Starting phenix.real_space_refine on Thu Jun 12 23:46:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxn_18733/06_2025/8qxn_18733_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxn_18733/06_2025/8qxn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qxn_18733/06_2025/8qxn_18733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxn_18733/06_2025/8qxn_18733.map" model { file = "/net/cci-nas-00/data/ceres_data/8qxn_18733/06_2025/8qxn_18733_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxn_18733/06_2025/8qxn_18733_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.188 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} 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: 10.61, per 1000 atoms: 0.73 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: 3.92 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.66 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: 4.27 Time building geometry restraints manager: 4.52 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=" C4 DCP B 705 " pdb=" C5 DCP B 705 " ideal model delta sigma weight residual 1.426 1.386 0.040 1.20e-02 6.94e+03 1.11e+01 bond pdb=" O1A DCP D 708 " pdb=" PA DCP D 708 " ideal model delta sigma weight residual 1.477 1.510 -0.033 1.00e-02 1.00e+04 1.06e+01 bond pdb=" O1A DCP B 705 " pdb=" PA DCP B 705 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.00e-02 1.00e+04 1.02e+01 bond pdb=" C4 DCP D 708 " pdb=" C5 DCP D 708 " ideal model delta sigma weight residual 1.426 1.388 0.038 1.20e-02 6.94e+03 9.82e+00 bond pdb=" C4' DCP B 705 " pdb=" O4' DCP B 705 " ideal model delta sigma weight residual 1.444 1.414 0.030 1.00e-02 1.00e+04 8.93e+00 ... (remaining 14801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 20019 3.81 - 7.62: 66 7.62 - 11.43: 1 11.43 - 15.24: 1 15.24 - 19.05: 3 Bond angle restraints: 20090 Sorted by residual: angle pdb=" PB DCP B 705 " pdb=" O3B DCP B 705 " pdb=" PG DCP B 705 " ideal model delta sigma weight residual 139.87 120.82 19.05 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB DCP D 708 " pdb=" O3B DCP D 708 " pdb=" PG DCP D 708 " ideal model delta sigma weight residual 139.87 122.00 17.87 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PA DCP B 705 " pdb=" O3A DCP B 705 " pdb=" PB DCP B 705 " ideal model delta sigma weight residual 136.83 120.00 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PA DCP D 708 " pdb=" O3A DCP D 708 " pdb=" PB DCP D 708 " ideal model delta sigma weight residual 136.83 122.82 14.01 1.00e+00 1.00e+00 1.96e+02 angle pdb=" O2G DCP D 708 " pdb=" PG DCP D 708 " pdb=" O3B DCP D 708 " ideal model delta sigma weight residual 104.48 110.98 -6.50 1.14e+00 7.76e-01 3.28e+01 ... (remaining 20085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.20: 8561 33.20 - 66.39: 258 66.39 - 99.59: 65 99.59 - 132.79: 6 132.79 - 165.98: 1 Dihedral angle restraints: 8891 sinusoidal: 3749 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 8888 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: 1.900 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.740 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 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 0.043 14809 Z= 0.152 Angle : 0.615 19.055 20096 Z= 0.393 Chirality : 0.053 1.402 2141 Planarity : 0.004 0.074 2542 Dihedral : 17.336 165.983 5580 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (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 TRP 0.012 0.001 TRP C 572 HIS 0.005 0.001 HIS A 233 PHE 0.010 0.001 PHE B 569 TYR 0.023 0.001 TYR C 315 ARG 0.006 0.000 ARG D 528 Details of bonding type rmsd hydrogen bonds : bond 0.19400 ( 686) hydrogen bonds : angle 5.64810 ( 1854) SS BOND : bond 0.00105 ( 3) SS BOND : angle 1.35585 ( 6) covalent geometry : bond 0.00265 (14806) covalent geometry : angle 0.61482 (20090) *********************** 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 : 1.596 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: 1.2598 time to fit residues: 555.5960 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 : 1.462 ------------------------------------------------------------------------------- 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 146 optimal weight: 0.6980 chunk 131 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 248 ASN B 327 ASN B 370 HIS C 303 ASN C 328 ASN C 447 GLN D 163 ASN D 327 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.188454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157399 restraints weight = 18303.430| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.83 r_work: 0.3632 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14809 Z= 0.162 Angle : 0.650 8.682 20096 Z= 0.339 Chirality : 0.047 0.178 2141 Planarity : 0.005 0.058 2542 Dihedral : 14.686 155.092 2168 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.68 % Allowed : 12.