Starting phenix.real_space_refine on Thu Aug 6 08:42:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxn_18733/08_2026/8qxn_18733_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxn_18733/08_2026/8qxn_18733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qxn_18733/08_2026/8qxn_18733_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxn_18733/08_2026/8qxn_18733_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qxn_18733/08_2026/8qxn_18733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxn_18733/08_2026/8qxn_18733.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.188 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 30 5.49 5 Mg 8 5.21 5 S 76 5.16 5 C 9185 2.51 5 N 2491 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14461 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3441 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 404} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3719 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3713 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 458, 3713 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 3794 Chain: "C" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3367 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 17, 'TRANS': 404} Chain breaks: 3 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3618 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 94 Unusual residues: {' FE': 1, ' MG': 1, 'DTP': 2, 'GTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 93 Unusual residues: {' FE': 1, ' MG': 2, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' FE': 1, ' MG': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 95 Unusual residues: {' FE': 1, ' MG': 4, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 3.86, per 1000 atoms: 0.27 Number of scatterers: 14461 At special positions: 0 Unit cell: (118.81, 94.83, 106.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 76 16.00 P 30 15.00 Mg 8 11.99 O 2667 8.00 N 2491 7.00 C 9185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 341 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS D 341 " - pdb=" SG CYS D 350 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 681.4 milliseconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3302 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 16 sheets defined 61.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.615A pdb=" N TYR A 154 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 155 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 186 removed outlier: 4.057A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 215 through 226 removed outlier: 5.582A pdb=" N ILE A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 232 through 248 removed outlier: 3.719A pdb=" N GLY A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 257 removed outlier: 3.559A pdb=" N TYR A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.690A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 5.069A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 330 through 337 removed outlier: 3.855A pdb=" N PHE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 373 Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.944A pdb=" N ILE A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.995A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 451 Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.826A pdb=" N TYR A 473 " --> pdb=" O ARG A 470 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLU A 474 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.605A pdb=" N ALA A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.514A pdb=" N ALA A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 164 through 186 Processing helix chain 'B' and resid 187 through 190 removed outlier: 3.848A pdb=" N GLN B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 214 through 226 removed outlier: 4.297A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE B 222 " --> pdb=" O ASP B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 232 through 249 removed outlier: 3.645A pdb=" N GLY B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 273 removed outlier: 4.558A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 272 " --> pdb=" O ILE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.953A pdb=" N SER B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 5.555A pdb=" N PHE B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 317 " --> pdb=" O TRP B 313 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 removed outlier: 4.088A pdb=" N PHE B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 4.420A pdb=" N ASN B 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 376 through 394 Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 410 through 414 removed outlier: 4.281A pdb=" N ILE B 413 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 424 through 432 removed outlier: 4.204A pdb=" N LEU B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 474 through 483 removed outlier: 4.553A pdb=" N LYS B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.833A pdb=" N VAL B 518 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.728A pdb=" N TYR C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 155 " --> pdb=" O GLY C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 186 removed outlier: 4.100A pdb=" N HIS C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.645A pdb=" N GLN C 190 " --> pdb=" O PRO C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.434A pdb=" N ASP C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 232 through 249 removed outlier: 3.598A pdb=" N GLY C 236 " --> pdb=" O THR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 257 Processing helix chain 'C' and resid 260 through 273 removed outlier: 4.097A pdb=" N CYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.647A pdb=" N SER C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE C 296 " --> pdb=" O ASN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 removed outlier: 3.600A pdb=" N TRP C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 337 removed outlier: 3.753A pdb=" N PHE C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 346 removed outlier: 3.545A pdb=" N ASN C 345 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 373 Processing helix chain 'C' and resid 376 through 394 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 411 through 414 removed outlier: 3.727A pdb=" N ASP C 414 " --> pdb=" O THR C 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 414' Processing helix chain 'C' and resid 415 through 421 removed outlier: 4.148A pdb=" N LYS C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 432 removed outlier: 4.264A pdb=" N LEU C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 438 through 450 Processing helix chain 'C' and resid 469 through 473 removed