Starting phenix.real_space_refine on Fri Jul 3 13:15:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxo_18734/07_2026/8qxo_18734_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxo_18734/07_2026/8qxo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qxo_18734/07_2026/8qxo_18734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxo_18734/07_2026/8qxo_18734.map" model { file = "/net/cci-nas-00/data/ceres_data/8qxo_18734/07_2026/8qxo_18734_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxo_18734/07_2026/8qxo_18734_neut.cif" } 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-dev-6108/lib/python3.11/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, 33 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 120 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'DCP': 1, 'DTP': 2, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'DCP': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Time building chain proxies: 3.75, per 1000 atoms: 0.26 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: 1.34 Conformation dependent library (CDL) restraints added in 627.0 milliseconds 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: 0.53 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: 2.18 Time building geometry restraints manager: 1.55 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=" O3B DCP D 704 " pdb=" PG DCP D 704 " ideal model delta sigma weight residual 1.746 1.608 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" O3B DCP B 704 " pdb=" PG DCP B 704 " ideal model delta sigma weight residual 1.746 1.609 0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" O3A DCP B 704 " pdb=" PB DCP B 704 " ideal model delta sigma weight residual 1.672 1.608 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C4 DCP D 704 " pdb=" N3 DCP D 704 " ideal model delta sigma weight residual 1.317 1.378 -0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" C4 DCP B 704 " pdb=" N3 DCP B 704 " ideal model delta sigma weight residual 1.317 1.378 -0.061 2.00e-02 2.50e+03 9.24e+00 ... (remaining 14625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 19613 2.45 - 4.89: 186 4.89 - 7.34: 31 7.34 - 9.79: 6 9.79 - 12.24: 3 Bond angle restraints: 19839 Sorted by residual: angle pdb=" PA DCP B 704 " pdb=" O3A DCP B 704 " pdb=" PB DCP B 704 " ideal model delta sigma weight residual 132.21 119.97 12.24 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O1A DCP D 704 " pdb=" PA DCP D 704 " pdb=" O2A DCP D 704 " ideal model delta sigma weight residual 121.40 110.74 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" O1A DCP B 704 " pdb=" PA DCP B 704 " pdb=" O2A DCP B 704 " ideal model delta sigma weight residual 121.40 110.85 10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" N LEU A 453 " pdb=" CA LEU A 453 " pdb=" C LEU A 453 " ideal model delta sigma weight residual 110.19 113.99 -3.80 1.24e+00 6.50e-01 9.40e+00 angle pdb=" PA DCP D 704 " pdb=" O3A DCP D 704 " pdb=" PB DCP D 704 " ideal model delta sigma weight residual 132.21 123.46 8.75 3.00e+00 1.11e-01 8.51e+00 ... (remaining 19834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.02: 8513 34.02 - 68.04: 250 68.04 - 102.06: 28 102.06 - 136.08: 3 136.08 - 170.10: 1 Dihedral angle restraints: 8795 sinusoidal: 3692 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 8792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1717 0.049 - 0.098: 292 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 3.000 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.910 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 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 0.138 14630 Z= 0.159 Angle : 0.622 12.236 19839 Z= 0.304 Chirality : 0.043 0.244 2121 Planarity : 0.006 0.221 2525 Dihedral : 16.366 170.101 5519 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 are 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/Z covalent geometry : bond 0.00323 / 0.16 (14630) covalent geometry : angle 0.62244 / 0.30 (19839) hydrogen bonds : bond 0.17883 / 12.70 ( 673) hydrogen bonds : angle 5.78419 / 4.02 ( 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 : 0.561 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: 0.8071 (ttp-110) cc_final: 0.7715 (ttp80) REVERT: D 506 ASP cc_start: 0.8738 (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: 0.1426 time to fit residues: 76.4186 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 : 0.535 ------------------------------------------------------------------------------- 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... ** 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 = 0.4055 r_free = 0.4055 