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1737 helix: 1.10 (0.18), residues: 898 sheet: 1.83 (0.59), residues: 94 loop : -0.64 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 572 HIS 0.010 0.002 HIS A 233 PHE 0.016 0.002 PHE A 213 TYR 0.039 0.002 TYR B 315 ARG 0.006 0.001 ARG D 528 Details of bonding type rmsd hydrogen bonds : bond 0.04989 ( 686) hydrogen bonds : angle 4.34153 ( 1854) SS BOND : bond 0.00424 ( 3) SS BOND : angle 2.21314 ( 6) covalent geometry : bond 0.00345 (14806) covalent geometry : angle 0.64892 (20090) *********************** 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 265 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 1.481 Fit side-chains REVERT: A 182 LEU cc_start: 0.7275 (tt) cc_final: 0.7067 (tp) REVERT: A 365 THR cc_start: 0.7638 (t) cc_final: 0.6933 (m) REVERT: A 375 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7686 (mt0) REVERT: A 455 LYS cc_start: 0.5818 (mmpt) cc_final: 0.5489 (mmtt) REVERT: B 288 LYS cc_start: 0.7322 (tppt) cc_final: 0.7033 (tmtt) REVERT: B 416 MET cc_start: 0.8025 (mmt) cc_final: 0.7741 (mmm) REVERT: B 472 ASP cc_start: 0.7204 (t70) cc_final: 0.6677 (t0) REVERT: B 539 GLN cc_start: 0.7099 (mm-40) cc_final: 0.6828 (mt0) REVERT: B 556 LYS cc_start: 0.7355 (mmtm) cc_final: 0.7137 (mmtt) REVERT: C 299 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6636 (pt0) REVERT: C 355 GLU cc_start: 0.4372 (mm-30) cc_final: 0.3939 (mm-30) REVERT: C 363 PHE cc_start: 0.7428 (m-10) cc_final: 0.7067 (m-10) REVERT: C 429 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: C 455 LYS cc_start: 0.6423 (mmmt) cc_final: 0.6088 (mmtm) REVERT: D 255 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7136 (pt0) REVERT: D 447 GLN cc_start: 0.8186 (tt0) cc_final: 0.7921 (tt0) REVERT: D 533 THR cc_start: 0.8752 (t) cc_final: 0.8272 (p) REVERT: D 556 LYS cc_start: 0.7559 (mtmt) cc_final: 0.7329 (mptp) outliers start: 39 outliers final: 16 residues processed: 256 average time/residue: 1.2621 time to fit residues: 354.2984 Evaluate side-chains 190 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 309 ASP 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 429 GLU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 184 GLU 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 519 SER Chi-restraints excluded: chain D residue 548 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 158 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 chunk 156 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS A 326 GLN A 364 HIS ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 ASN D 328 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.178932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147810 restraints weight = 25109.546| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.07 r_work: 0.3458 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14809 Z= 0.199 Angle : 0.676 8.675 20096 Z= 0.351 Chirality : 0.048 0.173 2141 Planarity : 0.005 0.053 2542 Dihedral : 14.101 158.041 2164 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.62 % Allowed : 13.28 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1737 helix: 0.89 (0.18), residues: 882 sheet: 1.82 (0.57), residues: 94 loop : -0.86 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 572 HIS 0.009 0.002 HIS D 243 PHE 0.019 0.002 PHE C 334 TYR 0.034 0.002 TYR B 315 ARG 0.007 0.001 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.06218 ( 686) hydrogen bonds : angle 4.47667 ( 1854) SS BOND : bond 0.00177 ( 3) SS BOND : angle 2.18284 ( 6) covalent geometry : bond 0.00470 (14806) covalent geometry : angle 0.67466 (20090) *********************** 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 247 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 1.565 Fit side-chains REVERT: A 299 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6690 (tt0) REVERT: A 398 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: A 551 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.5666 (mpt180) REVERT: B 288 LYS cc_start: 0.7578 (tppt) cc_final: 0.7341 (tmmt) REVERT: B 299 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7403 (mp0) REVERT: B 472 ASP cc_start: 0.7021 (t70) cc_final: 0.6510 (t0) REVERT: B 539 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7318 (mt0) REVERT: B 556 LYS cc_start: 