Starting phenix.real_space_refine on Sat Oct 11 12:03:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxn_18733/10_2025/8qxn_18733_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxn_18733/10_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_18733/10_2025/8qxn_18733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxn_18733/10_2025/8qxn_18733.map" model { file = "/net/cci-nas-00/data/ceres_data/8qxn_18733/10_2025/8qxn_18733_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxn_18733/10_2025/8qxn_18733_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.188 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 30 5.49 5 Mg 8 5.21 5 S 76 5.16 5 C 9185 2.51 5 N 2491 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14461 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3441 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 404} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3719 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3713 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 458, 3713 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 3794 Chain: "C" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3367 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 17, 'TRANS': 404} Chain breaks: 3 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3618 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 94 Unusual residues: {' FE': 1, ' MG': 1, 'DTP': 2, 'GTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 93 Unusual residues: {' FE': 1, ' MG': 2, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' FE': 1, ' MG': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 95 Unusual residues: {' FE': 1, ' MG': 4, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 4.40, per 1000 atoms: 0.30 Number of scatterers: 14461 At special positions: 0 Unit cell: (118.81, 94.83, 106.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 76 16.00 P 30 15.00 Mg 8 11.99 O 2667 8.00 N 2491 7.00 C 9185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 341 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS D 341 " - pdb=" SG CYS D 350 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 777.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3302 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 16 sheets defined 61.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.615A pdb=" N TYR A 154 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 155 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 186 removed outlier: 4.057A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 215 through 226 removed outlier: 5.582A pdb=" N ILE A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 232 through 248 removed outlier: 3.719A pdb=" N GLY A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 257 removed outlier: 3.559A pdb=" N TYR A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.690A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 5.069A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 330 through 337 removed outlier: 3.855A pdb=" N PHE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 373 Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.944A pdb=" N ILE A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.995A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 451 Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.826A pdb=" N TYR A 473 " --> pdb=" O ARG A 470 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLU A 474 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.605A pdb=" N ALA A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.514A pdb=" N ALA A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 164 through 186 Processing helix chain 'B' and resid 187 through 190 removed outlier: 3.848A pdb=" N GLN B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 214 through 226 removed outlier: 4.297A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE B 222 " --> pdb=" O ASP B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 232 through 249 removed outlier: 3.645A pdb=" N GLY B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 273 removed outlier: 4.558A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 272 " --> pdb=" O ILE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.953A pdb=" N SER B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 5.555A pdb=" N PHE B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 317 " --> pdb=" O TRP B 313 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 removed outlier: 4.088A pdb=" N PHE B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 4.420A pdb=" N ASN B 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 376 through 394 Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 410 through 414 removed outlier: 4.281A pdb=" N ILE B 413 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 424 through 432 removed outlier: 4.204A pdb=" N LEU B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 474 through 483 removed outlier: 4.553A pdb=" N LYS B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.833A pdb=" N VAL B 518 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.728A pdb=" N TYR C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 155 " --> pdb=" O GLY C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 186 removed outlier: 4.100A pdb=" N HIS C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.645A pdb=" N GLN C 190 " --> pdb=" O PRO