outlier: 3.927A pdb=" N TYR C 473 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 removed outlier: 4.398A pdb=" N LYS C 478 " --> pdb=" O GLU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 576 removed outlier: 3.708A pdb=" N TYR C 568 " --> pdb=" O ALA C 564 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.818A pdb=" N TYR D 154 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 186 removed outlier: 3.935A pdb=" N HIS D 167 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 214 through 221 removed outlier: 4.446A pdb=" N ASP D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 232 through 248 removed outlier: 3.604A pdb=" N GLY D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 260 through 273 removed outlier: 4.312A pdb=" N CYS D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 3.590A pdb=" N SER D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 298 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE D 300 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 324 removed outlier: 4.354A pdb=" N ALA D 317 " --> pdb=" O TRP D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 removed outlier: 4.277A pdb=" N PHE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 Processing helix chain 'D' and resid 355 through 373 Processing helix chain 'D' and resid 376 through 393 Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 410 through 414 removed outlier: 4.063A pdb=" N ILE D 413 " --> pdb=" O SER D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 421 removed outlier: 3.846A pdb=" N LYS D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 432 removed outlier: 4.340A pdb=" N LEU D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 438 through 451 removed outlier: 4.136A pdb=" N ILE D 444 " --> pdb=" O ASP D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 474 removed outlier: 4.415A pdb=" N GLU D 474 " --> pdb=" O GLU D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 558 through 577 removed outlier: 3.512A pdb=" N ARG D 576 " --> pdb=" O TRP D 572 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.524A pdb=" N LYS A 116 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 343 removed outlier: 3.524A pdb=" N CYS A 341 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 348 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 119 Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 340 removed outlier: 8.855A pdb=" N TYR B 521 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA B 351 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 460 removed outlier: 7.107A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 118 Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 341 removed outlier: 4.461A pdb=" N ARG C 339 " --> pdb=" O CYS C 350 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS C 350 " --> pdb=" O ARG C 339 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 399 through 400 Processing sheet with id=AB3, first strand: chain 'C' and resid 455 through 460 removed outlier: 3.562A pdb=" N CYS C 554 " --> pdb=" O LYS C 455 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 457 " --> pdb=" O VAL C 552 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL C 552 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU C 459 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE C 550 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 119 removed outlier: 3.524A pdb=" N LYS D 116 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 338 through 341 removed outlier: 8.305A pdb=" N TYR D 521 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 351 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 399 through 400 Processing sheet with id=AB7, first strand: chain 'D' and resid 455 through 459 removed outlier: 7.177A pdb=" N VAL D 552 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU D 459 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE D 550 " --> pdb=" O GLU D 459 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 499 " --> pdb=" O TYR D 553 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1854 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: 2.48 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4664 1.35 - 1.46: 3506 1.46 - 1.58: 6476 1.58 - 1.70: 46 1.70 - 1.82: 114 Bond restraints: 14806 Sorted by residual: bond pdb=" O3B DCP B 705 " pdb=" PG DCP B 705 " ideal model delta sigma weight residual 1.746 1.609 0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" O3B DCP D 708 " pdb=" PG DCP D 708 " ideal model delta sigma weight residual 1.746 1.614 0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" O3A DCP B 705 " pdb=" PB DCP B 705 " ideal model delta sigma weight residual 1.672 1.609 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C4 DCP B 705 " pdb=" N3 DCP B 705 " ideal model delta sigma weight residual 1.317 1.380 -0.063 2.00e-02 2.50e+03 9.84e+00 bond pdb=" O3A DCP D 708 " pdb=" PB DCP D 708 " ideal model delta sigma weight residual 1.672 1.611 0.061 2.00e-02 2.50e+03 9.37e+00 ... (remaining 14801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 19872 2.44 - 4.88: 176 4.88 - 7.33: 31 7.33 - 9.77: 7 9.77 - 12.21: 4 Bond angle restraints: 20090 Sorted by residual: angle pdb=" CG1 VAL A 457 " pdb=" CB VAL A 457 " pdb=" CG2 VAL A 457 " ideal model delta sigma weight residual 110.80 121.08 -10.28 2.20e+00 2.07e-01 2.18e+01 angle pdb=" CA VAL A 457 " pdb=" CB VAL A 457 " pdb=" CG2 VAL A 457 " ideal model delta sigma weight residual 110.40 117.48 -7.08 1.70e+00 3.46e-01 1.73e+01 angle pdb=" PA DCP B 705 " pdb=" O3A DCP B 705 " pdb=" PB DCP B 705 " ideal model delta sigma weight residual 132.21 120.00 12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C ASP B 314 " pdb=" N TYR B 315 " pdb=" CA TYR B 315 " ideal model delta sigma weight residual 120.72 114.45 6.27 1.67e+00 3.59e-01 1.41e+01 angle pdb=" CA VAL A 457 " pdb=" CB VAL A 457 " pdb=" CG1 VAL A 457 " ideal model delta sigma weight residual 110.40 116.55 -6.15 1.70e+00 3.46e-01 1.31e+01 ... (remaining 20085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.20: 8577 33.20 - 66.39: 259 66.39 - 99.59: 62 99.59 - 132.79: 6 132.79 - 165.98: 1 Dihedral angle restraints: 8905 sinusoidal: 3763 harmonic: 5142 Sorted by residual: dihedral pdb=" O3A GTP D 704 " pdb=" O3B GTP D 704 " pdb=" PB GTP D 704 " pdb=" PG GTP D 704 " ideal model delta sinusoidal sigma weight residual 303.79 137.81 165.98 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O3A GTP C 701 " pdb=" O3B GTP C 701 " pdb=" PB GTP C 701 " pdb=" PG GTP C 701 " ideal model delta sinusoidal sigma weight residual -56.21 64.49 -120.70 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" C4' GTP A 701 " pdb=" C5' GTP A 701 " pdb=" O5' GTP A 701 " pdb=" PA GTP A 701 " ideal model delta sinusoidal sigma weight residual 260.87 151.93 108.95 