Starting phenix.real_space_refine on Sun Jan 19 21:48:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxo_18734/01_2025/8qxo_18734_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxo_18734/01_2025/8qxo_18734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qxo_18734/01_2025/8qxo_18734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxo_18734/01_2025/8qxo_18734.map" model { file = "/net/cci-nas-00/data/ceres_data/8qxo_18734/01_2025/8qxo_18734_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxo_18734/01_2025/8qxo_18734_neut.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' FE': 1, ' MG': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 121 Unusual residues: {' FE': 1, 'DCP': 1, 'DTP': 2, 'GTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {' FE': 1, 'DCP': 1, 'GTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 10.93, per 1000 atoms: 0.76 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: 3.64 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 147 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: 4.55 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4646 1.35 - 1.46: 3403 1.46 - 1.58: 6429 1.58 - 1.70: 38 1.70 - 1.82: 114 Bond restraints: 14630 Sorted by residual: bond pdb=" C4' DCP B 704 " pdb=" O4' DCP B 704 " ideal model delta sigma weight residual 1.444 1.411 0.033 1.00e-02 1.00e+04 1.09e+01 bond pdb=" O1A DCP B 704 " pdb=" PA DCP B 704 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.00e-02 1.00e+04 1.06e+01 bond pdb=" O1A DCP D 704 " pdb=" PA DCP D 704 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.00e-02 1.00e+04 1.06e+01 bond pdb=" C4 DCP D 704 " pdb=" C5 DCP D 704 " ideal model delta sigma weight residual 1.426 1.389 0.037 1.20e-02 6.94e+03 9.37e+00 bond pdb=" O1B DCP D 704 " pdb=" PB DCP D 704 " ideal model delta sigma weight residual 1.477 1.511 -0.034 1.10e-02 8.26e+03 9.30e+00 ... (remaining 14625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 19806 4.44 - 8.88: 29 8.88 - 13.33: 0 13.33 - 17.77: 2 17.77 - 22.21: 2 Bond angle restraints: 19839 Sorted by residual: angle pdb=" PB DCP B 704 " pdb=" O3B DCP B 704 " pdb=" PG DCP B 704 " ideal model delta sigma weight residual 139.87 117.66 22.21 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PB DCP D 704 " pdb=" O3B DCP D 704 " pdb=" PG DCP D 704 " ideal model delta sigma weight residual 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PA DCP B 704 " pdb=" O3A DCP B 704 " pdb=" PB DCP B 704 " ideal model delta sigma weight residual 136.83 119.97 16.86 1.00e+00 1.00e+00 2.84e+02 angle pdb=" PA DCP D 704 " pdb=" O3A DCP D 704 " pdb=" PB DCP D 704 " ideal model delta sigma weight residual 136.83 123.46 13.37 1.00e+00 1.00e+00 1.79e+02 angle pdb=" O2G DCP B 704 " pdb=" PG DCP B 704 " pdb=" O3B DCP B 704 " ideal model delta sigma weight residual 104.48 110.28 -5.80 1.14e+00 7.76e-01 2.61e+01 ... (remaining 19834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.02: 8499 34.02 - 68.04: 250 68.04 - 102.06: 28 102.06 - 136.08: 3 136.08 - 170.10: 1 Dihedral angle restraints: 8781 sinusoidal: 3678 harmonic: 5103 Sorted by residual: dihedral pdb=" O3A GTP B 702 " pdb=" O3B GTP B 702 " pdb=" PB GTP B 702 " pdb=" PG GTP B 702 " ideal model delta sinusoidal sigma weight residual 303.79 133.69 170.10 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C4' GTP A 701 " pdb=" C5' GTP A 701 " pdb=" O5' GTP A 701 " pdb=" PA GTP A 701 " ideal model delta sinusoidal sigma weight residual 260.87 137.39 123.49 1 2.00e+01 2.50e-03 3.72e+01 dihedral pdb=" C4' GTP D 701 " pdb=" C5' GTP D 701 " pdb=" O5' GTP D 701 " pdb=" PA GTP D 701 " ideal model delta sinusoidal sigma weight residual 260.87 143.18 117.69 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 8778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1719 0.049 - 0.098: 290 0.098 - 0.146: 104 0.146 - 0.195: 4 0.195 - 0.244: 4 Chirality restraints: 2121 Sorted by residual: chirality pdb=" C3' DTP B 701 " pdb=" C2' DTP B 701 " pdb=" C4' DTP B 701 " pdb=" O3' DTP B 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C3' DTP B 705 " pdb=" C2' DTP B 705 " pdb=" C4' DTP B 705 " pdb=" O3' DTP B 705 " both_signs ideal model delta sigma weight residual False -2.68 -2.91 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C4' DTP B 705 " pdb=" C3' DTP B 705 " pdb=" C5' DTP B 705 " pdb=" O4' DTP B 705 " both_signs ideal model delta sigma weight residual False -2.50 -2.73 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2118 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DCP B 704 " -0.353 2.00e-02 2.50e+03 2.21e-01 1.10e+03 pdb=" C2 DCP B 704 " 0.026 2.00e-02 2.50e+03 pdb=" C4 DCP B 704 " -0.087 2.00e-02 2.50e+03 pdb=" C5 DCP B 704 " 0.068 2.00e-02 2.50e+03 pdb=" C6 DCP B 704 " 0.289 2.00e-02 2.50e+03 pdb=" N1 DCP B 704 " 0.051 2.00e-02 2.50e+03 pdb=" N3 DCP B 704 " -0.325 2.00e-02 2.50e+03 pdb=" N4 DCP B 704 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DCP B 704 " 0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCP D 704 " -0.016 2.00e-02 2.50e+03 7.27e-02 1.19e+02 pdb=" C2 DCP D 704 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DCP D 704 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DCP D 704 " 0.113 2.00e-02 2.50e+03 pdb=" C6 DCP D 704 " -0.017 2.00e-02 2.50e+03 pdb=" N1 DCP D 704 " -0.068 2.00e-02 2.50e+03 pdb=" N3 DCP D 704 " -0.120 2.00e-02 2.50e+03 pdb=" N4 DCP D 704 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DCP D 704 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 129 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO D 130 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 130 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 130 " 0.025 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 65 2.39 - 3.02: 8446 3.02 - 3.64: 21287 3.64 - 4.27: 30083 4.27 - 4.90: 51022 Nonbonded interactions: 110903 Sorted by model distance: nonbonded pdb=" O3B GTP A 701 " pdb="MG MG A 703 " model vdw 1.759 2.170 nonbonded pdb=" O2A GTP A 701 " pdb="MG MG A 703 " model vdw 1.802 2.170 nonbonded pdb="MG MG C 802 " pdb=" O2A GTP D 701 " model vdw 1.933 2.170 nonbonded pdb=" OD1 ASP A 311 " pdb="FE FE A 702 " model vdw 1.990 2.260 nonbonded pdb="MG MG C 802 " pdb=" O3B GTP D 701 " model vdw 2.005 2.170 ... (remaining 110898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 114 through 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 through 261 or (resid 262 and (nam \ e N or name CA or name C or name O or name CB )) or resid 263 through 275 or (re \ sid 276 and (name N or name CA or name C or name O or name CB )) or resid 285 th \ rough 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 through 291 or (resid 292 and (name N or name CA or name C or name \ O or name CB )) or resid 293 through 303 or (resid 304 through 305 and (name N \ or name CA or name C or name O or name CB )) or resid 306 through 325 or (resid \ 326 and (name N or name CA or name C or name O or name CB )) or resid 327 throug \ h 341 or (resid 342 and (name N or name CA or name C or name O or name CB )) or \ resid 343 or (resid 344 through 345 and (name N or name CA or name C or name O o \ r name CB )) or resid 346 through 397 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 399 through 434 or (resid 435 and (name N \ or name CA or name C or name O or name CB )) or resid 436 or resid 438 through 4 \ 64 or (resid 465 and (name N or name CA or name C or name O or name CB )) or res \ id 466 or (resid 467 and (name N or name CA or name C or name O or name CB )) or \ resid 468 or (resid 469 and (name N or name CA or name C or name O or name CB ) \ ) or resid 470 or (resid 471 and (name N or name CA or name C or name O or name \ CB )) or resid 472 through 473 or (resid 474 and (name N or name CA or name C or \ name O or name CB )) or resid 475 through 477 or (resid 478 and (name N or name \ CA or name C or name O or name CB )) or resid 479 through 485 or (resid 486 thr \ ough 490 and (name N or name CA or name C or name O or name CB )) or resid 491 o \ r (resid 492 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 93 or (resid 494 through 496 and (name N or name CA or name C or name O or name \ CB )) or resid 497 through 558 or (resid 559 through 560 and (name N or name CA \ or name C or name O or name CB )) or resid 561 through 577)) selection = (chain 'B' and (resid 114 through 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 through 261 or (resid 262 and (nam \ e N or name CA or name C or name O or name CB )) or resid 263 through 275 or (re \ sid 276 and (name N or name CA or name C or name O or name CB )) or resid 285 th \ rough 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 through 