.8333 (t70) cc_final: 0.7857 (t0) REVERT: A 189 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7899 (mm-30) REVERT: A 200 ARG cc_start: 0.7327 (tpm170) cc_final: 0.6974 (tpt90) REVERT: A 323 MET cc_start: 0.6901 (mmt) cc_final: 0.6498 (ptt) REVERT: A 434 LEU cc_start: 0.4649 (OUTLIER) cc_final: 0.4250 (tp) REVERT: B 56 TYR cc_start: 0.5853 (m-10) cc_final: 0.5504 (p90) REVERT: B 63 ARG cc_start: 0.7914 (mtm180) cc_final: 0.6923 (ptt-90) REVERT: B 70 MET cc_start: 0.7589 (mtp) cc_final: 0.6991 (mmp) REVERT: B 155 ASP cc_start: 0.8525 (t70) cc_final: 0.8220 (t0) REVERT: B 189 GLU cc_start: 0.8220 (pp20) cc_final: 0.7922 (pp20) REVERT: B 477 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7013 (tp) REVERT: C 127 ARG cc_start: 0.7500 (ttt180) cc_final: 0.6841 (ttp80) REVERT: C 189 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7478 (mm-30) REVERT: C 282 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8166 (mp) REVERT: C 301 TYR cc_start: 0.8003 (t80) cc_final: 0.7388 (t80) REVERT: C 330 MET cc_start: 0.5291 (OUTLIER) cc_final: 0.4887 (ppp) REVERT: C 504 MET cc_start: -0.2370 (mtt) cc_final: -0.3009 (pmm) REVERT: D 63 ARG cc_start: 0.7830 (mtm110) cc_final: 0.6992 (ttm-80) REVERT: D 95 GLU cc_start: 0.8073 (tp30) cc_final: 0.7821 (mm-30) REVERT: D 147 ASP cc_start: 0.8432 (t0) cc_final: 0.8063 (t0) REVERT: D 193 ARG cc_start: 0.6606 (mtm180) cc_final: 0.6174 (ttp-110) REVERT: D 323 MET cc_start: 0.6294 (mmm) cc_final: 0.5985 (mpt) REVERT: D 329 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.5765 (t80) outliers start: 43 outliers final: 16 residues processed: 155 average time/residue: 0.5878 time to fit residues: 101.2737 Evaluate side-chains 136 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 280 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 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: 8.9990 chunk 155 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 133 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 chunk 62 optimal weight: 0.1980 chunk 137 optimal weight: 1.9990 chunk 81 optimal weight: 30.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.210605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.111789 restraints weight = 19115.215| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.21 r_work: 0.3158 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3000 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= 0.121 Angle : 0.590 17.274 20611 Z= 0.306 Chirality : 0.043 0.170 2271 Planarity : 0.004 0.045 2550 Dihedral : 5.700 27.160 1999 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.48 % Rotamer: Outliers : 2.41 % Allowed : 18.89 % Favored : 78.70 % 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 aren not related in a simple way. whole: -1.73 (0.20), residues: 1763 helix: -1.20 (0.16), residues: 982 sheet: -1.56 (0.51), residues: 91 loop : -0.72 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 332 TYR 0.028 0.001 TYR A 355 PHE 0.016 0.001 PHE B 454 TRP 0.012 0.001 TRP B 68 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00270 (15221) covalent geometry : angle 0.58962 (20611) hydrogen bonds : bond 0.03828 ( 583) hydrogen bonds : angle 4.64416 ( 1575) Misc. bond : bond 0.00048 ( 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 163 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7099 (tmt170) cc_final: 0.6735 (ttt90) REVERT: A 137 PHE cc_start: 0.8132 (m-80) cc_final: 0.7921 (m-10) REVERT: A 189 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7875 (mm-30) REVERT: A 200 ARG cc_start: 0.7248 (tpm170) cc_final: 0.6905 (tpt90) REVERT: A 323 MET cc_start: 0.6900 (mmt) cc_final: 0.6514 (ptt) REVERT: A 434 LEU cc_start: 0.4619 (OUTLIER) cc_final: 0.4323 (tp) REVERT: B 56 TYR cc_start: 0.5729 (m-10) cc_final: 0.5455 (p90) REVERT: B 63 ARG cc_start: 0.7854 (mtm180) cc_final: 0.6865 (ptt-90) REVERT: B 70 MET cc_start: 0.7467 (mtp) cc_final: 0.6892 (mmp) REVERT: B 155 ASP cc_start: 0.8487 (t70) cc_final: 0.8189 (t0) REVERT: B 189 GLU