target = 0.183560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157804 restraints weight = 28499.450| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.05 r_work: 0.3559 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14630 Z= 0.155 Angle : 0.628 7.641 19839 Z= 0.319 Chirality : 0.048 0.367 2121 Planarity : 0.005 0.065 2525 Dihedral : 11.146 164.580 2109 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 2.36 % Allowed : 14.50 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.21), residues: 1728 helix: 1.36 (0.18), residues: 862 sheet: 1.97 (0.58), residues: 84 loop : -0.78 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 470 TYR 0.031 0.002 TYR B 315 PHE 0.023 0.002 PHE D 141 TRP 0.014 0.002 TRP B 285 HIS 0.010 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (14630) covalent geometry : angle 0.62806 / 0.32 (19839) hydrogen bonds : bond 0.04692 / 3.19 ( 673) hydrogen bonds : angle 4.46327 / 3.19 ( 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 240 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.577 Fit side-chains REVERT: A 254 MET cc_start: 0.7683 (ttm) cc_final: 0.7350 (ttm) REVERT: A 330 ASP cc_start: 0.8130 (t0) cc_final: 0.7919 (t0) REVERT: A 367 ASN cc_start: 0.7932 (m-40) cc_final: 0.7681 (m-40) REVERT: A 435 ASP cc_start: 0.6930 (m-30) cc_final: 0.6718 (m-30) REVERT: B 438 LEU cc_start: 0.8422 (mt) cc_final: 0.8156 (mt) REVERT: B 469 LYS cc_start: 0.7502 (mttt) cc_final: 0.6792 (mmmt) REVERT: B 505 MET cc_start: 0.7814 (ttp) cc_final: 0.7492 (ttm) REVERT: B 547 GLU cc_start: 0.7419 (pm20) cc_final: 0.6153 (tp30) REVERT: C 287 TYR cc_start: 0.7451 (m-80) cc_final: 0.7121 (m-80) REVERT: C 374 TYR cc_start: 0.7587 (m-80) cc_final: 0.6389 (m-80) REVERT: D 239 MET cc_start: 0.9053 (mtm) cc_final: 0.8797 (mtp) REVERT: D 371 ARG cc_start: 0.8244 (ttp-110) cc_final: 0.8008 (ttp80) REVERT: D 383 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: D 470 ARG cc_start: 0.7083 (tpt90) cc_final: 0.6855 (tpt170) outliers start: 34 outliers final: 19 residues processed: 229 average time/residue: 0.1438 time to fit residues: 46.6180 Evaluate side-chains 180 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 104 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.0010 chunk 136 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 HIS D 125 HIS D 539 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.176540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149950 restraints weight = 27052.260| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.07 r_work: 0.3524 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3704 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= 0.124 Angle : 0.545 6.368 19839 Z= 0.276 Chirality : 0.045 0.156 2121 Planarity : 0.004 0.050 2525 Dihedral : 10.743 161.914 2109 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 2.09 % Allowed : 16.32 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1728 helix: 1.48 (0.18), residues: 871 sheet: 2.33 (0.58), residues: 84 loop : -0.82 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.024 0.001 TYR B 315 PHE 0.017 0.001 PHE D 141 TRP 0.008 0.001 TRP B 313 HIS 0.007 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (14630) covalent geometry : angle 0.54517 / 0.28 (19839) hydrogen bonds : bond 0.04097 / 2.81 ( 673) hydrogen bonds : angle 4.19711 / 3.00 ( 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 : 0.563 Fit side-chains REVERT: A 367 ASN cc_start: 0.7941 (m-40) cc_final: 0.7649 (m-40) REVERT: B 271 GLN cc_start: 0.8528 (mt0) cc_final: 0.8274 (mt0) REVERT: B 469 LYS cc_start: 0.7612 (mttt) cc_final: 0.6887 (mmmt) REVERT: B 505 MET cc_start: 0.7832 (ttp) cc_final: 0.7564 (ttm) REVERT: B 547 GLU cc_start: 0.7777 (pm20) cc_final: 0.7216 (pt0) REVERT: C 287 TYR cc_start: 0.7645 (m-80) cc_final: 0.7318 (m-80) REVERT: C 374 TYR cc_start: 0.7649 (m-80) cc_final: 0.6496 (m-80) REVERT: C 424 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: C 497 ASP cc_start: 0.6361 (OUTLIER) cc_final: 0.6082 (t0) REVERT: C 555 LYS cc_start: 0.7683 (mmmm) cc_final: 0.7211 (mmtp) REVERT: D 239 MET cc_start: 0.8935 (mtm) cc_final: 0.8687 (mtp) REVERT: D 571 GLN cc_start: 0.7770 (tp40) cc_final: 0.7566 (tp40) outliers start: 30 outliers final: 23 residues processed: 191 average time/residue: 0.1424 time to fit residues: 38.5671 Evaluate side-chains 185 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 370 HIS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 552 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 194 ARG 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 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 