Starting phenix.real_space_refine on Sat Oct 11 11:42:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxo_18734/10_2025/8qxo_18734_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxo_18734/10_2025/8qxo_18734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qxo_18734/10_2025/8qxo_18734_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxo_18734/10_2025/8qxo_18734_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qxo_18734/10_2025/8qxo_18734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxo_18734/10_2025/8qxo_18734.map" } resolution = 3.43 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= 0.006 sd= 0.139 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 24 5.49 5 Mg 2 5.21 5 S 76 5.16 5 C 9076 2.51 5 N 2479 2.21 5 O 2630 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: 14291 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3412 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 17, 'TRANS': 399} Chain breaks: 2 Chain: "B" Number of atoms: 3704 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 457, 3698 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 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: 457, 3698 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 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: 3778 Chain: "C" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3318 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 17, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 71 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': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3607 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 20, 'TRANS': 436} 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: 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: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 121 Unusual residues: {' FE': 1, 'DCP': 1, 'DTP': 2, 'GTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {' FE': 1, 'DCP': 1, 'GTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.32, per 1000 atoms: 0.30 Number of scatterers: 14291 At special positions: 0 Unit cell: (117.72, 95.92, 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 24 15.00 Mg 2 11.99 O 2630 8.00 N 2479 7.00 C 9076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 705.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 16 sheets defined 60.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 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 removed outlier: 3.637A pdb=" N ILE A 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.646A pdb=" N TYR A 154 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 186 removed outlier: 4.022A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 removed outlier: 3.777A pdb=" N GLN A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 215 through 226 removed outlier: 5.357A 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 247 Processing helix chain 'A' and resid 249 through 257 removed outlier: 4.585A pdb=" N VAL A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.794A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 309 through 324 removed outlier: 3.534A pdb=" N TRP A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 removed outlier: 3.839A 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 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 433 removed outlier: 4.066A 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 450 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.905A pdb=" N TYR A 473 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.243A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (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: 3.760A pdb=" N GLN A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 568 " --> pdb=" O ALA A 564 " (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 removed outlier: 3.529A pdb=" N ILE B 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.593A pdb=" N TYR B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 186 removed outlier: 4.168A pdb=" N HIS B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 205 removed outlier: 3.636A pdb=" N CYS B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 removed outlier: 4.342A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 4.047A pdb=" N LEU B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 249 removed outlier: 3.748A pdb=" N GLY B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 271 removed outlier: 4.140A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 5.486A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.963A pdb=" N TRP B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 removed outlier: 4.179A pdb=" N PHE B 334 " --> pdb=" O ASP B 330 " (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 415 through 421 removed outlier: 4.054A pdb=" N LYS B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 433 removed outlier: 3.887A 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: 4.539A pdb=" N LYS B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 558 through 576 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: 3.629A pdb=" N GLY C 153 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR C 155 " --> pdb=" O GLY C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 186 removed outlier: 4.102A pdb=" N HIS C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.751A 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: 3.843A 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 248 Processing helix chain 'C' and resid 250 through 257 Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.934A pdb=" N CYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 295 Processing helix chain 'C' and resid 296 through 300 removed outlier: 3.894A pdb=" N GLU C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 Processing helix chain 'C' and resid 330 through 337 removed outlier: 3.706A pdb=" N PHE C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 355 through 373 Processing helix chain 'C' and resid 376 through 393 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 Processing helix chain 'C' and resid 415 through 421 removed outlier: 3.528A pdb=" N TYR C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 432 removed outlier: 4.077A 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 Processing helix chain 'C' and resid 474 through 483 removed outlier: 4.255A pdb=" N LYS C 478 " --> pdb=" O GLU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 576 Processing helix chain 'D' and resid 129 through 137 removed outlier: 3.545A pdb=" N ASP D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 163 through 186 removed outlier: 4.097A pdb=" N HIS D 167 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 removed outlier: 3.654A pdb=" N GLN D 190 " --> pdb=" O PRO D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 190' Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 214 through 220 removed outlier: 4.342A pdb=" N ASP D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.825A pdb=" N LEU D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 249 removed outlier: 3.659A pdb=" N GLY D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 260 through 273 removed outlier: 4.025A pdb=" N CYS D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 6.043A pdb=" N PHE D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 298 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 300 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 324 removed outlier: 3.799A pdb=" N TRP D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 324 " --> pdb=" O CYS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 removed outlier: 4.278A pdb=" N PHE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) 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 409 through 414 removed outlier: 3.922A pdb=" N ILE D 413 " --> pdb=" O SER D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 421 removed outlier: 4.025A pdb=" N LYS D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 432 removed outlier: 4.269A 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 450 Processing helix chain 'D' and resid 474 through 483 removed outlier: 4.316A pdb=" N LYS D 478 " --> pdb=" O GLU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 558 through 575 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.509A pdb=" N LYS A 116 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 343 removed outlier: 3.562A pdb=" N ARG A 348 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 459 removed outlier: 3.793A pdb=" N LYS A 455 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 554 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A 552 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU A 459 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE A 550 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 549 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 503 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 551 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 119 removed outlier: 3.620A pdb=" N LYS B 116 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 342 removed outlier: 3.527A pdb=" N ARG B 348 " --> pdb=" O CYS B 341 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N TYR B 521 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA B 351 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS B 522 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG B 528 " --> pdb=" O CYS B 522 " (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 459 removed outlier: 7.307A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 547 " --> pdb=" O MET B 505 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET B 505 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 118 removed outlier: 3.587A pdb=" N LYS C 116 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 342 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 456 through 459 removed outlier: 7.382A pdb=" N VAL C 552 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLU C 459 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 7.486A 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: 4.191A pdb=" N LYS D 116 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 128 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 338 through 343 removed outlier: 3.529A pdb=" N ARG D 339 " --> pdb=" O CYS D 350 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 348 " --> pdb=" O CYS D 341 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYR D 521 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.415A 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 456 673 hydrogen bonds defined for protein. 