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 8902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.280: 2140 0.280 - 0.561: 0 0.561 - 0.841: 0 0.841 - 1.122: 0 1.122 - 1.402: 1 Chirality restraints: 2141 Sorted by residual: chirality pdb=" CB VAL A 457 " pdb=" CA VAL A 457 " pdb=" CG1 VAL A 457 " pdb=" CG2 VAL A 457 " both_signs ideal model delta sigma weight residual False -2.63 -1.23 -1.40 2.00e-01 2.50e+01 4.91e+01 chirality pdb=" C3' DTP B 706 " pdb=" C2' DTP B 706 " pdb=" C4' DTP B 706 " pdb=" O3' DTP B 706 " both_signs ideal model delta sigma weight residual False -2.68 -2.93 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' DTP A 704 " pdb=" C2' DTP A 704 " pdb=" C4' DTP A 704 " pdb=" O3' DTP A 704 " both_signs ideal model delta sigma weight residual False -2.68 -2.93 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2138 not shown) Planarity restraints: 2542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DCP D 708 " -0.087 2.00e-02 2.50e+03 7.35e-02 1.22e+02 pdb=" C2 DCP D 708 " 0.019 2.00e-02 2.50e+03 pdb=" C4 DCP D 708 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DCP D 708 " 0.073 2.00e-02 2.50e+03 pdb=" C6 DCP D 708 " -0.054 2.00e-02 2.50e+03 pdb=" N1 DCP D 708 " 0.112 2.00e-02 2.50e+03 pdb=" N3 DCP D 708 " -0.124 2.00e-02 2.50e+03 pdb=" N4 DCP D 708 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DCP D 708 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCP B 705 " 0.001 2.00e-02 2.50e+03 5.29e-02 6.29e+01 pdb=" C2 DCP B 705 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DCP B 705 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DCP B 705 " -0.040 2.00e-02 2.50e+03 pdb=" C6 DCP B 705 " 0.108 2.00e-02 2.50e+03 pdb=" N1 DCP B 705 " -0.100 2.00e-02 2.50e+03 pdb=" N3 DCP B 705 " 0.031 2.00e-02 2.50e+03 pdb=" N4 DCP B 705 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DCP B 705 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 217 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C PHE A 217 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE A 217 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 218 " -0.012 2.00e-02 2.50e+03 ... (remaining 2539 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 94 2.47 - 3.08: 9984 3.08 - 3.69: 20489 3.69 - 4.29: 30207 4.29 - 4.90: 51687 Nonbonded interactions: 112461 Sorted by model distance: nonbonded pdb=" O1G DTP D 701 " pdb="MG MG D 702 " model vdw 1.867 2.170 nonbonded pdb=" O1B GTP C 701 " pdb="MG MG D 703 " model vdw 1.869 2.170 nonbonded pdb=" O1B DTP B 706 " pdb="MG MG D 703 " model vdw 1.869 2.170 nonbonded pdb=" O1G DTP B 706 " pdb="MG MG D 703 " model vdw 1.899 2.170 nonbonded pdb=" O1B DTP A 704 " pdb="MG MG B 704 " model vdw 1.905 2.170 ... (remaining 112456 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 114 through 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 through 261 or (resid 262 and (nam \ e N or name CA or name C or name O or name CB )) or resid 263 through 275 or (re \ sid 284 and (name N or name CA or name C or name O or name CB )) or resid 285 th \ rough 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 through 291 or (resid 292 and (name N or name CA or name C or name \ O or name CB )) or resid 293 through 303 or (resid 304 through 305 and (name N \ or name CA or name C or name O or name CB )) or resid 306 through 325 or (resid \ 326 and (name N or name CA or name C or name O or name CB )) or resid 327 throug \ h 341 or (resid 342 and (name N or name CA or name C or name O or name CB )) or \ resid 343 or (resid 344 through 345 and (name N or name CA or name C or name O o \ r name CB )) or resid 346 through 397 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 399 through 434 or (resid 435 and (name N \ or name CA or name C or name O or name CB )) or resid 436 or resid 438 through 4 \ 64 or (resid 465 and (name N or name CA or name C or name O or name CB )) or res \ id 466 or (resid 467 and (name N or name CA or name C or name O or name CB )) or \ resid 468 or (resid 469 and (name N or name CA or name C or name O or name CB ) \ ) or resid 470 or (resid 471 and (name N or name CA or name C or name O or name \ CB )) or resid 472 through 473 or (resid 474 and (name N or name CA or name C or \ name O or name CB )) or resid 475 through 477 or (resid 478 and (name N or name \ CA or name C or name O or name CB )) or resid 479 through 485 or (resid 486 thr \ ough 490 and (name N or name CA or name C or name O or name CB )) or resid 491 o \ r (resid 492 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 93 or (resid 494 through 496 and (name N or name CA or name C or name O or name \ CB )) or resid 497 through 558 or (resid 559 through 560 and (name N or name CA \ or name C or name O or name CB )) or resid 561 through 578 or resid 703)) selection = (chain 'B' and (resid 114 through 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 through 261 or (resid 262 and (nam \ e N or name CA or name C or name O or name CB )) or resid 263 through 275 or (re \ sid 276 and (name N or name CA or name C or name O or name CB )) or resid 285 th \ rough 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 through 291 or (resid 292 and (name N or name CA or name C or name \ O or name CB )) or resid 293 through 303 or (resid 304 through 305 and (name N \ or name CA or name C or name O or name CB )) or resid 306 through 325 or (resid \ 326 and (name N or name CA or name C or name O or name CB )) or resid 327 throug \ h 341 or (resid 342 and (name N or name CA or name C or name O or name CB )) or \ resid 343 or (resid 344 through 345 and (name N or name CA or name C or name O o \ r name CB )) or resid 346 through 370 or (resid 371 through 373 and (name N or n \ ame CA or name C or name O or name CB )) or resid 374 through 397 or (resid 398 \ and (name N or name CA or name C or name O or name CB )) or resid 399 through 43 \ 4 or (resid 435 and (name N or name CA or name C or name O or name CB )) or resi \ d 436 or resid 438 through 464 or (resid 465 and (name N or name CA or name C or \ name O or name CB )) or resid 466 or (resid 467 and (name N or name CA or name \ C or name O or name CB )) or resid 468 or (resid 469 and (name N or name CA or n \ ame C or name O or name CB )) or resid 470 or (resid 471 and (name N or name CA \ or name C or name O or name CB )) or resid 472 through 473 or (resid 474 and (na \ me N or name CA or name C or name O or name CB )) or resid 475 through 477 or (r \ esid 478 and (name N or name CA or name C or name O or name CB )) or resid 479 t \ hrough 485 or (resid 486 through 490 and (name N or name CA or name C or name O \ or name CB )) or resid 491 or (resid 492 and (name N or name CA or name C or nam \ e O or name CB )) or resid 493 through 505 or resid 518 through 521 or resid 545 \ through 575 or (resid 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 