Chi-restraints excluded: chain D residue 511 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 120 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.168712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142552 restraints weight = 27143.459| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.08 r_work: 0.3333 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14630 Z= 0.209 Angle : 0.646 7.526 19839 Z= 0.328 Chirality : 0.049 0.172 2121 Planarity : 0.005 0.048 2525 Dihedral : 10.753 158.615 2109 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.78 % Allowed : 16.39 % 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 are not related in a simple way. whole: 0.54 (0.21), residues: 1728 helix: 1.28 (0.18), residues: 862 sheet: 1.94 (0.50), residues: 114 loop : -1.00 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 164 TYR 0.031 0.002 TYR B 315 PHE 0.027 0.002 PHE D 141 TRP 0.018 0.002 TRP B 313 HIS 0.007 0.002 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (14630) covalent geometry : angle 0.64571 / 0.33 (19839) hydrogen bonds : bond 0.05547 / 3.79 ( 673) hydrogen bonds : angle 4.46038 / 3.20 ( 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 226 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 224 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7144 (mp) REVERT: B 119 ASN cc_start: 0.8196 (t0) cc_final: 0.7879 (t0) REVERT: B 142 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7075 (mp10) REVERT: B 405 LYS cc_start: 0.7660 (mttp) cc_final: 0.7402 (ttpt) REVERT: B 547 GLU cc_start: 0.8195 (pm20) cc_final: 0.7980 (pt0) REVERT: C 235 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8344 (tm-30) REVERT: C 287 TYR cc_start: 0.7736 (m-80) cc_final: 0.7507 (m-80) REVERT: C 336 LYS cc_start: 0.6792 (tttt) cc_final: 0.6412 (tttt) REVERT: C 385 MET cc_start: 0.8390 (mtp) cc_final: 0.7924 (mtt) REVERT: C 424 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: C 555 LYS cc_start: 0.7967 (mmmm) cc_final: 0.7581 (mmtp) REVERT: D 314 ASP cc_start: 0.8642 (t70) cc_final: 0.8401 (t0) REVERT: D 326 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7220 (mt0) REVERT: D 383 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8094 (m-30) outliers start: 55 outliers final: 30 residues processed: 212 average time/residue: 0.1363 time to fit residues: 40.0252 Evaluate side-chains 183 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 343 VAL 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 A residue 550 ILE 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 328 ASN Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 180 HIS Chi-restraints excluded: chain C residue 194 ARG 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 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 232 THR Chi-restraints excluded: chain D residue 315 TYR 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 511 GLU Chi-restraints excluded: chain D residue 550 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 71 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 139 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 GLN A 271 GLN A 303 ASN C 370 HIS ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS D 571 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.172730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.148372 restraints weight = 18680.615| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.43 r_work: 0.3475 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5008 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 : 0.540 6.309 19839 Z= 0.273 Chirality : 0.045 0.146 2121 Planarity : 0.004 0.050 2525 Dihedral : 10.350 157.090 2109 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.83 % Allowed : 17.94 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.21), residues: 1728 helix: 1.45 (0.18), residues: 870 sheet: 2.13 (0.51), residues: 114 loop : -0.92 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 348 TYR 0.023 0.001 TYR B 315 PHE 0.014 0.001 PHE D 141 TRP 0.009 0.001 TRP B 285 HIS 0.007 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (14630) covalent geometry : angle 0.53996 / 0.27 (19839) hydrogen bonds : bond 0.04069 / 2.79 ( 673) hydrogen bonds : angle 4.13460 / 2.97 ( 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 193 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 224 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6974 (mp) REVERT: A 288 LYS cc_start: 0.7438 (mmtp) cc_final: 0.7046 (tmtt) REVERT: A 346 GLU cc_start: 0.4251 (OUTLIER) cc_final: 0.3566 (pm20) REVERT: B 119 ASN cc_start: 0.8193 (t0) cc_final: 0.7929 (t0) REVERT: B 142 