cc_start: 0.8302 (pp20) cc_final: 0.7802 (pp20) REVERT: B 190 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7904 (mmtm) REVERT: B 301 TYR cc_start: 0.7726 (t80) cc_final: 0.7080 (m-80) REVERT: B 477 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7046 (tp) REVERT: C 127 ARG cc_start: 0.7457 (ttt180) cc_final: 0.6816 (ttp80) REVERT: C 301 TYR cc_start: 0.7921 (t80) cc_final: 0.7367 (t80) REVERT: C 504 MET cc_start: -0.2342 (mtt) cc_final: -0.2952 (pmm) REVERT: D 63 ARG cc_start: 0.7762 (mtm110) cc_final: 0.6940 (ttm-80) REVERT: D 69 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7945 (mt-10) REVERT: D 95 GLU cc_start: 0.8079 (tp30) cc_final: 0.7827 (mm-30) REVERT: D 147 ASP cc_start: 0.8411 (t0) cc_final: 0.8006 (t0) REVERT: D 193 ARG cc_start: 0.6560 (mtm180) cc_final: 0.6133 (ttp-110) REVERT: D 319 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.6242 (t80) REVERT: D 323 MET cc_start: 0.6524 (mmm) cc_final: 0.6097 (mmt) REVERT: D 329 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.5795 (t80) outliers start: 39 outliers final: 14 residues processed: 157 average time/residue: 0.6320 time to fit residues: 109.6754 Evaluate side-chains 136 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 319 PHE 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: 6.9990 chunk 95 optimal weight: 6.9990 chunk 133 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 38 optimal weight: 30.0000 chunk 131 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.208420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.108273 restraints weight = 19147.950| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.22 r_work: 0.3096 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2948 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= 0.209 Angle : 0.632 17.019 20611 Z= 0.327 Chirality : 0.046 0.174 2271 Planarity : 0.004 0.042 2550 Dihedral : 5.744 26.972 1999 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.09 % Favored : 92.85 % Rotamer: Outliers : 2.23 % Allowed : 19.20 % 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 aren not related in a simple way. whole: -1.69 (0.20), residues: 1763 helix: -1.19 (0.16), residues: 981 sheet: -1.44 (0.51), residues: 96 loop : -0.65 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 168 TYR 0.027 0.002 TYR A 355 PHE 0.017 0.001 PHE B 454 TRP 0.019 0.002 TRP B 68 HIS 0.004 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00493 (15221) covalent geometry : angle 0.63238 (20611) hydrogen bonds : bond 0.04218 ( 583) hydrogen bonds : angle 4.70012 ( 1575) Misc. bond : bond 0.00049 ( 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 153 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7118 (tmt170) cc_final: 0.6760 (ttt90) REVERT: A 137 PHE cc_start: 0.8177 (m-80) cc_final: 0.7967 (m-10) REVERT: A 155 ASP cc_start: 0.8294 (t70) cc_final: 0.7800 (t0) REVERT: A 189 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7851 (mm-30) REVERT: A 323 MET cc_start: 0.6877 (mmt) cc_final: 0.6471 (ptt) REVERT: A 434 LEU cc_start: 0.4615 (OUTLIER) cc_final: 0.4353 (tp) REVERT: B 56 TYR cc_start: 0.5823 (m-10) cc_final: 0.5560 (p90) REVERT: B 63 ARG cc_start: 0.7841 (mtm180) cc_final: 0.6848 (ptt-90) REVERT: B 70 MET cc_start: 0.7739 (mtp) cc_final: 0.7133 (mmp) REVERT: B 189 GLU cc_start: 0.8225 (pp20) cc_final: 0.7957 (pp20) REVERT: B 301 TYR cc_start: 0.7743 (t80) cc_final: 0.7084 (m-80) REVERT: B 477 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6987 (tp) REVERT: C 127 ARG cc_start: 0.7480 (ttt180) cc_final: 0.6832 (ttp80) REVERT: C 200 ARG cc_start: 0.5751 (tpt170) cc_final: 0.5342 (tpt170) REVERT: C 301 TYR cc_start: 0.8077 (t80) cc_final: 0.7667 (t80) REVERT: C 504 MET cc_start: -0.2224 (mtt) cc_final: -0.2831 (pmm) REVERT: D 63 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7034 (ttm-80) REVERT: D 69 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7916 (mt-10) REVERT: D 95 GLU cc_start: 0.8060 (tp30) cc_final: 0.7815 (mm-30) REVERT: D 147 ASP cc_start: 