578 or resid 703)) selection = (chain 'C' and (resid 114 through 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 through 275 or (resid 284 and (name N \ or name CA or name C or name O or name CB )) or resid 285 through 303 or (resid \ 304 through 305 and (name N or name CA or name C or name O or name CB )) or resi \ d 306 through 371 or (resid 372 through 373 and (name N or name CA or name C or \ name O or name CB )) or resid 374 through 436 or resid 438 through 466 or (resid \ 467 and (name N or name CA or name C or name O or name CB )) or resid 468 or (r \ esid 469 and (name N or name CA or name C or name O or name CB )) or resid 470 o \ r (resid 471 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 72 through 473 or (resid 474 and (name N or name CA or name C or name O or name \ CB )) or resid 475 through 575 or (resid 576 and (name N or name CA or name C or \ name O or name CB )) or resid 577 through 578 or resid 703)) selection = (chain 'D' and (resid 114 through 276 or resid 285 through 325 or (resid 326 and \ (name N or name CA or name C or name O or name CB )) or resid 327 through 370 o \ r (resid 371 through 373 and (name N or name CA or name C or name O or name CB ) \ ) or resid 374 through 436 or resid 438 through 486 or (resid 487 through 490 an \ d (name N or name CA or name C or name O or name CB )) or resid 491 through 505 \ or resid 518 through 521 or resid 545 through 575 or (resid 576 and (name N or n \ ame CA or name C or name O or name CB )) or resid 577 through 578 or resid 703)) \ } 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=0.50 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.620 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 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 : 0.003 0.137 14809 Z= 0.156 Angle : 0.609 12.208 20096 Z= 0.302 Chirality : 0.053 1.402 2141 Planarity : 0.004 0.074 2542 Dihedral : 17.264 165.983 5594 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.07 % Allowed : 0.13 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1737 helix: 1.54 (0.19), residues: 864 sheet: 1.89 (0.56), residues: 94 loop : -0.69 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 528 TYR 0.023 0.001 TYR C 315 PHE 0.010 0.001 PHE B 569 TRP 0.012 0.001 TRP C 572 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (14806) covalent geometry : angle 0.60833 / 0.30 (20090) SS BOND : bond 0.00105 / 0.04 ( 3) SS BOND : angle 1.35585 / 0.70 ( 6) hydrogen bonds : bond 0.19400 / 12.71 ( 686) hydrogen bonds : angle 5.64810 / 4.15 ( 1854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.6968 (tt) cc_final: 0.6689 (tp) REVERT: B 416 MET cc_start: 0.7630 (mmt) cc_final: 0.7212 (mmm) REVERT: D 385 MET cc_start: 0.8576 (mtp) cc_final: 0.8312 (mtm) outliers start: 0 outliers final: 2 residues processed: 403 average time/residue: 0.5426 time to fit residues: 240.0934 Evaluate side-chains 199 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS A 210 HIS A 326 GLN A 358 ASN A 447 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 327 ASN B 370 HIS ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN D 163 ASN D 327 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.180194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.149448 restraints weight = 16553.532| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.80 r_work: 0.3502 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14809 Z= 0.242 Angle : 0.777 11.434 20096 Z= 0.400 Chirality : 0.052 0.197 2141 Planarity : 0.006 0.061 2542 Dihedral : 14.931 155.275 2182 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.49 % Allowed : 11.80 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1737 helix: 0.70 (0.18), residues: 888 sheet: 1.51 (0.52), residues: 110 loop : -0.82 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 528 TYR 0.038 0.003 TYR B 315 PHE 0.022 0.002 PHE A 213 TRP 0.015 0.002 TRP C 572 HIS 0.012 0.003 HIS D 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (14806) covalent geometry : angle 0.77461 / 0.40 (20090) SS BOND : bond 0.01694 / 0.63 ( 3) SS BOND : angle 3.29551 / 2.00 ( 6) hydrogen bonds : bond 0.06764 / 4.61 ( 686) hydrogen bonds : angle 4.64076 / 3.37 ( 1854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.643 Fit side-chains REVERT: A 239 MET cc_start: 0.7423 (mtm) cc_final: 0.7212 (mtm) REVERT: A 334 PHE cc_start: 0.7939 (t80) cc_final: 0.7734 (t80) REVERT: A 375 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7842 (mt0) REVERT: A 429 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: A 551 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.5348 (mpt180) REVERT: A 555 LYS cc_start: 0.6905 (tmtt) cc_final: 0.6644 (mtpt) REVERT: B 288 LYS cc_start: 0.7540 (tppt) cc_final: 0.7199 (tmmt) REVERT: B 299 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7404 (mp0) REVERT: B 459 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7025 (pt0) REVERT: B 467 LYS cc_start: 0.6761 (ttmm) cc_final: 0.6515 (mttt) REVERT: B 472 ASP cc_start: 0.7124 (t70) cc_final: 0.6544 (t0) REVERT: B 505 MET cc_start: 0.8282 (mtm) cc_final: 0.8058 (mtp) REVERT: B 539 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7187 (mt0) REVERT: B 556 LYS cc_start: 0.7362 (mmtm) cc_final: 0.6486 (mttt) REVERT: B 571 GLN cc_start: 0.7825 (mm110) cc_final: 0.7401 (tm-30) REVERT: C 299 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6685 (pt0) REVERT: C 392 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7959 (ttmm) REVERT: D 148 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8813 (mmtm) REVERT: D 226 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7629 (mtm180) REVERT: D 255 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7355 (pt0) REVERT: D 337 PHE cc_start: 0.8388 (m-80) cc_final: 0.8154 (m-80) REVERT: D 340 VAL cc_start: 0.8376 (m) cc_final: 0.8117 (t) REVERT: D 408 ARG cc_start: 0.7936 (mtt-85) cc_final: 0.7590 (mtp180) REVERT: D 439 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7484 (mtpp) REVERT: D 447 GLN cc_start: 0.8397 (tt0) cc_final: 0.8153 (tt0) REVERT: D 455 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7659 (mmmm) REVERT: D 470 ARG cc_start: 0.7272 (mmm160) cc_final: 0.6706 (tpt170) REVERT: D 505 MET cc_start: 0.8075 (mmm) cc_final: 0.7784 (mmm) REVERT: D 511 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7071 (mm-30) REVERT: D 556 LYS cc_start: 0.7693 (mtmt) cc_final: 0.7355 (mptp) outliers start: 51 outliers final: 19 residues processed: 254 average time/residue: 0.6296 time to fit residues: 174.7649 Evaluate side-chains 188 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 519 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 93 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN C 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.179791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148280 