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7080 (mp10) REVERT: B 271 GLN cc_start: 0.8571 (mt0) cc_final: 0.8324 (mt0) REVERT: B 405 LYS cc_start: 0.7717 (mttp) cc_final: 0.7478 (ttpp) REVERT: B 469 LYS cc_start: 0.7605 (mmtt) cc_final: 0.6827 (mmmt) REVERT: B 571 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7675 (tp-100) REVERT: C 235 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8155 (tm-30) REVERT: C 254 MET cc_start: 0.7817 (mtm) cc_final: 0.7472 (mtm) REVERT: C 385 MET cc_start: 0.8314 (mtp) cc_final: 0.7911 (mtt) REVERT: C 405 LYS cc_start: 0.7472 (tptp) cc_final: 0.7158 (mtmm) REVERT: C 424 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8055 (m-30) REVERT: D 314 ASP cc_start: 0.8586 (t70) cc_final: 0.8369 (t0) REVERT: D 326 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7198 (mt0) REVERT: D 470 ARG cc_start: 0.7412 (tpt90) cc_final: 0.6768 (tpt170) outliers start: 41 outliers final: 28 residues processed: 184 average time/residue: 0.1442 time to fit residues: 37.1827 Evaluate side-chains 172 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 340 VAL 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 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 150 LEU Chi-restraints excluded: chain D residue 310 VAL 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 Chi-restraints excluded: chain D residue 511 GLU 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: 0.9990 chunk 113 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN B 571 GLN ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.171107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143296 restraints weight = 20816.841| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.09 r_work: 0.3394 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5208 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= 0.138 Angle : 0.550 6.601 19839 Z= 0.276 Chirality : 0.045 0.154 2121 Planarity : 0.004 0.049 2525 Dihedral : 10.273 154.041 2109 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.17 % Allowed : 18.27 % Favored : 78.56 % 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 are not related in a simple way. whole: 0.76 (0.21), residues: 1728 helix: 1.44 (0.18), residues: 871 sheet: 2.18 (0.51), residues: 110 loop : -0.90 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.024 0.001 TYR B 315 PHE 0.016 0.001 PHE C 454 TRP 0.008 0.001 TRP B 313 HIS 0.008 0.001 HIS C 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (14630) covalent geometry : angle 0.54988 / 0.28 (19839) hydrogen bonds : bond 0.04340 / 2.97 ( 673) hydrogen bonds : angle 4.13235 / 2.97 ( 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 195 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.4104 (OUTLIER) cc_final: 0.3484 (pm20) REVERT: B 119 ASN cc_start: 0.8386 (t0) cc_final: 0.8123 (t0) REVERT: B 142 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7149 (mp10) REVERT: B 271 GLN cc_start: 0.8551 (mt0) cc_final: 0.8238 (mt0) REVERT: B 405 LYS cc_start: 0.7715 (mttp) cc_final: 0.7346 (ttpp) REVERT: B 469 LYS cc_start: 0.7567 (mmtt) cc_final: 0.6776 (mmmt) REVERT: B 470 ARG cc_start: 0.7418 (tpt90) cc_final: 0.7198 (tpp-160) REVERT: C 369 LEU cc_start: 0.8336 (tt) cc_final: 0.7887 (tp) REVERT: C 380 ASN cc_start: 0.6989 (OUTLIER) cc_final: 0.6748 (m-40) REVERT: C 385 MET cc_start: 0.8334 (mtp) cc_final: 0.7986 (mtt) REVERT: C 405 LYS cc_start: 0.7560 (tptp) cc_final: 0.7192 (mtmm) REVERT: C 424 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: D 115 MET cc_start: 0.5837 (OUTLIER) cc_final: 0.5041 (tpt) REVERT: D 120 ASP cc_start: 0.7955 (t0) cc_final: 0.7252 (t70) REVERT: D 271 GLN cc_start: 0.8449 (mt0) cc_final: 0.8215 (mt0) REVERT: D 314 ASP cc_start: 0.8683 (t70) cc_final: 0.8464 (t70) REVERT: D 326 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7256 (mt0) REVERT: D 334 PHE cc_start: 0.8549 (t80) cc_final: 0.8304 (t80) outliers start: 46 outliers final: 34 residues processed: 184 average time/residue: 0.1375 time to fit residues: 35.3617 Evaluate side-chains 180 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 346 GLU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 422 LEU 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 195 ASP 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 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 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 310 VAL 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 511 GLU 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: 3.9990 chunk 71 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 169 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 