1872 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: 2.26 Time building geometry restraints manager: 1.65 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: 4646 1.35 - 1.46: 3403 1.46 - 1.58: 6429 1.58 - 1.70: 38 1.70 - 1.82: 114 Bond restraints: 14630 Sorted by residual: bond pdb=" C4' DCP B 704 " pdb=" O4' DCP B 704 " ideal model delta sigma weight residual 1.444 1.411 0.033 1.00e-02 1.00e+04 1.09e+01 bond pdb=" O1A DCP B 704 " pdb=" PA DCP B 704 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.00e-02 1.00e+04 1.06e+01 bond pdb=" O1A DCP D 704 " pdb=" PA DCP D 704 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.00e-02 1.00e+04 1.06e+01 bond pdb=" C4 DCP D 704 " pdb=" C5 DCP D 704 " ideal model delta sigma weight residual 1.426 1.389 0.037 1.20e-02 6.94e+03 9.37e+00 bond pdb=" O1B DCP D 704 " pdb=" PB DCP D 704 " ideal model delta sigma weight residual 1.477 1.511 -0.034 1.10e-02 8.26e+03 9.30e+00 ... (remaining 14625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 19806 4.44 - 8.88: 29 8.88 - 13.33: 0 13.33 - 17.77: 2 17.77 - 22.21: 2 Bond angle restraints: 19839 Sorted by residual: angle pdb=" PB DCP B 704 " pdb=" O3B DCP B 704 " pdb=" PG DCP B 704 " ideal model delta sigma weight residual 139.87 117.66 22.21 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PB DCP D 704 " pdb=" O3B DCP D 704 " pdb=" PG DCP D 704 " ideal model delta sigma weight residual 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PA DCP B 704 " pdb=" O3A DCP B 704 " pdb=" PB DCP B 704 " ideal model delta sigma weight residual 136.83 119.97 16.86 1.00e+00 1.00e+00 2.84e+02 angle pdb=" PA DCP D 704 " pdb=" O3A DCP D 704 " pdb=" PB DCP D 704 " ideal model delta sigma weight residual 136.83 123.46 13.37 1.00e+00 1.00e+00 1.79e+02 angle pdb=" O2G DCP B 704 " pdb=" PG DCP B 704 " pdb=" O3B DCP B 704 " ideal model delta sigma weight residual 104.48 110.28 -5.80 1.14e+00 7.76e-01 2.61e+01 ... (remaining 19834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.02: 8499 34.02 - 68.04: 250 68.04 - 102.06: 28 102.06 - 136.08: 3 136.08 - 170.10: 1 Dihedral angle restraints: 8781 sinusoidal: 3678 harmonic: 5103 Sorted by residual: dihedral pdb=" O3A GTP B 702 " pdb=" O3B GTP B 702 " pdb=" PB GTP B 702 " pdb=" PG GTP B 702 " ideal model delta sinusoidal sigma weight residual 303.79 133.69 170.10 1 2.00e+01 2.50e-03 4.76e+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 260.87 137.39 123.49 1 2.00e+01 2.50e-03 3.72e+01 dihedral pdb=" C4' GTP D 701 " pdb=" C5' GTP D 701 " pdb=" O5' GTP D 701 " pdb=" PA GTP D 701 " ideal model delta sinusoidal sigma weight residual 260.87 143.18 117.69 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 8778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1719 0.049 - 0.098: 290 0.098 - 0.146: 104 0.146 - 0.195: 4 0.195 - 0.244: 4 Chirality restraints: 2121 Sorted by residual: chirality pdb=" C3' DTP B 701 " pdb=" C2' DTP B 701 " pdb=" C4' DTP B 701 " pdb=" O3' DTP B 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C3' DTP B 705 " pdb=" C2' DTP B 705 " pdb=" C4' DTP B 705 " pdb=" O3' DTP B 705 " both_signs ideal model delta sigma weight residual False -2.68 -2.91 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C4' DTP B 705 " pdb=" C3' DTP B 705 " pdb=" C5' DTP B 705 " pdb=" O4' DTP B 705 " both_signs ideal model delta sigma weight residual False -2.50 -2.73 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2118 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DCP B 704 " -0.353 2.00e-02 2.50e+03 2.21e-01 1.10e+03 pdb=" C2 DCP B 704 " 0.026 2.00e-02 2.50e+03 pdb=" C4 DCP B 704 " -0.087 2.00e-02 2.50e+03 pdb=" C5 DCP B 704 " 0.068 2.00e-02 2.50e+03 pdb=" C6 DCP B 704 " 0.289 2.00e-02 2.50e+03 pdb=" N1 DCP B 704 " 0.051 2.00e-02 2.50e+03 pdb=" N3 DCP B 704 " -0.325 2.00e-02 2.50e+03 pdb=" N4 DCP B 704 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DCP B 704 " 0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCP D 704 " -0.016 2.00e-02 2.50e+03 7.27e-02 1.19e+02 pdb=" C2 DCP D 704 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DCP D 704 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DCP D 704 " 0.113 2.00e-02 2.50e+03 pdb=" C6 DCP D 704 " -0.017 2.00e-02 2.50e+03 pdb=" N1 DCP D 704 " -0.068 2.00e-02 2.50e+03 pdb=" N3 DCP D 704 " -0.120 2.00e-02 2.50e+03 pdb=" N4 DCP D 704 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DCP D 704 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 129 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO D 130 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 130 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 130 " 0.025 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 65 2.39 - 3.02: 8446 3.02 - 3.64: 21287 3.64 - 4.27: 30083 4.27 - 4.90: 51022 Nonbonded interactions: 110903 Sorted by model distance: nonbonded pdb=" O3B GTP A 701 " pdb="MG MG A 703 " model vdw 1.759 2.170 nonbonded pdb=" O2A GTP A 701 " pdb="MG MG A 703 " model vdw 1.802 2.170 nonbonded pdb="MG MG C 802 " pdb=" O2A GTP D 701 " model vdw 1.933 2.170 nonbonded pdb=" OD1 ASP A 311 " pdb="FE FE A 702 " model vdw 1.990 2.260 nonbonded pdb="MG MG C 802 " pdb=" O3B GTP D 701 " model vdw 2.005 2.170 ... (remaining 110898 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 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 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 577)) 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 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 through 468 or (resid 469 and (name N or name CA or name C or name O or n \ ame 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 n \ ame 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 through 490 and (name N or name CA or name C or name O or name CB )) or res \ id 491 or (resid 492 and (name N or name CA or name C or name O or name CB )) or \ resid 493 through 506 or resid 547 through 577)) 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 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 (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 5 \ 77)) 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 436 o \ r resid 438 through 486 or (resid 487 through 490 and (name N or name CA or name \ C or name O or name CB )) or resid 491 through 506 or resid 547 through 577)) } 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=0.34 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.260 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 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 0.047 14630 Z= 0.155 Angle : 0.634 22.210 19839 Z= 0.406 Chirality : 0.043 0.244 2121 Planarity : 0.006 0.221 2525 Dihedral : 16.427 170.101 5505 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.95 % Favored : 96.93 % Rotamer: Outliers : 0.13 % Allowed : 9.31 % Favored : 90.56 % 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 (0.21), residues: 1728 helix: 1.31 (0.19), residues: 879 sheet: 1.45 (0.60), residues: 79 loop : -0.78 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 528 TYR 0.022 0.001 TYR A 315 PHE 0.011 0.001 PHE B 316 TRP 0.007 0.001 TRP B 285 HIS 0.006 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00275 (14630) covalent geometry : angle 0.63364 (19839) hydrogen bonds : bond 0.17883 ( 673) hydrogen bonds : angle 5.78419 ( 1872) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 0.551 Fit side-chains REVERT: A 367 ASN cc_start: 0.7164 (m-40) cc_final: 0.6800 (m-40) REVERT: A 433 SER cc_start: 0.8513 (t) cc_final: 0.8254 (t) REVERT: A 455 LYS cc_start: 0.5482 (tppt) cc_final: 0.5193 (tttp) REVERT: B 235 GLN cc_start: 0.8008 (mt0) cc_final: 0.7501 (tt0) REVERT: B 285 TRP cc_start: 0.6454 (t60) cc_final: 0.5743 (t60) REVERT: B 396 TYR cc_start: 0.7681 (m-80) cc_final: 0.7196 (m-80) REVERT: B 469 LYS cc_start: 0.7504 (mttt) cc_final: 0.6827 (mmmt) REVERT: B 505 MET cc_start: 0.7500 (ttp) cc_final: 0.7252 (ttm) REVERT: B 547 GLU cc_start: 0.7215 (pm20) cc_final: 0.4814 (tp30) REVERT: C 155 TYR cc_start: 0.8069 (m-80) cc_final: 0.7654 (m-80) REVERT: C 348 ARG cc_start: 0.7056 (mmt90) cc_final: 0.6358 (ttt-90) REVERT: D 120 ASP cc_start: 0.6834 (m-30) cc_final: 0.6561 (m-30) REVERT: D 133 VAL cc_start: 0.7074 (t) cc_final: 0.6862 (t) REVERT: D 239 MET cc_start: 0.8051 (mtm) cc_final: 0.7676 (mtp) REVERT: D 371 ARG cc_start: 0.8070 (ttp-110) cc_final: 0.7715 (ttp80) REVERT: D 506 ASP cc_start: 0.8737 (p0) cc_final: 0.8294 (p0) REVERT: D 528 ARG cc_start: 0.6990 (mtm110) cc_final: 0.6568 (ttm-80) REVERT: D 539 GLN cc_start: 0.7014 (mt0) cc_final: 0.6606 (mt0) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.1528 time to fit residues: 80.8693 Evaluate side-chains 189 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 517 HIS B 539 GLN C 367 ASN C 447 GLN C 548 GLN D 321 HIS D 571 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.182499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158231 restraints weight = 28959.251| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.94 r_work: 0.3555 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14630 Z= 0.156 Angle : 0.619 7.965 19839 Z= 0.316 Chirality : 0.048 0.249 2121 Planarity : 0.005 0.077 2525 Dihedral : 10.889 164.347 2095 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.47 % Favored : 96.41 % Rotamer: Outliers : 2.36 % Allowed : 14.36 % Favored : 83.28 % 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: 0.70 (0.21), residues: 1728 helix: 1.39 (0.18), residues: 864 sheet: 2.01 (0.58), residues: 84 loop : -0.76 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 576 TYR 0.031 0.002 TYR B 315 PHE 0.022 0.002 PHE D 141 TRP 0.012 0.002 TRP B 285 HIS 0.007 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00358 (14630) covalent geometry : angle 0.61856 (19839) hydrogen bonds : bond 0.04805 ( 673) hydrogen bonds : angle 4.47168 ( 1872) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.482 Fit side-chains REVERT: A 254 MET cc_start: 0.7601 (ttm) cc_final: 0.7287 (ttm) REVERT: A 367 ASN cc_start: 0.7934 (m-40) cc_final: 0.7669 (m-40) REVERT: A 435 ASP cc_start: 0.6936 (m-30) cc_final: 0.6727 (m-30) REVERT: B 438 LEU cc_start: 0.8427 (mt) cc_final: 0.8161 (mt) REVERT: B 469 LYS cc_start: 0.7445 (mttt) cc_final: 0.6767 (mmmt) REVERT: B 505 MET cc_start: 0.7911 (ttp) cc_final: 0.7594 (ttm) REVERT: B 547 GLU cc_start: 0.7455 (pm20) cc_final: 0.6186 (tp30) REVERT: C 287 TYR cc_start: 0.7447 (m-80) cc_final: 0.7126 (m-80) REVERT: C 374 TYR cc_start: 0.7601 (m-80) cc_final: 0.6371 (m-80) REVERT: C 455 LYS cc_start: 0.5450 (mttm) cc_final: 0.5182 (mttm) REVERT: D 239 MET cc_start: 0.9066 (mtm) cc_final: 0.8815 (mtp) REVERT: D 371 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.8011 (ttp80) REVERT: D 383 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: D 470 ARG cc_start: 0.7197 (tpt90) cc_final: 0.6897 (tpt170) outliers start: 34 outliers final: 20 residues processed: 228 average time/residue: 0.1494 time to fit residues: 47.5791 Evaluate side-chains 180 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 40 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 138 optimal weight: 0.0670 chunk 123 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 HIS B 210 HIS D 125 HIS D 539 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.176954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151589 restraints weight = 27348.199| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.96 r_work: 0.3517 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14630 Z= 0.133 Angle : 0.555 6.249 19839 Z= 0.282 Chirality : 0.045 0.150 2121 Planarity : 0.004 0.050 2525 Dihedral : 10.401 161.421 2095 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 2.09 % Allowed : 16.05 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.21), residues: 1728 helix: 1.45 (0.18), residues: 877 sheet: 2.21 (0.52), residues: 104 loop : -0.86 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 576 TYR 0.023 0.001 TYR B 315 PHE 0.020 0.001 PHE D 141 TRP 0.009 0.001 TRP B 313 HIS 0.008 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00307 (14630) covalent geometry : angle 0.55531 (19839) hydrogen bonds : bond 0.04319 ( 673) hydrogen bonds : angle 4.23360 ( 1872) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.346 Fit side-chains REVERT: A 367 ASN cc_start: 0.8011 (m-40) cc_final: 0.7724 (m-40) REVERT: B 271 GLN cc_start: 0.8521 (mt0) cc_final: 0.8245 (mt0) REVERT: B 469 LYS cc_start: 0.7642 (mttt) cc_final: 0.6901 (mmmt) REVERT: B 505 MET cc_start: 0.7883 (ttp) cc_final: 0.7614 (ttm) REVERT: B 547 GLU cc_start: 0.7917 (pm20) cc_final: 0.7445 (pt0) REVERT: C 287 TYR cc_start: 0.7640 (m-80) cc_final: 0.7335 (m-80) REVERT: C 374 TYR cc_start: 0.7717 (m-80) cc_final: 0.6601 (m-80) REVERT: C 424 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: C 497 ASP cc_start: 0.6591 (OUTLIER) cc_final: 0.6357 (t0) REVERT: C 555 LYS cc_start: 0.7745 (mmmm) cc_final: 0.7307 (mmtp) REVERT: D 571 GLN cc_start: 0.7768 (tp40) cc_final: 0.7562 (tp40) outliers start: 30 outliers final: 21 residues processed: 192 average time/residue: 0.1453 time to fit residues: 39.5371 Evaluate side-chains 178 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 120 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 117 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN B 571 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.160051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133469 restraints weight = 27708.223| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.86 r_work: 0.3369 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14630 Z= 0.206 Angle : 0.655 7.746 19839 Z= 0.335 Chirality : 0.049 0.176 2121 Planarity : 0.005 0.051 2525 Dihedral : 10.689 157.798 2095 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.51 % Allowed : 16.66 % Favored : 79.84 % 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: 0.52 (0.21), residues: 1728 helix: 1.26 (0.18), residues: 860 sheet: 2.05 (0.51), residues: 114 loop : -1.02 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 470 TYR 0.031 0.002 TYR B 315 PHE 0.030 0.002 PHE D 141 TRP 0.019 0.002 TRP B 313 HIS 0.008 0.002 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00499 (14630) covalent geometry : angle 0.65462 (19839) hydrogen bonds : bond 0.05730 ( 673) hydrogen bonds : angle 4.50754 ( 1872) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 224 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7286 (mp) REVERT: A 314 ASP cc_start: 0.8215 (t0) cc_final: 0.7744 (t0) REVERT: B 119 ASN cc_start: 0.8262 (t0) cc_final: 0.7963 (t0) REVERT: B 142 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: B 469 LYS cc_start: 0.7485 (mttt) cc_final: 0.6858 (mmmt) REVERT: B 547 GLU cc_start: 0.8212 (pm20) cc_final: 0.7979 (pt0) REVERT: C 235 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8305 (tm-30) REVERT: C 287 TYR cc_start: 0.7752 (m-80) cc_final: 0.7538 (m-80) REVERT: C 336 LYS cc_start: 0.6802 (tttt) cc_final: 0.6472 (tttt) REVERT: C 369 LEU cc_start: 0.8251 (tt) cc_final: 0.7967 (tp) REVERT: C 380 ASN cc_start: 0.7244 (OUTLIER) cc_final: 0.6953 (m-40) REVERT: C 385 MET cc_start: 0.8344 (mtp) cc_final: 0.8017 (mtp) REVERT: C 405 LYS cc_start: 0.7345 (tptp) cc_final: 0.7127 (mtmm) REVERT: C 424 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: C 555 LYS cc_start: 0.7989 (mmmm) cc_final: 0.7695 (mmtp) REVERT: D 182 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8644 (mp) REVERT: D 326 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7164 (mt0) REVERT: D 470 ARG cc_start: 0.7431 (tpt90) cc_final: 0.6920 (tpt170) REVERT: D 539 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7253 (mt0) outliers start: 51 outliers final: 25 residues processed: 207 average time/residue: 0.1615 time to fit residues: 46.0476 Evaluate side-chains 179 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 539 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 71 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 271 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN C 370 HIS ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN D 571 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.169666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145221 restraints weight = 18887.448| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.50 r_work: 0.3450 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14630 Z= 0.145 Angle : 0.560 6.422 19839 Z= 0.285 Chirality : 0.046 0.153 2121 Planarity : 0.004 0.050 2525 Dihedral : 10.381 156.202 2095 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.49 % Allowed : 18.81 % Favored : 78.69 % 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: 0.65 (0.21), residues: 1728 helix: 1.36 (0.18), residues: 873 sheet: 2.10 (0.51), residues: 114 loop : -0.98 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 470 TYR 0.024 0.002 TYR B 315 PHE 0.015 0.001 PHE D 141 TRP 0.010 0.001 TRP B 285 HIS 0.007 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00345 (14630) covalent geometry : angle 0.56028 (19839) hydrogen bonds : bond 0.04490 ( 673) hydrogen bonds : angle 4.23355 ( 1872) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 224 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7326 (mp) REVERT: A 346 GLU cc_start: 0.4147 (OUTLIER) cc_final: 0.3490 (pm20) REVERT: B 119 ASN cc_start: 0.8282 (t0) cc_final: 0.8030 (t0) REVERT: B 142 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7110 (mp10) REVERT: B 271 GLN cc_start: 0.8588 (mt0) cc_final: 0.8267 (mt0) REVERT: B 469 LYS cc_start: 0.7556 (mttt) cc_final: 0.7354 (mmtt) REVERT: C 254 MET cc_start: 0.7896 (mtm) cc_final: 0.7571 (mtm) REVERT: C 385 MET cc_start: 0.8352 (mtp) cc_final: 0.7907 (mtt) REVERT: C 424 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: D 271 GLN cc_start: 0.8324 (mt0) cc_final: 0.7973 (mt0) REVERT: D 326 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7213 (mt0) REVERT: D 334 PHE cc_start: 0.8525 (t80) cc_final: 0.8252 (t80) outliers start: 36 outliers final: 26 residues processed: 178 average time/residue: 0.1517 time to fit residues: 37.0909 Evaluate side-chains 169 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 0.0570 chunk 113 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 157 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 271 GLN A 303 ASN ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.168825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.140977 restraints weight = 21118.740| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.00 r_work: 0.3465 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14630 Z= 0.111 Angle : 0.526 6.320 19839 Z= 0.267 Chirality : 0.044 0.152 2121 Planarity : 0.004 0.051 2525 Dihedral : 10.139 153.687 2095 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.03 % Allowed : 18.61 % Favored : 78.35 % 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: 0.79 (0.21), residues: 1728 helix: 1.50 (0.18), residues: 871 sheet: 2.36 (0.56), residues: 94 loop : -0.88 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.022 0.001 TYR B 315 PHE 0.014 0.001 PHE C 454 TRP 0.009 0.001 TRP A 285 HIS 0.010 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00255 (14630) covalent geometry : angle 0.52638 (19839) hydrogen bonds : bond 0.03871 ( 673) hydrogen bonds : angle 4.06173 ( 1872) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.3973 (OUTLIER) cc_final: 0.3381 (pm20) REVERT: A 442 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7934 (ttp80) REVERT: A 551 ARG cc_start: 0.5957 (mtm180) cc_final: 0.5427 (ptp-170) REVERT: B 119 ASN cc_start: 0.8206 (t0) cc_final: 0.7945 (t0) REVERT: B 142 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.6947 (mp10) REVERT: B 271 GLN cc_start: 0.8521 (mt0) cc_final: 0.8281 (mt0) REVERT: B 470 ARG cc_start: 0.6844 (tpp-160) cc_final: 0.6498 (tpt90) REVERT: C 369 LEU cc_start: 0.8221 (tt) cc_final: 0.7738 (tp) REVERT: C 371 ARG cc_start: 0.7477 (ptp-170) cc_final: 0.7208 (ptp-110) REVERT: C 385 MET cc_start: 0.8248 (mtp) cc_final: 0.7810 (mtt) REVERT: C 424 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7973 (m-30) REVERT: D 326 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7103 (mt0) outliers start: 44 outliers final: 29 residues processed: 189 average time/residue: 0.1336 time to fit residues: 35.7237 Evaluate side-chains 178 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 79 