0.7484 (mmtm) cc_final: 0.6600 (mttt) REVERT: B 571 GLN cc_start: 0.7730 (mm110) cc_final: 0.7318 (tm-30) REVERT: B 578 PHE cc_start: 0.6626 (m-10) cc_final: 0.6039 (m-10) REVERT: C 299 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6695 (tt0) REVERT: C 355 GLU cc_start: 0.5264 (mm-30) cc_final: 0.5026 (mm-30) REVERT: C 388 ASP cc_start: 0.8255 (t0) cc_final: 0.8055 (t0) REVERT: C 453 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7456 (mt) REVERT: D 326 GLN cc_start: 0.8228 (mt0) cc_final: 0.7966 (mt0) REVERT: D 340 VAL cc_start: 0.8210 (m) cc_final: 0.7778 (t) REVERT: D 429 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: D 439 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7456 (mtpp) REVERT: D 447 GLN cc_start: 0.8256 (tt0) cc_final: 0.7965 (tt0) REVERT: D 470 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6096 (tpt170) REVERT: D 472 ASP cc_start: 0.6912 (t0) cc_final: 0.6699 (t0) REVERT: D 511 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7001 (mm-30) REVERT: D 556 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7497 (mptp) REVERT: D 563 TYR cc_start: 0.6275 (OUTLIER) cc_final: 0.5668 (t80) outliers start: 53 outliers final: 27 residues processed: 234 average time/residue: 1.3052 time to fit residues: 335.2804 Evaluate side-chains 189 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 295 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 332 LYS 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 B residue 554 CYS Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 184 GLU 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 439 LYS Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain D residue 519 SER 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 133 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 364 HIS ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.179756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149323 restraints weight = 18652.481| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.62 r_work: 0.3464 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5156 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= 0.133 Angle : 0.582 7.605 20096 Z= 0.300 Chirality : 0.045 0.160 2141 Planarity : 0.004 0.041 2542 Dihedral : 13.417 149.778 2164 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.48 % Allowed : 16.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1737 helix: 1.21 (0.18), residues: 870 sheet: 1.84 (0.56), residues: 94 loop : -0.82 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 572 HIS 0.006 0.001 HIS A 233 PHE 0.013 0.001 PHE A 334 TYR 0.032 0.001 TYR B 315 ARG 0.004 0.000 ARG C 226 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 686) hydrogen bonds : angle 4.22692 ( 1854) SS BOND : bond 0.00124 ( 3) SS BOND : angle 1.66577 ( 6) covalent geometry : bond 0.00301 (14806) covalent geometry : angle 0.58126 (20090) *********************** 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 203 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.570 Fit side-chains REVERT: A 299 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6781 (tt0) REVERT: A 332 LYS cc_start: 0.7072 (mmtt) cc_final: 0.6716 (mmtm) REVERT: A 340 VAL cc_start: 0.7192 (OUTLIER) cc_final: 0.6955 (t) REVERT: A 429 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: A 505 MET cc_start: 0.3180 (mmm) cc_final: 0.2948 (mmm) REVERT: A 551 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.5613 (mpt180) REVERT: B 472 ASP cc_start: 0.7191 (t70) cc_final: 0.6567 (t0) REVERT: B 511 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7114 (mt-10) REVERT: B 539 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7422 (mt0) REVERT: B 556 LYS cc_start: 0.7431 (mmtm) cc_final: 0.6524 (mttt) REVERT: C 299 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6859 (tt0) REVERT: C 377 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7112 (mtpm) REVERT: C 388 ASP cc_start: 0.8420 (t0) cc_final: 0.8209 (t0) REVERT: D 271 GLN cc_start: 0.8588 (tt0) cc_final: 0.8194 (mt0) REVERT: D 285 TRP cc_start: 0.6629 (OUTLIER) cc_final: 0.5351 (t60) REVERT: D 326 GLN cc_start: 0.8282 (mt0) cc_final: 0.8065 (mt0) REVERT: D 340 VAL cc_start: 0.8233 (m) cc_final: 0.7812 (t) REVERT: D 447 GLN cc_start: 0.8314 (tt0) cc_final: 0.8025 (tt0) REVERT: D 470 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.5940 (tpt170) REVERT: D 472 ASP cc_start: 0.6998 (t0) cc_final: 0.6779 (t0) REVERT: D 511 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7086 (mm-30) REVERT: D 556 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7046 (mptp) outliers start: 36 outliers final: 17 residues processed: 196 average time/residue: 1.4738 time to fit residues: 318.4101 Evaluate side-chains 180 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 429 GLU 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 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 429 GLU 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 434 THR Chi-restraints excluded: chain D residue 506 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 364 HIS D 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.178507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147433 restraints weight = 20861.504| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.71 r_work: 0.3480 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 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 = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14809 Z= 0.140 Angle : 0.585 8.541 20096 Z= 0.301 Chirality : 0.045 0.156 2141 Planarity : 0.004 0.040 2542 Dihedral : 12.950 149.384 2164 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.95 % Allowed : 15.96 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1737 helix: 1.32 (0.18), residues: 858 sheet: 1.85 (0.56), residues: 94 loop : -0.75 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 572 HIS 0.008 0.001 HIS A 233 PHE 0.024 0.001 PHE C 334 TYR 0.031 0.002 TYR B 315 ARG 0.004 0.000 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 686) hydrogen bonds : angle 4.18566 ( 1854) SS BOND : bond 0.00162 ( 3) SS BOND : angle 1.47520 ( 6) covalent geometry : bond 0.00321 (14806) covalent geometry : angle 0.58477 (20090) *********************** 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 : 2.574 Fit side-chains REVERT: A 299 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6828 (tt0) REVERT: A 332 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6647 (mmtm) REVERT: A 340 VAL cc_start: 0.7192 (OUTLIER) cc_final: 0.6933 (t) REVERT: A 429 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: A 505 MET cc_start: 0.3326 (mmm) cc_final: 0.3103 (mmm) REVERT: A 551 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.5518 (mpt180) REVERT: B 229 VAL cc_start: 0.7689 (p) cc_final: 0.7176 (m) REVERT: B 230 LYS cc_start: 0.7862 (mmtp) cc_final: 0.7438 (mtmt) REVERT: B 299 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7288 (mt-10) REVERT: B 472 ASP cc_start: 0.7198 (t70) cc_final: 0.6569 (t0) REVERT: B 511 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6944 (mt-10) REVERT: B 539 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7537 (mt0) REVERT: B 556 LYS cc_start: 0.7272 (mmtm) cc_final: 0.6422 (mttt) REVERT: C 299 GLU cc_start: 0.7610 (mt-10) cc_final: 0.6926 (tt0) REVERT: C 355 GLU cc_start: 0.5422 (mm-30) cc_final: 0.5140 (mm-30) REVERT: C 388 ASP cc_start: 0.8453 (t0) cc_final: 0.8199 (t0) REVERT: C 429 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: C 551 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5506 (mpt180) REVERT: D 271 GLN cc_start: 0.8600 (tt0) cc_final: 0.8330 (mt0) REVERT: D 285 TRP cc_start: 0.6753 (OUTLIER) cc_final: 0.5485 (t60) REVERT: D 340 VAL cc_start: 0.8200 (m) cc_final: 0.7823 (t) REVERT: D 429 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: D 470 ARG cc_start: 0.6755 (mmm-85) cc_final: 0.6082 (tpt170) REVERT: D 497 ASP cc_start: 0.7738 (t0) cc_final: 0.7347 (t0) REVERT: D 501 ASP cc_start: 0.7716 (t0) cc_final: 0.7335 (t70) REVERT: D 563 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.5821 (t80) outliers start: 43 outliers final: 21 residues processed: 203 average time/residue: 1.6293 time to fit residues: 365.9774 Evaluate side-chains 179 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 429 GLU 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 B residue 554 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain C residue 552 VAL 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 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 563 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 123 optimal weight: 0.0070 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 326 GLN A 328 ASN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 149 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145727 restraints weight = 16678.675| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.55 r_work: 0.3426 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14809 Z= 0.182 Angle : 0.639 8.297 20096 Z= 0.329 Chirality : 0.047 0.170 2141 Planarity : 0.005 0.045 2542 Dihedral : 13.143 150.325 2164 