0.8400 (t0) cc_final: 0.8013 (t0) REVERT: D 193 ARG cc_start: 0.6598 (mtm180) cc_final: 0.6173 (ttp-110) REVERT: D 319 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.6119 (t80) REVERT: D 323 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6063 (mpm) REVERT: D 329 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.5787 (t80) outliers start: 36 outliers final: 17 residues processed: 143 average time/residue: 0.6051 time to fit residues: 95.7165 Evaluate side-chains 136 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 120 TYR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 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: 9.9990 chunk 171 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 chunk 75 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4599 r_free = 0.4599 target = 0.207991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.107667 restraints weight = 19229.391| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.23 r_work: 0.3091 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15222 Z= 0.218 Angle : 0.634 16.873 20611 Z= 0.328 Chirality : 0.046 0.173 2271 Planarity : 0.004 0.045 2550 Dihedral : 5.772 26.455 1999 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.98 % Favored : 92.97 % Rotamer: Outliers : 2.72 % Allowed : 19.32 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.20), residues: 1763 helix: -1.15 (0.16), residues: 976 sheet: -1.38 (0.51), residues: 96 loop : -0.65 (0.26), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 257 TYR 0.027 0.002 TYR A 355 PHE 0.017 0.001 PHE B 454 TRP 0.022 0.002 TRP B 68 HIS 0.007 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00514 (15221) covalent geometry : angle 0.63402 (20611) hydrogen bonds : bond 0.04213 ( 583) hydrogen bonds : angle 4.68733 ( 1575) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7151 (tmt170) cc_final: 0.6770 (ttt90) REVERT: A 137 PHE cc_start: 0.8177 (m-80) cc_final: 0.7973 (m-10) REVERT: A 155 ASP cc_start: 0.8331 (t70) cc_final: 0.7818 (t0) REVERT: A 189 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7888 (mm-30) REVERT: A 434 LEU cc_start: 0.4615 (OUTLIER) cc_final: 0.4356 (tp) REVERT: B 63 ARG cc_start: 0.7891 (mtm180) cc_final: 0.6940 (ptt-90) REVERT: B 65 TYR cc_start: 0.7541 (t80) cc_final: 0.7268 (t80) REVERT: B 70 MET cc_start: 0.7842 (mtp) cc_final: 0.7222 (mmp) REVERT: B 189 GLU cc_start: 0.8265 (pp20) cc_final: 0.7905 (pp20) REVERT: B 190 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8124 (mptp) REVERT: B 301 TYR cc_start: 0.7763 (t80) cc_final: 0.7116 (m-80) REVERT: B 477 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6788 (tp) REVERT: C 127 ARG cc_start: 0.7531 (ttt180) cc_final: 0.6852 (ttp80) REVERT: C 134 ARG cc_start: 0.9006 (mtp180) cc_final: 0.8789 (mtp180) REVERT: C 301 TYR cc_start: 0.8100 (t80) cc_final: 0.7728 (t80) REVERT: C 504 MET cc_start: -0.2099 (mtt) cc_final: -0.2782 (pmm) REVERT: D 63 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7034 (ttm-80) REVERT: D 69 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7954 (mt-10) REVERT: D 95 GLU cc_start: 0.8073 (tp30) cc_final: 0.7834 (mm-30) REVERT: D 147 ASP cc_start: 0.8421 (t0) cc_final: 0.8042 (t0) REVERT: D 193 ARG cc_start: 0.6640 (mtm180) cc_final: 0.6185 (ttp-110) REVERT: D 319 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.5964 (t80) REVERT: D 323 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.5930 (mpm) REVERT: D 329 PHE cc_start: 0.6369 (OUTLIER) cc_final: 0.5703 (t80) REVERT: D 360 MET cc_start: 0.6543 (mpt) cc_final: 0.6054 (ptm) outliers start: 44 outliers final: 25 residues processed: 149 average time/residue: 0.5773 time to fit residues: 95.7988 Evaluate side-chains 141 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ASN 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 B residue 73 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 190 LYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 97 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 