GLN C 370 HIS C 548 GLN D 125 HIS D 571 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.168045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139418 restraints weight = 23356.554| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.06 r_work: 0.3382 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5427 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= 0.122 Angle : 0.538 7.654 19839 Z= 0.270 Chirality : 0.045 0.156 2121 Planarity : 0.004 0.049 2525 Dihedral : 10.101 148.447 2109 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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 are not related in a simple way. whole: 0.90 (0.21), residues: 1728 helix: 1.58 (0.18), residues: 869 sheet: 2.22 (0.51), residues: 110 loop : -0.84 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.024 0.001 TYR B 315 PHE 0.016 0.001 PHE C 454 TRP 0.011 0.001 TRP A 285 HIS 0.008 0.001 HIS C 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (14630) covalent geometry : angle 0.53778 / 0.27 (19839) hydrogen bonds : bond 0.03990 / 2.75 ( 673) hydrogen bonds : angle 4.02540 / 2.90 ( 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 194 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.3959 (OUTLIER) cc_final: 0.3370 (pm20) REVERT: A 348 ARG cc_start: 0.4027 (ttt180) cc_final: 0.3621 (ttt-90) REVERT: A 442 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7931 (ttp80) REVERT: A 551 ARG cc_start: 0.5945 (mtm180) cc_final: 0.5455 (ptp-170) REVERT: B 119 ASN cc_start: 0.8211 (t0) cc_final: 0.7944 (t0) REVERT: B 142 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.6969 (mp10) REVERT: B 271 GLN cc_start: 0.8467 (mt0) cc_final: 0.8239 (mt0) REVERT: B 470 ARG cc_start: 0.7368 (tpt90) cc_final: 0.7093 (tpp-160) REVERT: C 369 LEU cc_start: 0.8231 (tt) cc_final: 0.7765 (tp) REVERT: C 380 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.6560 (m-40) REVERT: C 385 MET cc_start: 0.8295 (mtp) cc_final: 0.7926 (mtt) REVERT: C 405 LYS cc_start: 0.7463 (tptp) cc_final: 0.7184 (mtmm) REVERT: C 416 MET cc_start: 0.6475 (mmm) cc_final: 0.5793 (mmm) REVERT: C 424 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: D 115 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.4897 (tpt) REVERT: D 326 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7174 (mt0) REVERT: D 470 ARG cc_start: 0.7444 (tpt90) cc_final: 0.6793 (tpt170) outliers start: 46 outliers final: 31 residues processed: 184 average time/residue: 0.1297 time to fit residues: 34.2645 Evaluate side-chains 178 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 346 GLU 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 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 380 ASN 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 310 VAL 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 511 GLU Chi-restraints excluded: chain D residue 550 ILE 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: 0.5980 chunk 84 optimal weight: 0.1980 chunk 86 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 370 HIS C 548 GLN D 125 HIS D 271 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.172203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143988 restraints weight = 21339.464| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.19 r_work: 0.3470 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5520 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= 0.105 Angle : 0.514 6.289 19839 Z= 0.258 Chirality : 0.044 0.152 2121 Planarity : 0.004 0.049 2525 Dihedral : 9.905 142.616 2109 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.37 % Allowed : 18.48 % 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 are not related in a simple way. whole: 1.02 (0.21), residues: 1728 helix: 1.67 (0.18), residues: 869 sheet: 2.53 (0.56), residues: 90 loop : -0.72 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 348 TYR 0.023 0.001 TYR D 456 PHE 0.013 0.001 PHE C 454 TRP 0.015 0.001 TRP A 285 HIS 0.007 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (14630) covalent geometry : angle 0.51416 / 0.26 (19839) hydrogen bonds : bond 0.03646 / 2.50 ( 673) hydrogen bonds : angle 3.94340 / 2.84 ( 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 200 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 200 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7051 (mt0) REVERT: A 442 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7826 (ttp80) REVERT: A 505 MET cc_start: 0.4924 (mmt) cc_final: 0.4112 (ttm) REVERT: B 119 ASN cc_start: 0.8202 (t0) cc_final: 0.7928 (t0) REVERT: B 142 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: B 271 GLN