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.29 % Allowed : 16.50 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1737 helix: 1.14 (0.18), residues: 860 sheet: 1.64 (0.55), residues: 94 loop : -0.86 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 572 HIS 0.008 0.002 HIS A 233 PHE 0.014 0.002 PHE D 316 TYR 0.030 0.002 TYR B 315 ARG 0.005 0.001 ARG B 348 Details of bonding type rmsd hydrogen bonds : bond 0.05589 ( 686) hydrogen bonds : angle 4.30395 ( 1854) SS BOND : bond 0.00257 ( 3) SS BOND : angle 1.71605 ( 6) covalent geometry : bond 0.00435 (14806) covalent geometry : angle 0.63802 (20090) *********************** 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 213 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 1.532 Fit side-chains REVERT: A 230 LYS cc_start: 0.7636 (ptpp) cc_final: 0.6793 (tppt) REVERT: A 238 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7824 (t) REVERT: A 242 GLU cc_start: 0.8690 (tp30) cc_final: 0.8437 (mm-30) REVERT: A 299 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6971 (tt0) REVERT: A 328 ASN cc_start: 0.8196 (m-40) cc_final: 0.7964 (m110) REVERT: A 332 LYS cc_start: 0.7312 (mmtt) cc_final: 0.6898 (mmtm) REVERT: A 340 VAL cc_start: 0.7238 (OUTLIER) cc_final: 0.6981 (t) REVERT: A 360 TYR cc_start: 0.6162 (m-10) cc_final: 0.5790 (t80) REVERT: A 429 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: A 551 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.5554 (mtt180) REVERT: B 229 VAL cc_start: 0.7765 (p) cc_final: 0.7224 (m) REVERT: B 299 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7311 (mt-10) REVERT: B 328 ASN cc_start: 0.8079 (m110) cc_final: 0.7852 (m-40) REVERT: B 472 ASP cc_start: 0.7103 (t70) cc_final: 0.6513 (t0) REVERT: B 511 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6959 (mt-10) REVERT: B 539 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7611 (mt0) REVERT: B 556 LYS cc_start: 0.7144 (mmtm) cc_final: 0.6656 (mmtt) REVERT: C 239 MET cc_start: 0.7298 (mtm) cc_final: 0.7090 (mtm) REVERT: C 299 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6749 (tt0) REVERT: C 355 GLU cc_start: 0.5634 (mm-30) cc_final: 0.5432 (mm-30) REVERT: C 388 ASP cc_start: 0.8355 (t0) cc_final: 0.8083 (t0) REVERT: C 453 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7499 (mt) REVERT: C 551 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.5485 (mpt180) REVERT: D 271 GLN cc_start: 0.8562 (tt0) cc_final: 0.8267 (mt0) REVERT: D 285 TRP cc_start: 0.6705 (OUTLIER) cc_final: 0.5435 (t60) REVERT: D 340 VAL cc_start: 0.8273 (m) cc_final: 0.7864 (t) REVERT: D 429 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: D 455 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8042 (mmtm) REVERT: D 470 ARG cc_start: 0.6784 (mmm-85) cc_final: 0.6096 (tpt170) REVERT: D 497 ASP cc_start: 0.7759 (t0) cc_final: 0.7407 (t0) REVERT: D 501 ASP cc_start: 0.7795 (t0) cc_final: 0.7378 (t70) outliers start: 48 outliers final: 23 residues processed: 207 average time/residue: 1.3537 time to fit residues: 307.3177 Evaluate side-chains 182 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 429 GLU 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 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 B residue 554 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain C residue 552 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 77 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 164 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 149 GLN C 163 ASN ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.174157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144604 restraints weight = 16631.998| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.61 r_work: 0.3416 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6014 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= 0.198 Angle : 0.663 8.876 20096 Z= 0.342 Chirality : 0.047 0.173 2141 Planarity : 0.005 0.041 2542 Dihedral : 13.184 151.509 2164 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.09 % Allowed : 17.97 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1737 helix: 0.94 (0.18), residues: 866 sheet: 1.59 (0.55), residues: 94 loop : -0.92 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 572 HIS 0.009 0.002 HIS B 162 PHE 0.021 0.002 PHE C 334 TYR 0.029 0.002 TYR B 315 ARG 0.008 0.001 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.05873 ( 686) hydrogen bonds : angle 4.36792 ( 1854) SS BOND : bond 0.00203 ( 3) SS BOND : angle 1.84475 ( 6) covalent geometry : bond 0.00475 (14806) covalent geometry : angle 0.66251 (20090) *********************** 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 207 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7690 (mp0) cc_final: 0.7301 (mm-30) REVERT: A 230 LYS cc_start: 0.7699 (ptpp) cc_final: 0.6909 (tppt) REVERT: A 242 GLU cc_start: 0.8713 (tp30) cc_final: 0.8438 (mm-30) REVERT: A 299 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6998 (tt0) REVERT: A 332 LYS cc_start: 0.7400 (mmtt) cc_final: 0.6963 (mmtm) REVERT: A 340 VAL cc_start: 0.7271 (OUTLIER) cc_final: 0.6965 (t) REVERT: A 348 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.6143 (mtp85) REVERT: A 429 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: A 551 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.5656 (mtt180) REVERT: B 229 VAL cc_start: 0.7810 (p) cc_final: 0.7282 (m) REVERT: B 299 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 332 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8200 (mmtt) REVERT: B 472 ASP cc_start: 0.7240 (t70) cc_final: 0.6615 (t0) REVERT: B 511 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7043 (mt-10) REVERT: B 556 LYS cc_start: 0.7074 (mmtm) cc_final: 0.6581 (mmtt) REVERT: C 239 MET cc_start: 0.7428 (mtm) cc_final: 0.7217 (mtm) REVERT: C 299 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6796 (tt0) REVERT: C 388 ASP cc_start: 0.8344 (t0) cc_final: 0.8015 (t0) REVERT: C 453 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7620 (mt) REVERT: C 551 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.5581 (mpt180) REVERT: D 134 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7957 (mmm-85) REVERT: D 271 GLN cc_start: 0.8583 (tt0) cc_final: 0.8303 (mt0) REVERT: D 285 TRP cc_start: 0.6770 (OUTLIER) cc_final: 0.5358 (t60) REVERT: D 340 VAL cc_start: 0.8394 (m) cc_final: 0.7955 (t) REVERT: D 429 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: D 455 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8024 (mmtm) REVERT: D 470 ARG cc_start: 0.6794 (mmm-85) cc_final: 0.6276 (tpt170) REVERT: D 497 ASP cc_start: 0.7617 (t0) cc_final: 0.7249 (t0) REVERT: D 501 ASP cc_start: 0.7962 (t0) cc_final: 0.7335 (t70) outliers start: 45 outliers final: 24 residues processed: 204 average time/residue: 1.2585 time to fit residues: 283.1866 Evaluate side-chains 179 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 309 ASP 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 B residue 554 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 557 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 147 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 157 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 164 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 510 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.177833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148272 restraints weight = 18435.884| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.57 r_work: 0.3477 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6034 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 : 0.571 8.031 20096 Z= 0.294 Chirality : 0.044 0.153 2141 Planarity : 0.004 0.039 2542 Dihedral : 12.249 148.182 2164 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.08 % Allowed : 19.99 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1737 helix: 1.34 (0.18), residues: 862 sheet: 1.83 (0.55), residues: 94 loop : -0.77 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 572 HIS 0.005 0.001 HIS A 233 PHE 0.011 0.001 PHE B 165 TYR 0.024 0.001 TYR B 315 ARG 0.006 0.000 ARG C 566 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 686) hydrogen bonds : angle 4.12537 ( 1854) SS BOND : bond 0.00182 ( 3) SS BOND : angle 1.31373 ( 6) covalent geometry : bond 0.00263 (14806) covalent geometry : angle 0.57090 (20090) *********************** 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 193 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7567 (mp0) cc_final: 0.7312 (mm-30) REVERT: A 230 LYS cc_start: 0.7683 (ptpp) cc_final: 0.6884 (tppt) REVERT: A 242 GLU cc_start: 0.8650 (tp30) cc_final: 0.8380 (mm-30) REVERT: A 332 LYS cc_start: 0.7348 (mmtt) cc_final: 0.7006 (mmtm) REVERT: A 340 VAL cc_start: 0.7131 (OUTLIER) cc_final: 0.6879 (t) REVERT: A 429 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: B 229 VAL cc_start: 0.7763 (p) cc_final: 0.7256 (m) REVERT: B 299 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7277 (mt-10) REVERT: B 472 ASP cc_start: 0.7085 (t70) cc_final: 0.6502 (t0) REVERT: B 511 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7024 (mt-10) REVERT: B 539 