C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.434A pdb=" N ASP C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 232 through 249 removed outlier: 3.598A pdb=" N GLY C 236 " --> pdb=" O THR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 257 Processing helix chain 'C' and resid 260 through 273 removed outlier: 4.097A pdb=" N CYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.647A pdb=" N SER C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE C 296 " --> pdb=" O ASN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 removed outlier: 3.600A pdb=" N TRP C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 337 removed outlier: 3.753A pdb=" N PHE C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 346 removed outlier: 3.545A pdb=" N ASN C 345 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 373 Processing helix chain 'C' and resid 376 through 394 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 411 through 414 removed outlier: 3.727A pdb=" N ASP C 414 " --> pdb=" O THR C 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 414' Processing helix chain 'C' and resid 415 through 421 removed outlier: 4.148A pdb=" N LYS C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 432 removed outlier: 4.264A pdb=" N LEU C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 438 through 450 Processing helix chain 'C' and resid 469 through 473 removed outlier: 3.927A pdb=" N TYR C 473 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 removed outlier: 4.398A pdb=" N LYS C 478 " --> pdb=" O GLU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 576 removed outlier: 3.708A pdb=" N TYR C 568 " --> pdb=" O ALA C 564 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.818A pdb=" N TYR D 154 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 186 removed outlier: 3.935A pdb=" N HIS D 167 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 214 through 221 removed outlier: 4.446A pdb=" N ASP D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 232 through 248 removed outlier: 3.604A pdb=" N GLY D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 260 through 273 removed outlier: 4.312A pdb=" N CYS D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 3.590A pdb=" N SER D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 298 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE D 300 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 324 removed outlier: 4.354A pdb=" N ALA D 317 " --> pdb=" O TRP D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 removed outlier: 4.277A pdb=" N PHE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 Processing helix chain 'D' and resid 355 through 373 Processing helix chain 'D' and resid 376 through 393 Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 410 through 414 removed outlier: 4.063A pdb=" N ILE D 413 " --> pdb=" O SER D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 421 removed outlier: 3.846A pdb=" N LYS D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 432 removed outlier: 4.340A pdb=" N LEU D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 438 through 451 removed outlier: 4.136A pdb=" N ILE D 444 " --> pdb=" O ASP D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 474 removed outlier: 4.415A pdb=" N GLU D 474 " --> pdb=" O GLU D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 558 through 577 removed outlier: 3.512A pdb=" N ARG D 576 " --> pdb=" O TRP D 572 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.524A pdb=" N LYS A 116 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 343 removed outlier: 3.524A pdb=" N CYS A 341 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 348 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 119 Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 340 removed outlier: 8.855A pdb=" N TYR B 521 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA B 351 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 460 removed outlier: 7.107A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 118 Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 341 removed outlier: 4.461A pdb=" N ARG C 339 " --> pdb=" O CYS C 350 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS C 350 " --> pdb=" O ARG C 339 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 399 through 400 Processing sheet with id=AB3, first strand: chain 'C' and resid 455 through 460 removed outlier: 3.562A pdb=" N CYS C 554 " --> pdb=" O LYS C 455 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 457 " --> pdb=" O VAL C 552 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL C 552 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU C 459 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE C 550 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 119 removed outlier: 3.524A pdb=" N LYS D 116 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 338 through 341 removed outlier: 8.305A pdb=" N TYR D 521 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 351 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 399 through 400 Processing sheet with id=AB7, first strand: chain 'D' and resid 455 through 459 removed outlier: 7.177A pdb=" N VAL D 552 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU D 459 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE D 550 " --> pdb=" O GLU D 459 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 499 " --> pdb=" O TYR D 553 