restraints weight = 23675.596| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.87 r_work: 0.3429 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14809 Z= 0.157 Angle : 0.606 8.997 20096 Z= 0.313 Chirality : 0.046 0.174 2141 Planarity : 0.004 0.048 2542 Dihedral : 13.809 148.355 2178 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.95 % Allowed : 14.22 % Favored : 82.83 % 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 are not related in a simple way. whole: 0.32 (0.20), residues: 1737 helix: 1.01 (0.18), residues: 882 sheet: 1.77 (0.56), residues: 94 loop : -0.92 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 566 TYR 0.034 0.002 TYR B 315 PHE 0.020 0.002 PHE C 334 TRP 0.012 0.001 TRP C 572 HIS 0.007 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (14806) covalent geometry : angle 0.60535 / 0.31 (20090) SS BOND : bond 0.00828 / 0.39 ( 3) SS BOND : angle 1.41089 / 0.71 ( 6) hydrogen bonds : bond 0.05100 / 3.49 ( 686) hydrogen bonds : angle 4.29635 / 3.10 ( 1854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.567 Fit side-chains REVERT: A 299 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6968 (tt0) REVERT: A 334 PHE cc_start: 0.7904 (t80) cc_final: 0.7654 (t80) REVERT: B 459 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7183 (pt0) REVERT: B 472 ASP cc_start: 0.7054 (t70) cc_final: 0.6530 (t0) REVERT: B 505 MET cc_start: 0.8111 (mtm) cc_final: 0.7884 (mtp) REVERT: B 539 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7338 (mt0) REVERT: B 556 LYS cc_start: 0.7323 (mmtm) cc_final: 0.6890 (mmtt) REVERT: B 571 GLN cc_start: 0.7628 (mm110) cc_final: 0.7271 (tm-30) REVERT: C 299 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6733 (tt0) REVERT: C 429 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: D 326 GLN cc_start: 0.7957 (mt0) cc_final: 0.7741 (mt0) REVERT: D 408 ARG cc_start: 0.7847 (mtt-85) cc_final: 0.7626 (mtp180) REVERT: D 429 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: D 447 GLN cc_start: 0.8212 (tt0) cc_final: 0.7913 (tt0) REVERT: D 470 ARG cc_start: 0.7287 (mmm160) cc_final: 0.6380 (tpt170) REVERT: D 505 MET cc_start: 0.7999 (mmm) cc_final: 0.7771 (mmm) REVERT: D 563 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5610 (t80) outliers start: 43 outliers final: 17 residues processed: 215 average time/residue: 0.6200 time to fit residues: 146.5117 Evaluate side-chains 180 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 548 GLN Chi-restraints excluded: chain D residue 563 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 116 optimal weight: 4.9990 chunk 110 optimal weight: 0.0770 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 13 optimal weight: 0.0170 chunk 75 optimal weight: 0.0670 chunk 109 optimal weight: 0.0030 chunk 26 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN A 548 GLN B 510 GLN C 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.184638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153938 restraints weight = 29306.280| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.58 r_work: 0.3501 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (21 function evaluations) r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14809 Z= 0.099 Angle : 0.527 6.537 20096 Z= 0.270 Chirality : 0.043 0.163 2141 Planarity : 0.004 0.037 2542 Dihedral : 12.747 143.863 2178 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.01 % Allowed : 16.23 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.21), residues: 1737 helix: 1.38 (0.19), residues: 880 sheet: 1.93 (0.56), residues: 94 loop : -0.79 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 226 TYR 0.028 0.001 TYR B 315 PHE 0.011 0.001 PHE B 165 TRP 0.008 0.001 TRP C 572 HIS 0.006 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (14806) covalent geometry : angle 0.52657 / 0.27 (20090) SS BOND : bond 0.00124 / 0.06 ( 3) SS BOND : angle 1.16250 / 0.58 ( 6) hydrogen bonds : bond 0.03595 / 2.45 ( 686) hydrogen bonds : angle 4.02544 / 2.89 ( 1854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.415 Fit side-chains REVERT: A 299 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7117 (tt0) REVERT: A 334 PHE cc_start: 0.7958 (t80) cc_final: 0.7704 (t80) REVERT: A 455 LYS cc_start: 0.6370 (OUTLIER) cc_final: 0.6032 (mmtm) REVERT: B 288 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7464 (tmmt) REVERT: B 455 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7455 (mmtm) REVERT: B 472 ASP cc_start: 0.7079 (t70) cc_final: 0.6517 (t0) REVERT: B 505 MET cc_start: 0.8103 (mtm) cc_final: 0.7854 (mtp) REVERT: B 511 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7004 (mt-10) REVERT: B 539 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7359 (mt0) REVERT: B 556 LYS cc_start: 0.7381 (mmtm) cc_final: 0.6468 (mttt) REVERT: C 299 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6801 (tt0) REVERT: C 429 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: D 285 TRP cc_start: 0.6553 (OUTLIER) cc_final: 0.5376 (t60) REVERT: D 340 VAL cc_start: 0.8038 (m) cc_final: 0.7702 (t) REVERT: D 408 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7684 (mtp180) REVERT: D 447 GLN cc_start: 0.8128 (tt0) cc_final: 0.7874 (tt0) REVERT: D 470 ARG cc_start: 0.7206 (mmm160) cc_final: 0.6402 (tpt170) REVERT: D 556 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7708 (mtpt) REVERT: D 563 TYR cc_start: 0.6142 (OUTLIER) cc_final: 0.5550 (t80) outliers start: 29 outliers final: 13 residues processed: 199 average time/residue: 0.5750 time to fit residues: 125.5039 Evaluate side-chains 184 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 285 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 548 GLN Chi-restraints excluded: chain D residue 563 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 17 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN B 328 ASN B 510 GLN C 149 GLN C 163 ASN D 271 GLN D 328 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.177872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146582 restraints weight = 20040.669| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.67 r_work: 0.3479 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14809 Z= 0.160 Angle : 0.608 9.485 20096 Z= 0.313 Chirality : 0.046 0.175 2141 Planarity : 0.004 0.040 2542 Dihedral : 13.044 144.731 2178 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.95 % Allowed : 15.83 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1737 helix: 1.31 (0.18), residues: 858 sheet: 1.81 (0.55), residues: 94 loop : -0.80 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 576 TYR 0.033 0.002 TYR B 315 PHE 0.024 0.002 PHE C 334 TRP 0.012 0.001 TRP C 572 HIS 0.008 0.002 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (14806) covalent geometry : angle 0.60717 / 0.31 (20090) SS BOND : bond 0.00242 / 