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 HIS C 548 GLN D 125 HIS D 271 GLN D 571 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.170844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.143114 restraints weight = 23431.423| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.24 r_work: 0.3437 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 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 = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14630 Z= 0.123 Angle : 0.537 7.133 19839 Z= 0.271 Chirality : 0.045 0.167 2121 Planarity : 0.004 0.049 2525 Dihedral : 10.135 148.389 2095 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.17 % Allowed : 18.68 % Favored : 78.15 % 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: 0.93 (0.21), residues: 1728 helix: 1.58 (0.18), residues: 868 sheet: 2.23 (0.51), residues: 114 loop : -0.82 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.023 0.001 TYR B 315 PHE 0.015 0.001 PHE C 454 TRP 0.014 0.001 TRP A 285 HIS 0.008 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00291 (14630) covalent geometry : angle 0.53698 (19839) hydrogen bonds : bond 0.04076 ( 673) hydrogen bonds : angle 4.04046 ( 1872) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.3934 (OUTLIER) cc_final: 0.3334 (pm20) REVERT: A 348 ARG cc_start: 0.4015 (ttt180) cc_final: 0.3626 (ttt-90) REVERT: A 442 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7930 (ttp80) REVERT: A 551 ARG cc_start: 0.5910 (mtm180) cc_final: 0.5440 (ptp-170) REVERT: B 119 ASN cc_start: 0.8245 (t0) cc_final: 0.7971 (t0) REVERT: B 142 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: B 271 GLN cc_start: 0.8513 (mt0) cc_final: 0.8284 (mt0) REVERT: C 385 MET cc_start: 0.8285 (mtp) cc_final: 0.7903 (mtt) REVERT: C 424 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: C 503 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6481 (tp) REVERT: D 326 GLN cc_start: 0.7283 (mm-40) cc_final: 0.7030 (mt0) REVERT: D 383 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: D 470 ARG cc_start: 0.7539 (tpt90) cc_final: 0.6884 (tpt170) outliers start: 46 outliers final: 31 residues processed: 172 average time/residue: 0.1335 time to fit residues: 32.8173 Evaluate side-chains 175 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 36 optimal weight: 0.0000 chunk 84 optimal weight: 0.0570 chunk 86 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 85 optimal weight: 1.9990 overall best weight: 0.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 GLN C 370 HIS C 548 GLN D 125 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.172500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.145185 restraints weight = 21429.858| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.13 r_work: 0.3409 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14630 Z= 0.101 Angle : 0.511 6.376 19839 Z= 0.258 Chirality : 0.044 0.162 2121 Planarity : 0.004 0.049 2525 Dihedral : 9.965 144.437 2095 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.56 % Allowed : 19.02 % Favored : 78.42 % 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: 1728 helix: 1.65 (0.18), residues: 869 sheet: 2.51 (0.56), residues: 90 loop : -0.74 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.021 0.001 TYR D 315 PHE 0.012 0.001 PHE C 454 TRP 0.011 0.001 TRP A 285 HIS 0.014 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00228 (14630) covalent geometry : angle 0.51079 (19839) hydrogen bonds : bond 0.03605 ( 673) hydrogen bonds : angle 3.93670 ( 1872) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7891 (ttp80) REVERT: A 551 ARG cc_start: 0.5936 (mtm180) cc_final: 0.5530 (ptp-170) REVERT: B 119 ASN cc_start: 0.8187 (t0) cc_final: 0.7918 (t0) REVERT: B 142 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7015 (mp10) REVERT: B 271 GLN cc_start: 0.8448 (mt0) cc_final: 0.8215 (mt0) REVERT: C 371 ARG cc_start: 0.7459 (ptp-170) cc_final: 0.7179 (ptp-110) REVERT: C 385 MET cc_start: 0.8225 (mtp) cc_final: 0.7827 (mtt) REVERT: C 424 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7962 (m-30) REVERT: D 125 HIS cc_start: 0.8019 (m90) cc_final: 0.7812 (m170) REVERT: D 271 GLN cc_start: 0.8346 (mt0) cc_final: 0.8113 (mt0) REVERT: D 470 ARG cc_start: 0.7443 (tpt90) cc_final: 0.6872 (tpt170) outliers start: 37 outliers final: 26 residues processed: 175 average time/residue: 0.1304 time to fit residues: 32.6277 Evaluate side-chains 163 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 139 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 77 optimal weight: 0.0040 chunk 92 optimal weight: 2.