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1854 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.44 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.21), residues: 1737 helix: 1.54 (0.19), residues: 864 sheet: 1.89 (0.56), residues: 94 loop : -0.69 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 528 TYR 0.023 0.001 TYR C 315 PHE 0.010 0.001 PHE B 569 TRP 0.012 0.001 TRP C 572 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00265 (14806) covalent geometry : angle 0.61482 (20090) SS BOND : bond 0.00105 ( 3) SS BOND : angle 1.35585 ( 6) hydrogen bonds : bond 0.19400 ( 686) hydrogen bonds : angle 5.64810 ( 1854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.6968 (tt) cc_final: 0.6689 (tp) REVERT: B 416 MET cc_start: 0.7630 (mmt) cc_final: 0.7212 (mmm) REVERT: D 385 MET cc_start: 0.8576 (mtp) cc_final: 0.8312 (mtm) outliers start: 0 outliers final: 2 residues processed: 403 average time/residue: 0.6381 time to fit residues: 280.4834 Evaluate side-chains 199 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 327 ASN B 370 HIS C 303 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN D 163 ASN D 327 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.180064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149053 restraints weight = 16530.918| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.90 r_work: 0.3509 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14809 Z= 0.246 Angle : 0.777 11.571 20096 Z= 0.403 Chirality : 0.052 0.209 2141 Planarity : 0.006 0.061 2542 Dihedral : 14.810 156.172 2168 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.62 % Allowed : 11.94 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.20), residues: 1737 helix: 0.66 (0.18), residues: 888 sheet: 1.44 (0.52), residues: 114 loop : -0.82 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 528 TYR 0.041 0.003 TYR B 315 PHE 0.022 0.002 PHE A 213 TRP 0.016 0.002 TRP C 572 HIS 0.013 0.003 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00561 (14806) covalent geometry : angle 0.77552 (20090) SS BOND : bond 0.00648 ( 3) SS BOND : angle 3.08222 ( 6) hydrogen bonds : bond 0.06684 ( 686) hydrogen bonds : angle 4.64511 ( 1854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 0.448 Fit side-chains REVERT: A 239 MET cc_start: 0.7418 (mtm) cc_final: 0.7197 (mtm) REVERT: A 294 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6854 (mtmm) REVERT: A 366 ARG cc_start: 0.7638 (ttm170) cc_final: 0.7433 (ttp-170) REVERT: A 375 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7836 (mt0) REVERT: A 429 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: A 551 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.5359 (mpt180) REVERT: A 555 LYS cc_start: 0.6902 (tmtt) cc_final: 0.6628 (mtpt) REVERT: B 288 LYS cc_start: 0.7519 (tppt) cc_final: 0.7218 (tmtt) REVERT: B 299 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7392 (mp0) REVERT: B 472 ASP cc_start: 0.7108 (t70) cc_final: 0.6543 (t0) REVERT: B 505 MET cc_start: 0.8281 (mtm) cc_final: 0.8058 (mtp) REVERT: B 539 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7290 (mt0) REVERT: B 556 LYS cc_start: 0.7392 (mmtm) cc_final: 0.6515 (mttt) REVERT: C 299 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6692 (pt0) REVERT: C 355 GLU cc_start: 0.4937 (mm-30) cc_final: 0.4162 (mp0) REVERT: C 392 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7954 (ttmm) REVERT: C 426 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.7084 (mm) REVERT: D 148 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8820 (mmtm) REVERT: D 255 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7344 (pt0) REVERT: D 337 PHE cc_start: 0.8385 (m-80) cc_final: 0.8149 (m-80) REVERT: D 340 VAL cc_start: 0.8408 (m) cc_final: 0.8110 (t) REVERT: D 408 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7587 (mtp180) REVERT: D 439 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7483 (mtpp) REVERT: D 447 GLN cc_start: 0.8417 (tt0) cc_final: 0.8172 (tt0) REVERT: D 470 ARG cc_start: 0.7279 (mmm160) cc_final: 0.6569 (tpt170) REVERT: D 472 ASP cc_start: 0.7049 (t0) cc_final: 0.6844 (t0) REVERT: D 505 MET cc_start: 0.8068 (mmm) cc_final: 0.7775 (mmm) REVERT: D 511 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7071 (mm-30) REVERT: D 556 LYS cc_start: 0.7650 (mtmt) cc_final: 0.7323 (mptp) outliers start: 53 outliers final: 19 residues processed: 255 average time/residue: 0.6783 time to fit residues: 188.0287 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 : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 392 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 519 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 93 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 248 ASN C 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.180653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149022 restraints weight = 23657.706| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.87 r_work: 0.3451 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14809 Z= 0.142 Angle : 0.590 8.471 20096 Z= 0.306 Chirality : 0.045 0.168 2141 Planarity : 0.004 0.047 2542 Dihedral : 13.558 148.005 2164 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.95 % Allowed : 14.35 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.20), residues: 1737 helix: 1.04 (0.18), residues: 884 sheet: 1.86 (0.57), residues: 94 loop : -0.88 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 566 