cc_start: 0.8398 (mt0) cc_final: 0.8186 (mt0) REVERT: B 470 ARG cc_start: 0.7319 (tpt90) cc_final: 0.7103 (tpp-160) REVERT: B 505 MET cc_start: 0.7826 (ttm) cc_final: 0.7608 (mtp) REVERT: C 362 MET cc_start: 0.6723 (tmm) cc_final: 0.6132 (ttt) REVERT: C 369 LEU cc_start: 0.8176 (tt) cc_final: 0.7697 (tp) REVERT: C 380 ASN cc_start: 0.6818 (OUTLIER) cc_final: 0.6412 (m-40) REVERT: C 385 MET cc_start: 0.8251 (mtp) cc_final: 0.7877 (mtt) REVERT: C 405 LYS cc_start: 0.7430 (tptp) cc_final: 0.7190 (mtmm) REVERT: C 424 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: D 115 MET cc_start: 0.5831 (OUTLIER) cc_final: 0.4997 (tpt) REVERT: D 149 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: D 271 GLN cc_start: 0.8350 (mt0) cc_final: 0.8103 (mt0) REVERT: D 326 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7158 (mt0) REVERT: D 470 ARG cc_start: 0.7460 (tpt90) cc_final: 0.6846 (tpt170) outliers start: 49 outliers final: 35 residues processed: 191 average time/residue: 0.1185 time to fit residues: 33.3506 Evaluate side-chains 182 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 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 200 GLN 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 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 311 ASP 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 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 149 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 310 VAL 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 445 LEU Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 550 ILE 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: 0.6980 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 0.0870 chunk 152 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 92 optimal weight: 2.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 370 HIS C 548 GLN D 125 HIS D 571 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.173064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.144468 restraints weight = 23296.318| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.25 r_work: 0.3475 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5592 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 : 0.512 6.463 19839 Z= 0.257 Chirality : 0.044 0.157 2121 Planarity : 0.004 0.047 2525 Dihedral : 9.768 134.415 2109 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.24 % Allowed : 18.34 % 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 are not related in a simple way. whole: 1.15 (0.21), residues: 1728 helix: 1.75 (0.18), residues: 869 sheet: 2.34 (0.51), 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 0.010 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (14630) covalent geometry : angle 0.51225 / 0.26 (19839) hydrogen bonds : bond 0.03497 / 2.40 ( 673) hydrogen bonds : angle 3.89260 / 2.82 ( 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 191 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 200 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7095 (mt0) REVERT: A 442 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7840 (ttp80) REVERT: A 505 MET cc_start: 0.4943 (mmt) cc_final: 0.4128 (ttm) REVERT: B 119 ASN cc_start: 0.8220 (t0) cc_final: 0.7954 (t0) REVERT: B 142 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.6950 (mp10) REVERT: B 271 GLN cc_start: 0.8386 (mt0) cc_final: 0.8176 (mt0) REVERT: B 470 ARG cc_start: 0.7371 (tpt90) cc_final: 0.7153 (tpp-160) REVERT: C 362 MET cc_start: 0.6714 (tmm) cc_final: 0.6100 (ttt) REVERT: C 369 LEU cc_start: 0.8165 (tt) cc_final: 0.7684 (tp) REVERT: C 380 ASN cc_start: 0.6822 (OUTLIER) cc_final: 0.6328 (m-40) REVERT: C 385 MET cc_start: 0.8260 (mtp) cc_final: 0.7908 (mtt) REVERT: C 424 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: C 503 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6428 (tp) REVERT: D 115 MET cc_start: 0.5747 (OUTLIER) cc_final: 0.4924 (tpt) REVERT: D 125 HIS cc_start: 0.8061 (m90) cc_final: 0.7767 (m170) REVERT: D 149 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: D 470 ARG cc_start: 0.7303 (tpt90) cc_final: 0.6847 (tpt170) REVERT: D 497 ASP cc_start: 0.7098 (m-30) cc_final: 0.6512 (t0) outliers start: 47 outliers final: 36 residues processed: 183 average time/residue: 0.1269 time to fit residues: 33.4498 Evaluate side-chains 181 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 200 GLN 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 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 311 ASP Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 370 HIS 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 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 