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7626 (mt0) REVERT: B 556 LYS cc_start: 0.6943 (mmtm) cc_final: 0.6463 (mmtt) REVERT: C 353 ASP cc_start: 0.7078 (p0) cc_final: 0.6659 (m-30) REVERT: C 362 MET cc_start: 0.7860 (ttt) cc_final: 0.7549 (ttt) REVERT: C 388 ASP cc_start: 0.8333 (t0) cc_final: 0.8108 (t0) REVERT: C 429 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: D 271 GLN cc_start: 0.8463 (tt0) cc_final: 0.8186 (mt0) REVERT: D 285 TRP cc_start: 0.6715 (OUTLIER) cc_final: 0.5398 (t60) REVERT: D 340 VAL cc_start: 0.8132 (m) cc_final: 0.7826 (t) REVERT: D 429 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: D 470 ARG cc_start: 0.6625 (mmm-85) cc_final: 0.5999 (tpt170) REVERT: D 497 ASP cc_start: 0.7563 (t0) cc_final: 0.7160 (t0) REVERT: D 501 ASP cc_start: 0.7879 (t0) cc_final: 0.7438 (t70) outliers start: 30 outliers final: 16 residues processed: 188 average time/residue: 1.9219 time to fit residues: 399.6442 Evaluate side-chains 175 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain B residue 309 ASP 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 237 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 429 GLU 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 429 GLU Chi-restraints excluded: chain D residue 434 THR 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 129 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.177839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.148033 restraints weight = 18784.746| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.81 r_work: 0.3445 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14809 Z= 0.130 Angle : 0.591 8.975 20096 Z= 0.303 Chirality : 0.044 0.156 2141 Planarity : 0.004 0.039 2542 Dihedral : 11.965 148.900 2164 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.81 % Allowed : 20.25 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1737 helix: 1.37 (0.18), residues: 864 sheet: 1.88 (0.55), residues: 94 loop : -0.73 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 572 HIS 0.006 0.001 HIS A 233 PHE 0.024 0.001 PHE C 334 TYR 0.026 0.001 TYR B 315 ARG 0.007 0.000 ARG B 352 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 686) hydrogen bonds : angle 4.11657 ( 1854) SS BOND : bond 0.00182 ( 3) SS BOND : angle 1.40223 ( 6) covalent geometry : bond 0.00296 (14806) covalent geometry : angle 0.59109 (20090) *********************** 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 189 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7539 (mp0) cc_final: 0.7187 (mm-30) REVERT: A 230 LYS cc_start: 0.7723 (ptpp) cc_final: 0.6890 (tppt) REVERT: A 242 GLU cc_start: 0.8688 (tp30) cc_final: 0.8453 (mm-30) REVERT: A 299 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6932 (tt0) REVERT: A 332 LYS cc_start: 0.7275 (mmtt) cc_final: 0.6941 (mmtm) REVERT: A 340 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6857 (t) REVERT: A 361 ASP cc_start: 0.7772 (m-30) cc_final: 0.7293 (m-30) REVERT: A 388 ASP cc_start: 0.8239 (t0) cc_final: 0.8023 (t0) REVERT: A 429 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: B 472 ASP cc_start: 0.7162 (t70) cc_final: 0.6422 (t0) REVERT: B 511 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7030 (mt-10) REVERT: B 539 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7607 (mt0) REVERT: B 556 LYS cc_start: 0.7103 (mmtm) cc_final: 0.6647 (mmtt) REVERT: C 353 ASP cc_start: 0.7006 (p0) cc_final: 0.6712 (m-30) REVERT: C 388 ASP cc_start: 0.8315 (t0) cc_final: 0.8047 (t0) REVERT: C 429 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: C 551 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.5556 (mpt180) REVERT: D 271 GLN cc_start: 0.8482 (tt0) cc_final: 0.8212 (mt0) REVERT: D 285 TRP cc_start: 0.6737 (OUTLIER) cc_final: 0.5400 (t60) REVERT: D 340 VAL cc_start: 0.8144 (m) cc_final: 0.7830 (t) REVERT: D 429 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: D 470 ARG cc_start: 0.6638 (mmm-85) cc_final: 0.5995 (tpt170) REVERT: D 497 ASP cc_start: 0.7684 (t0) cc_final: 0.7163 (t0) REVERT: D 501 ASP cc_start: 0.7924 (t0) cc_final: 0.7336 (t70) REVERT: D 556 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7564 (ptmt) outliers start: 26 outliers final: 17 residues processed: 185 average time/residue: 1.4536 time to fit residues: 294.4851 Evaluate side-chains 175 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 309 ASP 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 C residue 237 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 551 ARG 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 429 GLU 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 103 optimal weight: 4.9990 chunk 132 optimal weight: 0.2980 chunk 166 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 71 optimal weight: 0.0470 chunk 171 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.0000 chunk 66 optimal weight: 0.8980 overall best weight: 0.