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 548 GLN C 370 HIS C 548 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143351 restraints weight = 23437.415| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.41 r_work: 0.3379 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14630 Z= 0.107 Angle : 0.518 6.911 19839 Z= 0.261 Chirality : 0.044 0.162 2121 Planarity : 0.004 0.049 2525 Dihedral : 9.802 136.095 2095 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.56 % Allowed : 18.95 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.21), residues: 1728 helix: 1.69 (0.18), residues: 869 sheet: 2.29 (0.50), residues: 110 loop : -0.68 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.025 0.001 TYR D 456 PHE 0.012 0.001 PHE C 454 TRP 0.011 0.001 TRP A 285 HIS 0.006 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00245 (14630) covalent geometry : angle 0.51755 (19839) hydrogen bonds : bond 0.03652 ( 673) hydrogen bonds : angle 3.91029 ( 1872) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 442 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7920 (ttp80) REVERT: B 119 ASN cc_start: 0.8258 (t0) cc_final: 0.7980 (t0) REVERT: B 142 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7017 (mp10) REVERT: B 271 GLN cc_start: 0.8469 (mt0) cc_final: 0.8240 (mt0) REVERT: C 385 MET cc_start: 0.8291 (mtp) cc_final: 0.7897 (mtt) REVERT: C 405 LYS cc_start: 0.7436 (tptp) cc_final: 0.7161 (mtmm) REVERT: C 424 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: C 497 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6544 (t0) REVERT: D 125 HIS cc_start: 0.8030 (m90) cc_final: 0.7770 (m170) REVERT: D 149 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: D 271 GLN cc_start: 0.8362 (mt0) cc_final: 0.8111 (mt0) REVERT: D 383 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: D 470 ARG cc_start: 0.7477 (tpt90) cc_final: 0.6960 (tpt170) outliers start: 37 outliers final: 28 residues processed: 167 average time/residue: 0.1252 time to fit residues: 29.8184 Evaluate side-chains 165 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 50 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 166 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 144 optimal weight: 0.0470 chunk 154 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.170054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143649 restraints weight = 21549.315| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.73 r_work: 0.3403 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14630 Z= 0.131 Angle : 0.544 7.406 19839 Z= 0.275 Chirality : 0.045 0.157 2121 Planarity : 0.004 0.047 2525 Dihedral : 9.776 128.747 2095 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.56 % Allowed : 19.35 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.21), residues: 1728 helix: 1.66 (0.18), residues: 867 sheet: 2.15 (0.50), residues: 110 loop : -0.71 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 348 TYR 0.024 0.001 TYR D 456 PHE 0.014 0.001 PHE C 454 TRP 0.012 0.001 TRP A 285 HIS 0.007 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00313 (14630) covalent geometry : angle 0.54388 (19839) hydrogen bonds : bond 0.04229 ( 673) hydrogen bonds : angle 4.01018 ( 1872) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.556 Fit side-chains REVERT: A 234 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: A 442 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8008 (ttp80) REVERT: B 119 ASN cc_start: 0.8459 (t0) cc_final: 0.8256 (t0) REVERT: B 142 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7144 (mp10) REVERT: B 271 GLN cc_start: 0.8528 (mt0) cc_final: 0.8257 (mt0) REVERT: C 369 LEU cc_start: 0.8186 (tt) cc_final: 0.7771 (tp) REVERT: C 385 MET cc_start: 0.8376 (mtp) cc_final: 0.8001 (mtt) REVERT: C 405 LYS cc_start: 0.7600 (tptp) cc_final: 0.7240 (mtmm) REVERT: C 424 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: C 497 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6616 (t0) REVERT: D 125 HIS cc_start: 0.8142 (m90) cc_final: 0.7908 (m-70) REVERT: D 149 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8562 (tt0) REVERT: D 271 GLN cc_start: 0.8483 (mt0) cc_final: 0.8247 (mt0) REVERT: D 334 PHE cc_start: 0.8490 (t80) cc_final: 0.8233 (t80) REVERT: D 383 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: D 497 ASP cc_start: 0.7363 (m-30) cc_final: 0.6588 (t0) outliers start: 37 outliers final: 26 residues processed: 165 average time/residue: 0.1379 time to fit residues: 32.0241 Evaluate side-chains 165 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 146 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 120 optimal weight: 0.0040 chunk 134 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.169756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142155 restraints weight = 21614.022| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.97 r_work: 0.3466 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14630 Z= 0.115 Angle : 0.529 8.986 19839 Z= 0.267 Chirality : 0.044 0.160 2121 Planarity : 0.004 0.048 2525 Dihedral : 9.589 128.320 2095 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.43 % Allowed : 19.62 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.21), residues: 1728 helix: 1.69 (0.18), residues: 869 sheet: 2.13 (0.50), residues: 110 loop : -0.68 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 348 TYR 0.026 0.001 TYR D 456 PHE 0.013 0.001 PHE C 454 TRP 0.011 0.001 TRP A 285 HIS 0.006 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00268 (14630) covalent geometry : angle 0.52945 (19839) hydrogen bonds : bond 0.03830 ( 673) hydrogen bonds : angle 3.95410 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3117.58 seconds wall clock time: 54 minutes 18.22 seconds (3258.22 seconds total)