115 MET 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 310 VAL 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 445 LEU Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 550 ILE 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: 0.5980 chunk 120 optimal weight: 0.0050 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 166 optimal weight: 0.0070 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 370 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.173003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144823 restraints weight = 21329.772| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.10 r_work: 0.3413 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5630 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= 0.100 Angle : 0.517 7.463 19839 Z= 0.258 Chirality : 0.044 0.158 2121 Planarity : 0.004 0.048 2525 Dihedral : 9.589 128.636 2109 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.90 % Allowed : 18.95 % 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 are not related in a simple way. whole: 1.16 (0.21), residues: 1728 helix: 1.76 (0.18), residues: 869 sheet: 2.57 (0.56), residues: 90 loop : -0.63 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 348 TYR 0.027 0.001 TYR D 456 PHE 0.012 0.001 PHE C 454 TRP 0.011 0.001 TRP A 285 HIS 0.007 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (14630) covalent geometry : angle 0.51656 / 0.26 (19839) hydrogen bonds : bond 0.03455 / 2.38 ( 673) hydrogen bonds : angle 3.87357 / 2.80 ( 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 181 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7091 (mt0) REVERT: A 333 ARG cc_start: 0.7425 (ttt180) cc_final: 0.7025 (ttm170) REVERT: A 442 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7828 (ttp80) REVERT: A 505 MET cc_start: 0.4705 (mmt) cc_final: 0.3889 (ttm) REVERT: B 119 ASN cc_start: 0.8190 (t0) cc_final: 0.7908 (t0) REVERT: B 142 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.6990 (mp10) REVERT: B 271 GLN cc_start: 0.8364 (mt0) cc_final: 0.8153 (mt0) REVERT: C 362 MET cc_start: 0.6624 (tmm) cc_final: 0.6030 (ttt) REVERT: C 380 ASN cc_start: 0.6750 (OUTLIER) cc_final: 0.6254 (m-40) REVERT: C 385 MET cc_start: 0.8274 (mtp) cc_final: 0.7903 (mtt) REVERT: C 424 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: C 503 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6405 (tp) REVERT: D 115 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.4965 (tpt) REVERT: D 149 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: D 470 ARG cc_start: 0.7267 (tpt90) cc_final: 0.6851 (tpt170) REVERT: D 497 ASP cc_start: 0.7092 (m-30) cc_final: 0.6498 (t0) outliers start: 42 outliers final: 33 residues processed: 174 average time/residue: 0.1221 time to fit residues: 30.3397 Evaluate side-chains 174 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 200 GLN 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 C residue 224 LEU 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 370 HIS 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 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 115 MET 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 310 VAL 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 445 LEU Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 550 ILE 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: 0.6980 chunk 108 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 370 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.142742 restraints weight = 21344.773| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.03 r_work: 0.3471 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5725 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= 0.127 Angle : 0.544 7.416 19839 Z= 0.272 Chirality : 0.045 0.151 2121 Planarity : 0.004 0.047 2525 Dihedral : 9.581 126.547 2109 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.24 % Allowed : 18.68 % 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 are not related in a simple way. whole: 1.07 (0.21), residues: 1728 helix: 1.68 (0.18), residues: 870 sheet: 2.16 (0.50), residues: 110 loop : -0.68 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 348 TYR 0.027 0.001 TYR D 456 PHE 0.015 0.001 PHE C 454 TRP 0.010 0.001 TRP A 285 HIS 0.009 0.001 HIS C 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (14630) covalent geometry : angle 0.54396 / 0.27 (19839) hydrogen bonds : bond 0.04017 / 2.75 ( 673) hydrogen bonds : angle 3.97981 / 2.88 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3000.25 seconds wall clock time: 52 minutes 16.10 seconds (3136.10 seconds total)