TYR 0.033 0.002 TYR B 315 PHE 0.020 0.001 PHE C 334 TRP 0.011 0.001 TRP C 572 HIS 0.007 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00324 (14806) covalent geometry : angle 0.58932 (20090) SS BOND : bond 0.00906 ( 3) SS BOND : angle 1.65696 ( 6) hydrogen bonds : bond 0.04880 ( 686) hydrogen bonds : angle 4.27565 ( 1854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.513 Fit side-chains REVERT: A 299 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6928 (tt0) REVERT: A 557 VAL cc_start: 0.6006 (OUTLIER) cc_final: 0.5801 (m) REVERT: B 299 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7226 (mp0) REVERT: B 472 ASP cc_start: 0.7036 (t70) cc_final: 0.6506 (t0) REVERT: B 505 MET cc_start: 0.8124 (mtm) cc_final: 0.7874 (mtp) REVERT: B 539 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7313 (mt0) REVERT: B 556 LYS cc_start: 0.7399 (mmtm) cc_final: 0.6968 (mmtt) REVERT: B 571 GLN cc_start: 0.7726 (mm110) cc_final: 0.7396 (tm-30) REVERT: C 299 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6712 (tt0) REVERT: C 355 GLU cc_start: 0.5198 (mm-30) cc_final: 0.4958 (mm-30) REVERT: C 429 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: D 429 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: D 447 GLN cc_start: 0.8214 (tt0) cc_final: 0.7926 (tt0) REVERT: D 470 ARG cc_start: 0.7276 (mmm160) cc_final: 0.6656 (tpt170) REVERT: D 472 ASP cc_start: 0.6896 (t0) cc_final: 0.6656 (t0) REVERT: D 556 LYS cc_start: 0.7770 (mtmt) cc_final: 0.7485 (mptp) REVERT: D 563 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.5644 (t80) outliers start: 43 outliers final: 17 residues processed: 214 average time/residue: 0.5910 time to fit residues: 138.6149 Evaluate side-chains 181 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 557 VAL 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 C residue 127 GLU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 548 GLN Chi-restraints excluded: chain D residue 563 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 116 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- 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 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.174322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142955 restraints weight = 29285.668| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.54 r_work: 0.3358 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14809 Z= 0.219 Angle : 0.699 9.352 20096 Z= 0.361 Chirality : 0.049 0.213 2141 Planarity : 0.005 0.052 2542 Dihedral : 13.841 150.737 2164 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.69 % Allowed : 15.49 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.20), residues: 1737 helix: 0.68 (0.18), residues: 884 sheet: 1.58 (0.56), residues: 94 loop : -1.07 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 348 TYR 0.034 0.002 TYR B 315 PHE 0.016 0.002 PHE A 213 TRP 0.015 0.001 TRP C 572 HIS 0.009 0.002 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00524 (14806) covalent geometry : angle 0.69831 (20090) SS BOND : bond 0.00446 ( 3) SS BOND : angle 2.27878 ( 6) hydrogen bonds : bond 0.06596 ( 686) hydrogen bonds : angle 4.54908 ( 1854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7681 (ptpp) cc_final: 0.6801 (tppt) REVERT: A 299 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7061 (tt0) REVERT: A 332 LYS cc_start: 0.7195 (mmtt) cc_final: 0.6728 (mmtm) REVERT: A 366 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7457 (ttp-170) REVERT: A 551 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.5069 (mtt180) REVERT: A 557 VAL cc_start: 0.6389 (OUTLIER) cc_final: 0.6171 (m) REVERT: B 229 VAL cc_start: 0.7768 (p) cc_final: 0.7283 (m) REVERT: B 288 LYS cc_start: 0.7778 (tmmt) cc_final: 0.7541 (mmtm) REVERT: B 299 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7477 (mp0) REVERT: B 340 VAL cc_start: 0.7892 (m) cc_final: 0.7553 (t) REVERT: B 472 ASP cc_start: 0.7020 (t70) cc_final: 0.6444 (t0) REVERT: B 505 MET cc_start: 0.8138 (mtm) cc_final: 0.7885 (mtp) REVERT: B 511 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7003 (mt-10) REVERT: B 539 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7577 (mt0) REVERT: B 556 LYS cc_start: 0.7293 (mmtm) cc_final: 0.6365 (mttt) REVERT: B 571 GLN cc_start: 0.7635 (mm110) cc_final: 0.7402 (tm-30) REVERT: B 576 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7138 (tpp80) REVERT: C 299 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6818 (tt0) REVERT: C 355 GLU cc_start: 0.5592 (mm-30) cc_final: 0.5261 (mm-30) REVERT: C 453 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7503 (mt) REVERT: C 551 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.5446 (mpt180) REVERT: D 285 TRP cc_start: 0.6632 (OUTLIER) cc_final: 0.5405 (t60) REVERT: D 429 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: D 439 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7638 (mtpp) REVERT: D 455 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8144 (mmtm) REVERT: D 470 ARG cc_start: 0.7318 (mmm160) cc_final: 0.6578 (tpt170) REVERT: D 472 ASP cc_start: 0.7028 (t0) cc_final: 0.6793 (t0) REVERT: D 501 ASP cc_start: 0.7854 (t0) cc_final: 0.7476 (t70) outliers start: 54 outliers final: 28 residues processed: 226 average time/residue: 0.6508 time to fit residues: 160.9164 Evaluate side-chains 192 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 455 LYS Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 