0.12 ( 3) SS BOND : angle 1.60250 / 0.87 ( 6) hydrogen bonds : bond 0.05240 / 3.59 ( 686) hydrogen bonds : angle 4.23078 / 3.03 ( 1854) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 299 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6904 (tt0) REVERT: A 332 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6795 (mmtm) REVERT: A 440 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.7075 (m-30) REVERT: A 455 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6184 (mmtm) REVERT: A 551 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.5636 (mpt180) REVERT: B 229 VAL cc_start: 0.7785 (p) cc_final: 0.7260 (m) REVERT: B 299 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 455 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7530 (mmtm) REVERT: B 472 ASP cc_start: 0.7136 (t70) cc_final: 0.6527 (t0) REVERT: B 505 MET cc_start: 0.8209 (mtm) cc_final: 0.7975 (mtp) REVERT: B 511 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7000 (mt-10) REVERT: B 539 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7549 (mt0) REVERT: B 556 LYS cc_start: 0.7273 (mmtm) cc_final: 0.6781 (mmtt) REVERT: B 576 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7564 (tpp80) REVERT: C 299 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6883 (tt0) REVERT: C 328 ASN cc_start: 0.8198 (m110) cc_final: 0.7434 (m110) REVERT: C 355 GLU cc_start: 0.4999 (mm-30) cc_final: 0.4798 (mm-30) REVERT: C 429 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: D 148 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8825 (mmtm) REVERT: D 285 TRP cc_start: 0.6808 (OUTLIER) cc_final: 0.5578 (t60) REVERT: D 340 VAL cc_start: 0.8253 (m) cc_final: 0.7856 (t) REVERT: D 408 ARG cc_start: 0.8073 (mtt-85) cc_final: 0.7651 (mtp180) REVERT: D 429 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: D 447 GLN cc_start: 0.8310 (tt0) cc_final: 0.8001 (tt0) REVERT: D 470 ARG cc_start: 0.7264 (mmm160) cc_final: 0.6341 (tpt170) REVERT: D 501 ASP cc_start: 0.7907 (t0) cc_final: 0.7534 (t70) REVERT: D 563 TYR cc_start: 0.6443 (OUTLIER) cc_final: 0.5809 (t80) outliers start: 43 outliers final: 24 residues processed: 203 average time/residue: 0.5843 time to fit residues: 130.1664 Evaluate side-chains 186 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 285 TRP Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 548 GLN Chi-restraints excluded: chain D residue 563 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 169 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN A 326 GLN B 510 GLN C 149 GLN C 328 ASN ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.177374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146915 restraints weight = 18707.635| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.58 r_work: 0.3491 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14809 Z= 0.157 Angle : 0.602 8.261 20096 Z= 0.310 Chirality : 0.046 0.167 2141 Planarity : 0.004 0.041 2542 Dihedral : 12.943 145.053 2178 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.02 % Allowed : 16.30 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1737 helix: 1.30 (0.18), residues: 858 sheet: 1.73 (0.54), residues: 94 loop : -0.81 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 576 TYR 0.029 0.002 TYR B 315 PHE 0.011 0.001 PHE A 213 TRP 0.011 0.001 TRP C 572 HIS 0.007 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (14806) covalent geometry : angle 0.60140 / 0.31 (20090) SS BOND : bond 0.00281 / 0.13 ( 3) SS BOND : angle 1.58823 / 0.89 ( 6) hydrogen bonds : bond 0.05026 / 3.45 ( 686) hydrogen bonds : angle 4.20389 / 3.01 ( 1854) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.569 Fit side-chains REVERT: A 230 LYS cc_start: 0.7615 (ptpp) cc_final: 0.6750 (tppt) REVERT: A 299 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6926 (tt0) REVERT: A 332 LYS cc_start: 0.7194 (mmtt) cc_final: 0.6805 (mmtm) REVERT: A 360 TYR cc_start: 0.6110 (m-10) cc_final: 0.5793 (t80) REVERT: A 429 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: A 440 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.7057 (m-30) REVERT: A 455 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6308 (mmtm) REVERT: A 551 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.5663 (mpt180) REVERT: B 229 VAL cc_start: 0.7814 (p) cc_final: 0.7324 (m) REVERT: B 299 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7329 (mt-10) REVERT: B 455 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7484 (mmtm) REVERT: B 472 ASP cc_start: 0.7114 (t70) cc_final: 0.6517 (t0) REVERT: B 505 MET cc_start: 0.8205 (mtm) cc_final: 0.7981 (mtp) REVERT: B 511 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6991 (mt-10) REVERT: B 539 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7586 (mt0) REVERT: B 556 LYS cc_start: 0.7234 (mmtm) cc_final: 0.6686 (mmtt) REVERT: B 576 ARG cc_start: 0.7777 (tpp80) cc_final: 0.7488 (tpp80) REVERT: C 299 GLU cc_start: 0.7553 (mt-10) cc_final: 0.6994 (tt0) REVERT: C 429 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: D 285 TRP cc_start: 0.6687 (OUTLIER) cc_final: 0.5441 (t60) REVERT: D 340 VAL cc_start: 0.8315 (m) cc_final: 0.7908 (t) REVERT: D 408 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7666 (mtp180) REVERT: D 429 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: D 470 ARG cc_start: 0.7272 (mmm160) cc_final: 0.6399 (tpt170) REVERT: D 501 ASP cc_start: 0.7856 (t0) cc_final: 0.7499 (t70) REVERT: D 563 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5706 (t80) outliers start: 44 outliers final: 23 residues processed: 201 average time/residue: 0.5931 time to fit residues: 130.4298 Evaluate side-chains 179 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 285 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain D residue 548 GLN Chi-restraints excluded: chain D residue 563 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 7 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 0.0870 chunk 138 optimal weight: 0.0570 chunk 34 optimal weight: 6.9990 chunk 143 optimal weight: 0.0020 chunk 16 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN B 510 GLN C 149 GLN C 328 ASN D 271 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.181915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.152026 restraints weight = 18749.662| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.59 r_work: 0.3508 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14809 Z= 0.104 Angle : 0.538 8.027 20096 Z= 0.275 Chirality : 0.043 0.147 2141 Planarity : 0.004 0.041 2542 Dihedral : 11.876 141.162 2178 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.15 % Allowed : 17.57 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1737 helix: 1.63 (0.19), residues: 858 sheet: 1.89 (0.54), residues: 94 loop : -0.64 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 566 TYR 0.024 