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: 8.9990 chunk 72 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 161 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN ** 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 = 0.4608 r_free = 0.4608 target = 0.208976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.108950 restraints weight = 19239.749| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.25 r_work: 0.3154 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15222 Z= 0.174 Angle : 0.616 16.781 20611 Z= 0.317 Chirality : 0.045 0.169 2271 Planarity : 0.004 0.041 2550 Dihedral : 5.656 26.350 1999 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.81 % Favored : 93.14 % Rotamer: Outliers : 2.41 % Allowed : 19.75 % Favored : 77.83 % 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 aren not related in a simple way. whole: -1.51 (0.21), residues: 1763 helix: -1.05 (0.16), residues: 983 sheet: -1.37 (0.52), residues: 96 loop : -0.58 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.027 0.001 TYR A 355 PHE 0.020 0.001 PHE A 485 TRP 0.018 0.001 TRP B 68 HIS 0.008 0.001 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00409 (15221) covalent geometry : angle 0.61612 (20611) hydrogen bonds : bond 0.04046 ( 583) hydrogen bonds : angle 4.62736 ( 1575) Misc. bond : bond 0.00051 ( 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 150 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8081 (m-10) cc_final: 0.7578 (m-90) REVERT: A 96 ARG cc_start: 0.7176 (tmt170) cc_final: 0.6807 (ttt90) REVERT: A 137 PHE cc_start: 0.8135 (m-80) cc_final: 0.7909 (m-10) REVERT: A 155 ASP cc_start: 0.8378 (t70) cc_final: 0.7886 (t0) REVERT: A 189 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7921 (mm-30) REVERT: A 434 LEU cc_start: 0.4634 (OUTLIER) cc_final: 0.4392 (tp) REVERT: B 63 ARG cc_start: 0.7846 (mtm180) cc_final: 0.6893 (ptt-90) REVERT: B 70 MET cc_start: 0.7801 (mtp) cc_final: 0.7156 (mmp) REVERT: B 189 GLU cc_start: 0.8261 (pp20) cc_final: 0.8007 (pp20) REVERT: B 301 TYR cc_start: 0.7761 (t80) cc_final: 0.7112 (m-80) REVERT: B 477 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6637 (tp) REVERT: C 127 ARG cc_start: 0.7505 (ttt180) cc_final: 0.6831 (ttp80) REVERT: C 134 ARG cc_start: 0.9020 (mtp180) cc_final: 0.8804 (mtp180) REVERT: C 281 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7590 (t0) REVERT: C 282 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8163 (mp) REVERT: C 301 TYR cc_start: 0.8082 (t80) cc_final: 0.7660 (t80) REVERT: C 504 MET cc_start: -0.2048 (mtt) cc_final: -0.2728 (pmm) REVERT: D 63 ARG cc_start: 0.7785 (mtm110) cc_final: 0.6983 (ttm-80) REVERT: D 95 GLU cc_start: 0.8078 (tp30) cc_final: 0.7839 (mm-30) REVERT: D 147 ASP cc_start: 0.8405 (t0) cc_final: 0.8025 (t0) REVERT: D 193 ARG cc_start: 0.6618 (mtm180) cc_final: 0.6170 (ttp-110) REVERT: D 319 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.5877 (t80) REVERT: D 323 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.5997 (mpm) REVERT: D 329 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.5665 (t80) REVERT: D 360 MET cc_start: 0.6654 (mpt) cc_final: 0.6163 (ptm) outliers start: 39 outliers final: 21 residues processed: 143 average time/residue: 0.5918 time to fit residues: 94.0059 Evaluate side-chains 137 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ASN 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 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 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 281 ASN Chi-restraints excluded: chain C residue 282 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 109 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.210342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.111502 restraints weight = 19249.547| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.23 r_work: 0.3147 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3352 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= 0.123 Angle : 0.599 16.785 