146 TYR 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 478 LYS Chi-restraints excluded: chain B residue 576 ARG Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 440 ASP 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 180 HIS Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 285 TRP Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 439 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 C 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.177296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.146333 restraints weight = 20119.886| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.73 r_work: 0.3414 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14809 Z= 0.138 Angle : 0.588 9.811 20096 Z= 0.304 Chirality : 0.045 0.159 2141 Planarity : 0.004 0.041 2542 Dihedral : 12.992 147.168 2164 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.82 % Allowed : 17.51 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.20), residues: 1737 helix: 1.17 (0.18), residues: 860 sheet: 1.77 (0.55), residues: 94 loop : -0.96 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 305 TYR 0.028 0.001 TYR B 315 PHE 0.023 0.001 PHE C 334 TRP 0.010 0.001 TRP C 572 HIS 0.006 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00314 (14806) covalent geometry : angle 0.58799 (20090) SS BOND : bond 0.00184 ( 3) SS BOND : angle 1.39421 ( 6) hydrogen bonds : bond 0.04681 ( 686) hydrogen bonds : angle 4.24017 ( 1854) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7639 (ptpp) cc_final: 0.6745 (tppt) REVERT: A 299 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6910 (tt0) REVERT: A 332 LYS cc_start: 0.7300 (mmtt) cc_final: 0.6858 (mmtm) REVERT: A 366 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7560 (ttp-170) REVERT: A 457 VAL cc_start: 0.7710 (t) cc_final: 0.7333 (t) REVERT: A 551 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.5225 (mtt180) REVERT: B 229 VAL cc_start: 0.7776 (p) cc_final: 0.7254 (m) REVERT: B 288 LYS cc_start: 0.7699 (tmmt) cc_final: 0.7494 (mmtm) REVERT: B 299 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7428 (mt-10) REVERT: B 455 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7540 (mmtm) REVERT: B 472 ASP cc_start: 0.7094 (t70) cc_final: 0.6490 (t0) REVERT: B 505 MET cc_start: 0.8224 (mtm) cc_final: 0.7997 (mtp) REVERT: B 511 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7033 (mt-10) REVERT: B 539 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7607 (mt0) REVERT: B 556 LYS cc_start: 0.7215 (mmtm) cc_final: 0.6259 (mtpt) REVERT: C 299 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6923 (tt0) REVERT: C 355 GLU cc_start: 0.5631 (mm-30) cc_final: 0.5178 (mm-30) REVERT: D 271 GLN cc_start: 0.8585 (tt0) cc_final: 0.8318 (mt0) REVERT: D 285 TRP cc_start: 0.6671 (OUTLIER) cc_final: 0.5402 (t60) REVERT: D 340 VAL cc_start: 0.8184 (m) cc_final: 0.7805 (t) REVERT: D 429 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: D 470 ARG cc_start: 0.7314 (mmm160) cc_final: 0.6390 (tpt170) REVERT: D 472 ASP cc_start: 0.7129 (t0) cc_final: 0.6886 (t0) REVERT: D 501 ASP cc_start: 0.8097 (t0) cc_final: 0.7713 (t70) REVERT: D 556 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7865 (mtpt) outliers start: 41 outliers final: 21 residues processed: 206 average time/residue: 0.6595 time to fit residues: 148.2367 Evaluate side-chains 180 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain 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 548 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 169 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 328 ASN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 510 GLN D 328 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.178746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148683 restraints weight = 18838.269| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.69 r_work: 0.3485 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14809 Z= 0.125 Angle : 0.571 7.791 20096 Z= 0.294 Chirality : 0.044 0.152 2141 Planarity : 0.004 0.040 2542 Dihedral : 12.484 145.195 2164 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.09 % Allowed : 17.64 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.20), residues: 1737 helix: 1.32 (0.19), residues: 862 sheet: 1.81 (0.54), residues: 94 loop : -0.82 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 305 TYR 0.027 0.001 TYR B 315 PHE 0.011 0.001 PHE B 165 TRP 0.009 0.001 TRP C 572 HIS 0.006 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00280 (14806) covalent geometry : angle 0.57037 (20090) SS BOND : bond 0.00065 ( 3) SS BOND : angle 1.30677 ( 6) hydrogen bonds : bond 0.04407 ( 686) hydrogen bonds : angle 4.12587 ( 1854) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7594 (ptpp) cc_final: 0.6798 (tppt) REVERT: A 242 GLU cc_start: 0.8688 (tp30) cc_final: 0.8454 (mm-30) REVERT: A 299 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6958 (tt0) REVERT: A 332 LYS cc_start: 0.7307 (mmtt) cc_final: 0.6927 (mmtm) REVERT: A 366 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7536 (ttp-170) REVERT: A 457 VAL cc_start: 0.7233 (t) cc_final: 0.6999 (t) REVERT: B 299 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7299 (mt-10) REVERT: B 455 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7597 (mmtm) REVERT: B 472 ASP cc_start: 0.7070 (t70) cc_final: 0.6487 (t0) REVERT: B 478 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7557 (mppt) REVERT: B 505 MET cc_start: 0.8187 (mtm) cc_final: 0.7956 (mtp) REVERT: B 511 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7000 (mt-10) REVERT: B 539 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7644 (mt0) REVERT: B 556 LYS cc_start: 0.6987 (mmtm) cc_final: 0.6098 (mtpt) REVERT: C 299 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6935 (tt0) REVERT: C 355 GLU cc_start: 0.5958 (mm-30) cc_final: 0.5704 (mm-30) REVERT: C 429 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: D 271 GLN cc_start: 0.8559 (tt0) cc_final: 0.8275 (mt0) REVERT: D 285 TRP cc_start: 0.6629 (OUTLIER) cc_final: 0.5376 (t60) REVERT: D 340 VAL cc_start: 0.8176 (m) cc_final: 0.7841 (t) REVERT: D 470 ARG cc_start: 0.7263 (mmm160) cc_final: 0.6376 (tpt170) REVERT: D 472 ASP cc_start: 0.7097 (t0) cc_final: 0.6891 (t0) REVERT: D 501 ASP cc_start: 0.8018 (t0) cc_final: 0.7643 (t70) outliers start: 45 outliers final: 26 residues processed: 208 average time/residue: 0.6792 time to fit residues: 154.1531 Evaluate side-chains 181 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain B residue 262 GLU 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 478 LYS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 285 TRP Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 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 7 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 143 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.174723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144649 restraints weight = 18756.182| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.56 r_work: 0.3414 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14809 Z= 0.186 Angle : 0.643 9.659 20096 Z= 0.331 Chirality : 0.047 0.175 2141 Planarity : 0.005 0.040 2542 Dihedral : 12.726 146.626 2164 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.22 % Allowed : 18.18 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.20), residues: 1737 helix: 1.10 (0.18), residues: 864 sheet: 1.72 (0.55), residues: 94 loop : -0.89 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 352 TYR 0.029 0.002 TYR B 315 PHE 0.021 0.002 PHE C 334 TRP 0.011 0.001 TRP C 572 HIS 0.008 0.002 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00444 (14806) covalent geometry : angle 0.64191 (20090) SS BOND : bond 0.00232 ( 3) SS BOND : angle 1.75901 ( 6) hydrogen bonds : bond 0.05626 ( 686) hydrogen bonds : angle 4.29643 ( 1854) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7517 (mp0) cc_final: 0.7253 (mm-30) REVERT: A 230 LYS cc_start: 0.7695 (ptpp) cc_final: 0.6892 (tppt) REVERT: A 242 GLU cc_start: 0.8728 (tp30) cc_final: 0.8480 (mm-30) REVERT: A 299 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6882 (tt0) REVERT: A 332 LYS cc_start: 0.7367 (mmtt) cc_final: 0.6973 (mmtm) REVERT: A 339 ARG cc_start: 0.7041 (ttt90) cc_final: 0.6214 (ttm-80) REVERT: A 360 TYR cc_start: 0.6127 (m-10) cc_final: 0.5708 (t80) REVERT: A 366 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7578 (ttp-170) REVERT: A 455 LYS cc_start: 0.6471 (OUTLIER) cc_final: 0.6150 (mptp) REVERT: A 551 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.5426 (mtt180) REVERT: B 299 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7467 (mt-10) REVERT: B 455 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7559 (mmtm) REVERT: B 472 ASP cc_start: 0.7107 (t70) cc_final: 0.6508 (t0) REVERT: B 478 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7510 (mtpt) REVERT: B 505 MET cc_start: 0.8214 (mtm) cc_final: 0.7984 (mtp) REVERT: B 511 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6981 (mt-10) REVERT: B 556 LYS cc_start: 0.6948 (mmtm) cc_final: 0.6495 (mmtt) REVERT: C 355 GLU cc_start: 0.6160 (mm-30) cc_final: 0.5932 (mm-30) REVERT: C 453 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7546 (mt) REVERT: C 551 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.5521 (mpt180) REVERT: D 134 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7944 (mmm-85) REVERT: D 271 GLN cc_start: 0.8528 (tt0) cc_final: 0.8239 (mt0) REVERT: D 285 TRP cc_start: 0.6732 (OUTLIER) cc_final: 0.5408 (t60) REVERT: D 340 VAL cc_start: 0.8323 (m) cc_final: 0.7891 (t) REVERT: D 429 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: D 455 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7989 (mmtm) REVERT: D 470 ARG cc_start: 0.7310 (mmm160) cc_final: 0.6387 (tpt170) REVERT: D 472 ASP cc_start: 0.7099 (t0) cc_final: 0.6894 (t0) REVERT: D 501 ASP cc_start: 0.8132 (t0) cc_final: 0.7609 (t70) outliers start: 47 outliers final: 32 residues processed: 204 average time/residue: 0.6900 time to fit residues: 153.4492 Evaluate side-chains 192 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 262 GLU 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 449 GLU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 478 LYS 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 290 ARG 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 134 ARG Chi-restraints excluded: chain D residue 146 TYR 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 548 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 144 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 123 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 171 optimal weight: 0.5980 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 306 ASN B 510 GLN C 