0.001 TYR B 315 PHE 0.023 0.001 PHE C 334 TRP 0.007 0.001 TRP C 572 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (14806) covalent geometry : angle 0.53820 / 0.28 (20090) SS BOND : bond 0.00106 / 0.05 ( 3) SS BOND : angle 1.09540 / 0.57 ( 6) hydrogen bonds : bond 0.03651 / 2.50 ( 686) hydrogen bonds : angle 3.97395 / 2.85 ( 1854) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.520 Fit side-chains REVERT: A 230 LYS cc_start: 0.7526 (ptpp) cc_final: 0.6719 (tppt) REVERT: A 299 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6861 (tt0) REVERT: A 332 LYS cc_start: 0.7191 (mmtt) cc_final: 0.6835 (mmtm) REVERT: A 429 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: A 455 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6280 (mmtm) REVERT: B 229 VAL cc_start: 0.7774 (p) cc_final: 0.7280 (m) REVERT: B 299 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7171 (mt-10) REVERT: B 472 ASP cc_start: 0.7069 (t70) cc_final: 0.6451 (t0) REVERT: B 505 MET cc_start: 0.8193 (mtm) cc_final: 0.7943 (mtp) REVERT: B 511 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7080 (mt-10) REVERT: B 539 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7626 (mt0) REVERT: B 556 LYS cc_start: 0.7064 (mmtm) cc_final: 0.6148 (mtpt) REVERT: B 576 ARG cc_start: 0.7726 (tpp80) cc_final: 0.7378 (tpp80) REVERT: C 299 GLU cc_start: 0.7591 (mt-10) cc_final: 0.6939 (tt0) REVERT: C 355 GLU cc_start: 0.5333 (mm-30) cc_final: 0.4624 (tp30) REVERT: D 285 TRP cc_start: 0.6648 (OUTLIER) cc_final: 0.5413 (t60) REVERT: D 340 VAL cc_start: 0.8024 (m) cc_final: 0.7727 (t) REVERT: D 408 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7654 (mtp180) REVERT: D 470 ARG cc_start: 0.7186 (mmm160) cc_final: 0.6248 (tpt170) REVERT: D 501 ASP cc_start: 0.7886 (t0) cc_final: 0.7663 (t70) REVERT: D 563 TYR cc_start: 0.6351 (OUTLIER) cc_final: 0.5676 (t80) outliers start: 31 outliers final: 16 residues processed: 192 average time/residue: 0.5546 time to fit residues: 116.3689 Evaluate side-chains 172 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 285 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 548 GLN Chi-restraints excluded: chain D residue 563 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 144 optimal weight: 0.0770 chunk 140 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 171 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.9865 > 50:) overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN B 510 GLN C 149 GLN ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.176271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146022 restraints weight = 19971.009| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.59 r_work: 0.3454 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14809 Z= 0.172 Angle : 0.626 8.031 20096 Z= 0.321 Chirality : 0.046 0.181 2141 Planarity : 0.004 0.041 2542 Dihedral : 12.477 143.323 2178 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.41 % Allowed : 17.77 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1737 helix: 1.30 (0.18), residues: 864 sheet: 1.79 (0.54), residues: 94 loop : -0.73 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 566 TYR 0.030 0.002 TYR B 315 PHE 0.013 0.002 PHE A 213 TRP 0.011 0.001 TRP C 572 HIS 0.008 0.002 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (14806) covalent geometry : angle 0.62507 / 0.32 (20090) SS BOND : bond 0.00177 / 0.08 ( 3) SS BOND : angle 1.62163 / 0.90 ( 6) hydrogen bonds : bond 0.05365 / 3.68 ( 686) hydrogen bonds : angle 4.21176 / 3.02 ( 1854) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.676 Fit side-chains REVERT: A 193 GLU cc_start: 0.7339 (mp0) cc_final: 0.6981 (mm-30) REVERT: A 230 LYS cc_start: 0.7604 (ptpp) cc_final: 0.6812 (tppt) REVERT: A 242 GLU cc_start: 0.8624 (tp30) cc_final: 0.8377 (mm-30) REVERT: A 299 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6713 (tt0) REVERT: A 332 LYS cc_start: 0.7229 (mmtt) cc_final: 0.6889 (mmtm) REVERT: A 360 TYR cc_start: 0.5903 (m-10) cc_final: 0.5525 (t80) REVERT: A 429 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: A 455 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6400 (mmtm) REVERT: A 551 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5345 (mtt180) REVERT: B 229 VAL cc_start: 0.7782 (p) cc_final: 0.7376 (m) REVERT: B 299 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7142 (mt-10) REVERT: B 472 ASP cc_start: 0.6956 (t70) cc_final: 0.6382 (t0) REVERT: B 474 GLU cc_start: 0.7545 (mp0) cc_final: 0.7145 (pm20) REVERT: B 505 MET cc_start: 0.8080 (mtm) cc_final: 0.7834 (mtp) REVERT: B 511 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7022 (mt-10) REVERT: B 539 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7574 (mt0) REVERT: B 556 LYS cc_start: 0.6869 (mmtm) cc_final: 0.6095 (mtpt) REVERT: B 576 ARG cc_start: 0.7695 (tpp80) cc_final: 0.7292 (tpp80) REVERT: C 299 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6819 (tt0) REVERT: C 355 GLU cc_start: 0.5527 (mm-30) cc_final: 0.4943 (tp30) REVERT: D 134 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7801 (mmm-85) REVERT: D 285 TRP cc_start: 0.6619 (OUTLIER) cc_final: 0.5388 (t60) REVERT: D 340 VAL cc_start: 0.8278 (m) cc_final: 0.7923 (t) REVERT: D 408 ARG cc_start: 0.7909 (mtt-85) cc_final: 0.7567 (mtp180) REVERT: D 429 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: D 455 LYS cc_start: 0.8335 (mmmt) cc_final: 0.7924 (mmtm) REVERT: D 470 ARG cc_start: 0.7171 (mmm160) cc_final: 0.6296 (tpt170) REVERT: D 501 ASP cc_start: 0.7812 (t0) cc_final: 0.7283 (t70) outliers start: 35 outliers final: 20 residues processed: 196 average time/residue: 0.6245 time to fit residues: 134.1974 Evaluate side-chains 180 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 285 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 548 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN B 510 GLN C 149 GLN D 271 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.178996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147940 restraints weight = 18862.481| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.94 r_work: 0.3490 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14809 Z= 0.118 Angle : 0.570 7.255 20096 Z= 0.292 Chirality : 0.044 0.170 2141 Planarity : 0.004 0.040 2542 Dihedral : 11.989 141.388 2178 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.68 % Allowed : 19.18 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1737 helix: 1.50 (0.19), residues: 864 sheet: 1.92 (0.54), residues: 94 loop : -0.67 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 566 TYR 0.025 0.001 TYR B 315 PHE 0.023 0.001 PHE C 334 TRP 0.009 0.001 TRP C 572 HIS 0.006 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (14806) covalent geometry : angle 0.57006 / 0.29 (20090) SS BOND : bond 0.00153 / 0.07 ( 3) SS BOND : angle 1.14378 / 0.61 ( 