20611 Z= 0.306 Chirality : 0.044 0.164 2271 Planarity : 0.003 0.046 2550 Dihedral : 5.508 27.326 1999 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.13 % Favored : 93.82 % Rotamer: Outliers : 1.80 % Allowed : 20.62 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.21), residues: 1763 helix: -0.87 (0.17), residues: 985 sheet: -1.28 (0.52), residues: 96 loop : -0.52 (0.26), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.028 0.001 TYR B 196 PHE 0.015 0.001 PHE B 454 TRP 0.016 0.001 TRP B 68 HIS 0.007 0.001 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00279 (15221) covalent geometry : angle 0.59920 (20611) hydrogen bonds : bond 0.03761 ( 583) hydrogen bonds : angle 4.53124 ( 1575) Misc. bond : bond 0.00052 ( 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 144 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8085 (m-10) cc_final: 0.7651 (m-90) REVERT: A 96 ARG cc_start: 0.7122 (tmt170) cc_final: 0.6790 (ttt90) REVERT: A 137 PHE cc_start: 0.8098 (m-80) cc_final: 0.7878 (m-10) REVERT: A 155 ASP cc_start: 0.8234 (t70) cc_final: 0.7767 (t0) REVERT: A 189 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7919 (mm-30) REVERT: A 434 LEU cc_start: 0.4767 (OUTLIER) cc_final: 0.4497 (tp) REVERT: B 63 ARG cc_start: 0.7780 (mtm180) cc_final: 0.6858 (ptt-90) REVERT: B 70 MET cc_start: 0.7669 (mtp) cc_final: 0.7085 (mmp) REVERT: B 155 ASP cc_start: 0.8519 (t70) cc_final: 0.8247 (t0) REVERT: B 189 GLU cc_start: 0.8236 (pp20) cc_final: 0.7979 (pp20) REVERT: B 301 TYR cc_start: 0.7711 (t80) cc_final: 0.7103 (m-80) REVERT: B 477 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6617 (tp) REVERT: C 127 ARG cc_start: 0.7512 (ttt180) cc_final: 0.6830 (ttp80) REVERT: C 282 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8214 (mp) REVERT: C 301 TYR cc_start: 0.8016 (t80) cc_final: 0.7509 (t80) REVERT: C 504 MET cc_start: -0.1941 (mtt) cc_final: -0.2625 (pmm) REVERT: D 63 ARG cc_start: 0.7748 (mtm110) cc_final: 0.7113 (ttm-80) REVERT: D 95 GLU cc_start: 0.8061 (tp30) cc_final: 0.7782 (tm-30) REVERT: D 147 ASP cc_start: 0.8371 (t0) cc_final: 0.7966 (t0) REVERT: D 193 ARG cc_start: 0.6627 (mtm180) cc_final: 0.6182 (ttp-110) REVERT: D 319 PHE cc_start: 0.6495 (OUTLIER) cc_final: 0.5877 (t80) REVERT: D 323 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6006 (mpm) REVERT: D 329 PHE cc_start: 0.6371 (OUTLIER) cc_final: 0.5634 (t80) REVERT: D 360 MET cc_start: 0.6674 (mpt) cc_final: 0.6227 (ptm) outliers start: 29 outliers final: 17 residues processed: 140 average time/residue: 0.6391 time to fit residues: 98.7244 Evaluate side-chains 135 residues out of total 1615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 330 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 109 optimal weight: 0.0670 chunk 132 optimal weight: 0.0010 chunk 113 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.211177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.113235 restraints weight = 19050.734| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.21 r_work: 0.3219 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15222 Z= 0.111 Angle : 0.588 16.610 20611 Z= 0.300 Chirality : 0.043 0.172 2271 Planarity : 0.003 0.042 2550 Dihedral : 5.319 26.454 1999 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 1.73 % Allowed : 20.87 % 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 aren not related in a simple way. whole: -1.12 (0.21), residues: 1763 helix: -0.69 (0.17), residues: 984 sheet: -1.20 (0.52), residues: 96 loop : -0.48 (0.26), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.029 0.001 TYR B 196 PHE 0.020 0.001 PHE D 329 TRP 0.012 0.001 TRP C 64 HIS 0.006 0.001 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00248 (15221) covalent geometry : angle 0.58752 (20611) hydrogen bonds : bond 0.03658 ( 583) hydrogen bonds : angle 4.43929 ( 1575) Misc. bond : bond 0.00054 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9848.14 seconds wall clock time: 167 minutes 40.63 seconds (10060.63 seconds total)