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.177100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146946 restraints weight = 20038.790| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.67 r_work: 0.3464 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.003 0.034 14809 Z= 0.126 Angle : 0.574 8.750 20096 Z= 0.295 Chirality : 0.044 0.154 2141 Planarity : 0.004 0.039 2542 Dihedral : 12.137 145.459 2164 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.48 % Allowed : 19.85 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.20), residues: 1737 helix: 1.31 (0.19), residues: 862 sheet: 1.80 (0.55), residues: 94 loop : -0.78 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 352 TYR 0.026 0.001 TYR B 315 PHE 0.011 0.001 PHE B 165 TRP 0.009 0.001 TRP C 572 HIS 0.006 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00283 (14806) covalent geometry : angle 0.57393 (20090) SS BOND : bond 0.00096 ( 3) SS BOND : angle 1.25286 ( 6) hydrogen bonds : bond 0.04398 ( 686) hydrogen bonds : angle 4.12421 ( 1854) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7612 (mp0) cc_final: 0.7312 (mm-30) REVERT: A 230 LYS cc_start: 0.7668 (ptpp) cc_final: 0.6846 (tppt) REVERT: A 242 GLU cc_start: 0.8698 (tp30) cc_final: 0.8459 (mm-30) REVERT: A 299 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6850 (tt0) REVERT: A 332 LYS cc_start: 0.7357 (mmtt) cc_final: 0.6989 (mmtm) REVERT: A 339 ARG cc_start: 0.6985 (ttt90) cc_final: 0.6323 (ttm-80) REVERT: A 366 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7540 (ttp-170) REVERT: A 455 LYS cc_start: 0.6484 (OUTLIER) cc_final: 0.6158 (mptp) REVERT: A 456 TYR cc_start: 0.7044 (t80) cc_final: 0.6772 (t80) REVERT: B 299 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 455 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7574 (mmtm) REVERT: B 472 ASP cc_start: 0.7083 (t70) cc_final: 0.6462 (t0) REVERT: B 505 MET cc_start: 0.8199 (mtm) cc_final: 0.7965 (mtp) REVERT: B 511 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 556 LYS cc_start: 0.6912 (mmtm) cc_final: 0.6441 (mmtt) REVERT: C 353 ASP cc_start: 0.7140 (p0) cc_final: 0.6662 (m-30) REVERT: C 429 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: C 551 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.5519 (mpt180) REVERT: D 271 GLN cc_start: 0.8519 (tt0) cc_final: 0.8241 (mt0) REVERT: D 285 TRP cc_start: 0.6681 (OUTLIER) cc_final: 0.5340 (t60) REVERT: D 340 VAL cc_start: 0.8197 (m) cc_final: 0.7864 (t) REVERT: D 429 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: D 470 ARG cc_start: 0.7282 (mmm160) cc_final: 0.6341 (tpt170) REVERT: D 501 ASP cc_start: 0.8101 (t0) cc_final: 0.7735 (t70) outliers start: 36 outliers final: 25 residues processed: 197 average time/residue: 0.6531 time to fit residues: 140.4017 Evaluate side-chains 187 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 262 GLU 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 449 GLU 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 290 ARG 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 400 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 506 ASP Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 548 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 99 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 326 GLN B 510 GLN C 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.148062 restraints weight = 18946.691| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.69 r_work: 0.3485 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14809 Z= 0.113 Angle : 0.563 8.461 20096 Z= 0.288 Chirality : 0.044 0.165 2141 Planarity : 0.004 0.039 2542 Dihedral : 11.743 144.071 2164 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.15 % Allowed : 20.32 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.21), residues: 1737 helix: 1.44 (0.19), residues: 862 sheet: 1.91 (0.55), residues: 94 loop : -0.68 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 352 TYR 0.025 0.001 TYR B 315 PHE 0.023 0.001 PHE C 334 TRP 0.008 0.001 TRP C 572 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00249 (14806) covalent geometry : angle 0.56267 (20090) SS BOND : bond 0.00096 ( 3) SS BOND : angle 1.11393 ( 6) hydrogen bonds : bond 0.04085 ( 686) hydrogen bonds : angle 4.04417 ( 1854) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7565 (mp0) cc_final: 0.7298 (mm-30) REVERT: A 230 LYS cc_start: 0.7673 (ptpp) cc_final: 0.6857 (tppt) REVERT: A 242 GLU cc_start: 0.8698 (tp30) cc_final: 0.8454 (mm-30) REVERT: A 299 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6837 (tt0) REVERT: A 332 LYS cc_start: 0.7299 (mmtt) cc_final: 0.6994 (mmtm) REVERT: A 366 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7558 (ttp-170) REVERT: A 455 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6195 (mptp) REVERT: A 456 TYR cc_start: 0.7035 (t80) cc_final: 0.6804 (t80) REVERT: B 299 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7310 (mt-10) REVERT: B 455 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7600 (mmtm) REVERT: B 472 ASP cc_start: 0.7083 (t70) cc_final: 0.6326 (t0) REVERT: B 505 MET cc_start: 0.8193 (mtm) cc_final: 0.7966 (mtp) REVERT: B 511 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7231 (mt-10) REVERT: B 539 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7643 (mt0) REVERT: B 556 LYS cc_start: 0.6932 (mmtm) cc_final: 0.6448 (mmtt) REVERT: C 299 GLU cc_start: 0.7658 (mt-10) cc_final: 0.6975 (tt0) REVERT: C 353 ASP cc_start: 