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN C 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.179801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.156091 restraints weight = 21051.444| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.34 r_work: 0.3574 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- 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 = 0.44 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14809 Z= 0.100 Angle : 0.551 7.758 20096 Z= 0.282 Chirality : 0.043 0.147 2141 Planarity : 0.004 0.039 2542 Dihedral : 10.976 142.060 2164 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.21 % Allowed : 20.99 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1737 helix: 1.67 (0.19), residues: 864 sheet: 2.15 (0.55), residues: 94 loop : -0.56 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 572 HIS 0.005 0.001 HIS A 233 PHE 0.023 0.001 PHE C 334 TYR 0.020 0.001 TYR B 315 ARG 0.007 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 686) hydrogen bonds : angle 3.91750 ( 1854) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.19488 ( 6) covalent geometry : bond 0.00211 (14806) covalent geometry : angle 0.55084 (20090) ********************** 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 186 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 1.517 Fit side-chains REVERT: A 193 GLU cc_start: 0.7392 (mp0) cc_final: 0.7182 (mm-30) REVERT: A 230 LYS cc_start: 0.7607 (ptpp) cc_final: 0.6898 (tppt) REVERT: A 242 GLU cc_start: 0.8584 (tp30) cc_final: 0.8370 (mm-30) REVERT: A 299 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6876 (tt0) REVERT: A 332 LYS cc_start: 0.7288 (mmtt) cc_final: 0.7010 (mmtm) REVERT: A 361 ASP cc_start: 0.7444 (m-30) cc_final: 0.7175 (m-30) REVERT: B 342 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6900 (tm-30) REVERT: B 472 ASP cc_start: 0.6849 (t70) cc_final: 0.6286 (t0) REVERT: B 511 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6947 (mt-10) REVERT: B 539 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7533 (mt0) REVERT: B 556 LYS cc_start: 0.7033 (mmtm) cc_final: 0.6575 (mmtt) REVERT: C 250 ILE cc_start: 0.8825 (mp) cc_final: 0.8612 (mm) REVERT: C 299 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6745 (tt0) REVERT: C 353 ASP cc_start: 0.7081 (p0) cc_final: 0.6865 (m-30) REVERT: D 285 TRP cc_start: 0.6706 (OUTLIER) cc_final: 0.5384 (t60) REVERT: D 470 ARG cc_start: 0.6490 (mmm-85) cc_final: 0.5815 (tpt170) REVERT: D 497 ASP cc_start: 0.7609 (t0) cc_final: 0.7013 (t0) REVERT: D 501 ASP cc_start: 0.7531 (t0) cc_final: 0.7313 (t70) outliers start: 17 outliers final: 9 residues processed: 183 average time/residue: 1.2471 time to fit residues: 251.8857 Evaluate side-chains 163 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 265 ILE 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 548 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 25 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 131 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 89 optimal weight: 0.0970 chunk 172 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3940 r_free = 0.3940 target = 0.174788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.152715 restraints weight = 24425.013| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.45 r_work: 0.3448 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 : 0.003 0.035 14809 Z= 0.120 Angle : 0.583 8.868 20096 Z= 0.299 Chirality : 0.044 0.154 2141 Planarity : 0.004 0.039 2542 Dihedral : 11.069 145.474 2164 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.41 % Allowed : 21.33 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1737 helix: 1.57 (0.19), residues: 866 sheet: 2.16 (0.55), residues: 94 loop : -0.51 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.006 0.001 HIS A 233 PHE 0.011 0.001 PHE B 165 TYR 0.025 0.001 TYR B 315 ARG 0.007 0.001 ARG B 352 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 686) hydrogen bonds : angle 4.02115 ( 1854) SS BOND : bond 0.00138 ( 3) SS BOND : angle 1.40219 ( 6) covalent geometry : bond 0.00271 (14806) covalent geometry : angle 0.58273 (20090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11170.95 seconds wall clock time: 197 minutes 44.54 seconds (11864.54 seconds total)