6) hydrogen bonds : bond 0.04142 / 2.84 ( 686) hydrogen bonds : angle 4.06457 / 2.92 ( 1854) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.619 Fit side-chains REVERT: A 193 GLU cc_start: 0.7449 (mp0) cc_final: 0.7130 (mm-30) REVERT: A 230 LYS cc_start: 0.7651 (ptpp) cc_final: 0.6753 (tppt) REVERT: A 242 GLU cc_start: 0.8730 (tp30) cc_final: 0.8466 (mm-30) REVERT: A 299 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6840 (tt0) REVERT: A 332 LYS cc_start: 0.7200 (mmtt) cc_final: 0.6844 (mmtm) REVERT: A 360 TYR cc_start: 0.6087 (m-10) cc_final: 0.5600 (t80) REVERT: A 429 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: A 455 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6436 (mmtm) REVERT: B 229 VAL cc_start: 0.7790 (p) cc_final: 0.7288 (m) REVERT: B 299 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7214 (mt-10) REVERT: B 472 ASP cc_start: 0.7082 (t70) cc_final: 0.6449 (t0) REVERT: B 474 GLU cc_start: 0.7671 (mp0) cc_final: 0.7135 (pm20) REVERT: B 505 MET cc_start: 0.8178 (mtm) cc_final: 0.7951 (mtp) REVERT: B 511 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7128 (mt-10) REVERT: B 539 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7595 (mt0) REVERT: B 556 LYS cc_start: 0.6878 (mmtm) cc_final: 0.6093 (mtpt) REVERT: B 576 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7354 (tpp80) REVERT: C 299 GLU cc_start: 0.7661 (mt-10) cc_final: 0.6953 (tt0) REVERT: C 355 GLU cc_start: 0.5512 (mm-30) cc_final: 0.4818 (tp30) REVERT: D 285 TRP cc_start: 0.6629 (OUTLIER) cc_final: 0.5332 (t60) REVERT: D 340 VAL cc_start: 0.8131 (m) cc_final: 0.7804 (t) REVERT: D 408 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7608 (mtp180) REVERT: D 470 ARG cc_start: 0.7091 (mmm160) cc_final: 0.6070 (tpt170) REVERT: D 501 ASP cc_start: 0.7966 (t0) cc_final: 0.7590 (t70) outliers start: 24 outliers final: 15 residues processed: 175 average time/residue: 0.6374 time to fit residues: 122.4498 Evaluate side-chains 166 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 285 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 548 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 33 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 83 optimal weight: 0.0980 chunk 75 optimal weight: 0.4980 chunk 76 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN C 149 GLN D 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.180053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149216 restraints weight = 25382.483| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.96 r_work: 0.3471 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14809 Z= 0.111 Angle : 0.558 6.928 20096 Z= 0.285 Chirality : 0.044 0.152 2141 Planarity : 0.004 0.040 2542 Dihedral : 11.419 137.782 2178 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.95 % Allowed : 19.05 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1737 helix: 1.62 (0.19), residues: 860 sheet: 2.02 (0.54), residues: 94 loop : -0.57 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 566 TYR 0.024 0.001 TYR B 315 PHE 0.010 0.001 PHE B 165 TRP 0.009 0.001 TRP C 572 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (14806) covalent geometry : angle 0.55774 / 0.29 (20090) SS BOND : bond 0.00099 / 0.05 ( 3) SS BOND : angle 1.12680 / 0.57 ( 6) hydrogen bonds : bond 0.03854 / 2.64 ( 686) hydrogen bonds : angle 3.97103 / 2.85 ( 1854) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.495 Fit side-chains REVERT: A 193 GLU cc_start: 0.7319 (mp0) cc_final: 0.6933 (mm-30) REVERT: A 230 LYS cc_start: 0.7605 (ptpp) cc_final: 0.6796 (tppt) REVERT: A 242 GLU cc_start: 0.8613 (tp30) cc_final: 0.8366 (mm-30) REVERT: A 299 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6799 (tt0) REVERT: A 332 LYS cc_start: 0.7225 (mmtt) cc_final: 0.6948 (mmtm) REVERT: A 360 TYR cc_start: 0.5976 (m-10) cc_final: 0.5603 (t80) REVERT: A 429 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: A 455 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6454 (mmtm) REVERT: B 229 VAL cc_start: 0.7750 (p) cc_final: 0.7274 (m) REVERT: B 472 ASP cc_start: 0.6951 (t70) cc_final: 0.6385 (t0) REVERT: B 474 GLU cc_start: 0.7481 (mp0) cc_final: 0.7155 (pm20) REVERT: B 505 MET cc_start: 0.8032 (mtm) cc_final: 0.7790 (mtp) REVERT: B 511 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6963 (mt-10) REVERT: B 539 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7571 (mt0) REVERT: B 556 LYS cc_start: 0.6969 (mmtm) cc_final: 0.6223 (mtpt) REVERT: B 576 ARG cc_start: 0.7674 (tpp80) cc_final: 0.7361 (tpp80) REVERT: C 299 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6848 (tt0) REVERT: C 355 GLU cc_start: 0.5448 (mm-30) cc_final: 0.4844 (tp30) REVERT: C 551 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.5565 (mpt180) REVERT: D 134 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7829 (mmm-85) REVERT: D 285 TRP cc_start: 0.6663 (OUTLIER) cc_final: 0.5407 (t60) REVERT: D 340 VAL cc_start: 0.7988 (m) cc_final: 0.7777 (t) REVERT: D 408 ARG cc_start: 0.7951 (mtt-85) cc_final: 0.7589 (mtp180) REVERT: D 470 ARG cc_start: 0.6973 (mmm160) cc_final: 0.6015 (tpt170) REVERT: D 501 ASP cc_start: 0.7646 (t0) cc_final: 0.7255 (t70) REVERT: D 556 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7291 (ptmt) outliers start: 28 outliers final: 19 residues processed: 186 average time/residue: 0.5621 time to fit residues: 115.2327 Evaluate side-chains 174 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 285 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 548 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 23 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN B 326 GLN B 510 GLN C 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.170305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150274 restraints weight = 20963.160| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.40 r_work: 0.3420 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14809 Z= 0.205 Angle : 0.674 8.220 20096 Z= 0.346 Chirality : 0.048 0.196 2141 Planarity : 0.005 0.041 2542 Dihedral : 12.643 145.156 2178 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.01 % Allowed : 19.52 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1737 helix: 1.15 (0.18), residues: 864 sheet: 1.78 (0.55), residues: 94 loop : -0.78 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 305 TYR 0.031 0.002 TYR B 315 PHE 0.021 0.002 PHE C 334 TRP 0.013 0.002 TRP C 572 HIS 0.010 0.002 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (14806) covalent geometry : angle 0.67338 / 0.35 (20090) SS BOND : bond 0.00234 / 0.11 ( 3) SS BOND : angle 1.71835 / 0.97 ( 6) hydrogen bonds : bond 0.05992 / 4.12 ( 686) hydrogen bonds : angle 4.35045 / 3.12 ( 1854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4538.56 seconds wall clock time: 77 minutes 58.33 seconds (4678.33 seconds total)