0.7111 (p0) cc_final: 0.6657 (m-30) REVERT: C 355 GLU cc_start: 0.6035 (mm-30) cc_final: 0.5772 (mm-30) REVERT: C 429 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: C 551 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.5502 (mpt180) REVERT: D 115 MET cc_start: 0.7441 (tpt) cc_final: 0.7146 (tpt) REVERT: D 271 GLN cc_start: 0.8524 (tt0) cc_final: 0.8239 (mt0) REVERT: D 285 TRP cc_start: 0.6727 (OUTLIER) cc_final: 0.5449 (t60) REVERT: D 328 ASN cc_start: 0.7480 (p0) cc_final: 0.6757 (p0) REVERT: D 340 VAL cc_start: 0.8080 (m) cc_final: 0.7818 (t) REVERT: D 429 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: D 470 ARG cc_start: 0.7090 (mmm160) cc_final: 0.6100 (tpt170) REVERT: D 501 ASP cc_start: 0.8089 (t0) cc_final: 0.7730 (t70) outliers start: 31 outliers final: 18 residues processed: 195 average time/residue: 0.6775 time to fit residues: 144.3269 Evaluate side-chains 181 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 455 LYS Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 551 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 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 33 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 76 optimal weight: 0.0570 chunk 97 optimal weight: 0.0980 chunk 37 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.179538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149266 restraints weight = 25467.496| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.04 r_work: 0.3461 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14809 Z= 0.106 Angle : 0.550 8.720 20096 Z= 0.282 Chirality : 0.043 0.143 2141 Planarity : 0.004 0.039 2542 Dihedral : 11.203 140.998 2164 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.61 % Allowed : 20.86 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.21), residues: 1737 helix: 1.59 (0.19), residues: 862 sheet: 2.08 (0.55), residues: 94 loop : -0.58 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 352 TYR 0.023 0.001 TYR B 315 PHE 0.012 0.001 PHE C 363 TRP 0.007 0.001 TRP C 572 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00225 (14806) covalent geometry : angle 0.54966 (20090) SS BOND : bond 0.00172 ( 3) SS BOND : angle 1.11820 ( 6) hydrogen bonds : bond 0.03646 ( 686) hydrogen bonds : angle 3.98221 ( 1854) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7379 (mp0) cc_final: 0.7153 (mm-30) REVERT: A 230 LYS cc_start: 0.7601 (ptpp) cc_final: 0.6855 (tppt) REVERT: A 242 GLU cc_start: 0.8579 (tp30) cc_final: 0.8346 (mm-30) REVERT: A 299 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6718 (tt0) REVERT: A 332 LYS cc_start: 0.7325 (mmtt) cc_final: 0.7062 (mmtm) REVERT: A 366 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7405 (ttt180) REVERT: A 455 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.6180 (mptp) REVERT: A 456 TYR cc_start: 0.7002 (t80) cc_final: 0.6776 (t80) REVERT: B 326 GLN cc_start: 0.7689 (mt0) cc_final: 0.6879 (mp10) REVERT: B 472 ASP cc_start: 0.6863 (t70) cc_final: 0.6272 (t0) REVERT: B 505 MET cc_start: 0.8052 (mtm) cc_final: 0.7818 (mtp) REVERT: B 511 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7021 (mt-10) REVERT: B 539 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7592 (mt0) REVERT: B 556 LYS cc_start: 0.6874 (mmtm) cc_final: 0.6410 (mmtt) REVERT: C 299 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6835 (tt0) REVERT: C 353 ASP cc_start: 0.7115 (p0) cc_final: 0.6752 (m-30) REVERT: C 551 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.5455 (mpt180) REVERT: D 115 MET cc_start: 0.7069 (tpt) cc_final: 0.6791 (tpt) REVERT: D 470 ARG cc_start: 0.7026 (mmm160) cc_final: 0.6100 (tpt170) REVERT: D 501 ASP cc_start: 0.7675 (t0) cc_final: 0.7303 (t70) outliers start: 23 outliers final: 14 residues processed: 187 average time/residue: 0.6844 time to fit residues: 139.6306 Evaluate side-chains 169 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 455 LYS 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 127 GLU 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 290 ARG Chi-restraints excluded: chain C residue 551 ARG Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 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 23 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 C 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.170087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.144948 restraints weight = 20963.535| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.58 r_work: 0.3414 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14809 Z= 0.191 Angle : 0.650 9.265 20096 Z= 0.334 Chirality : 0.047 0.192 2141 Planarity : 0.005 0.041 2542 Dihedral : 12.260 144.868 2164 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.74 % Allowed : 20.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.20), residues: 1737 helix: 1.20 (0.18), residues: 862 sheet: 1.71 (0.55), residues: 94 loop : -0.73 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 352 TYR 0.030 0.002 TYR B 315 PHE 0.013 0.002 PHE A 213 TRP 0.011 0.001 TRP C 572 HIS 0.009 0.002 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00459 (14806) covalent geometry : angle 0.64972 (20090) SS BOND : bond 0.00232 ( 3) SS BOND : angle 1.87140 ( 6) hydrogen bonds : bond 0.05748 ( 686) hydrogen bonds : angle 4.28309 ( 1854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5326.51 seconds wall clock time: 91 minutes 24.09 seconds (5484.09 seconds total)