291 or (resid 292 and (name N or name CA or name C or name \ O or name CB )) or resid 293 through 303 or (resid 304 through 305 and (name N \ or name CA or name C or name O or name CB )) or resid 306 through 325 or (resid \ 326 and (name N or name CA or name C or name O or name CB )) or resid 327 throug \ h 341 or (resid 342 and (name N or name CA or name C or name O or name CB )) or \ resid 343 or (resid 344 through 345 and (name N or name CA or name C or name O o \ r name CB )) or resid 346 through 397 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 399 through 434 or (resid 435 and (name N \ or name CA or name C or name O or name CB )) or resid 436 or resid 438 through 4 \ 64 or (resid 465 and (name N or name CA or name C or name O or name CB )) or res \ id 466 through 468 or (resid 469 and (name N or name CA or name C or name O or n \ ame CB )) or resid 470 or (resid 471 and (name N or name CA or name C or name O \ or name CB )) or resid 472 through 473 or (resid 474 and (name N or name CA or n \ ame C or name O or name CB )) or resid 475 through 477 or (resid 478 and (name N \ or name CA or name C or name O or name CB )) or resid 479 through 485 or (resid \ 486 through 490 and (name N or name CA or name C or name O or name CB )) or res \ id 491 or (resid 492 and (name N or name CA or name C or name O or name CB )) or \ resid 493 through 506 or resid 547 through 577)) selection = (chain 'C' and (resid 114 through 227 or (resid 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 through 275 or (resid 284 and (name N \ or name CA or name C or name O or name CB )) or resid 285 through 303 or (resid \ 304 through 305 and (name N or name CA or name C or name O or name CB )) or resi \ d 306 through 436 or resid 438 through 466 or (resid 467 and (name N or name CA \ or name C or name O or name CB )) or resid 468 or (resid 469 and (name N or name \ CA or name C or name O or name CB )) or resid 470 or (resid 471 and (name N or \ name CA or name C or name O or name CB )) or resid 472 through 473 or (resid 474 \ and (name N or name CA or name C or name O or name CB )) or resid 475 through 5 \ 77)) selection = (chain 'D' and (resid 114 through 276 or resid 285 through 325 or (resid 326 and \ (name N or name CA or name C or name O or name CB )) or resid 327 through 436 o \ r resid 438 through 486 or (resid 487 through 490 and (name N or name CA or name \ C or name O or name CB )) or resid 491 through 506 or resid 547 through 577)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.34 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 35.130 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14630 Z= 0.180 Angle : 0.634 22.210 19839 Z= 0.406 Chirality : 0.043 0.244 2121 Planarity : 0.006 0.221 2525 Dihedral : 16.427 170.101 5505 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.95 % Favored : 96.93 % Rotamer: Outliers : 0.13 % Allowed : 9.31 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (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 TRP 0.007 0.001 TRP B 285 HIS 0.006 0.001 HIS B 233 PHE 0.011 0.001 PHE B 316 TYR 0.022 0.001 TYR A 315 ARG 0.009 0.000 ARG D 528 *********************** 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 : 1.608 Fit side-chains REVERT: A 367 ASN cc_start: 0.7164 (m-40) cc_final: 0.6800 (m-40) REVERT: A 433 SER cc_start: 0.8513 (t) cc_final: 0.8254 (t) REVERT: A 455 LYS cc_start: 0.5482 (tppt) cc_final: 0.5193 (tttp) REVERT: B 235 GLN cc_start: 0.8008 (mt0) cc_final: 0.7501 (tt0) REVERT: B 285 TRP cc_start: 0.6454 (t60) cc_final: 0.5743 (t60) REVERT: B 396 TYR cc_start: 0.7681 (m-80) cc_final: 0.7196 (m-80) REVERT: B 469 LYS cc_start: 0.7504 (mttt) cc_final: 0.6827 (mmmt) REVERT: B 505 MET cc_start: 0.7500 (ttp) cc_final: 0.7252 (ttm) REVERT: B 547 GLU cc_start: 0.7215 (pm20) cc_final: 0.4814 (tp30) REVERT: C 155 TYR cc_start: 0.8069 (m-80) cc_final: 0.7654 (m-80) REVERT: C 348 ARG cc_start: 0.7056 (mmt90) cc_final: 0.6358 (ttt-90) REVERT: D 120 ASP cc_start: 0.6834 (m-30) cc_final: 0.6561 (m-30) REVERT: D 133 VAL cc_start: 0.7074 (t) cc_final: 0.6862 (t) REVERT: D 239 MET cc_start: 0.8051 (mtm) cc_final: 0.7676 (mtp) REVERT: D 371 ARG cc_start: 0.8070 (ttp-110) cc_final: 0.7715 (ttp80) REVERT: D 506 ASP cc_start: 0.8737 (p0) cc_final: 0.8294 (p0) REVERT: D 528 ARG cc_start: 0.6990 (mtm110) cc_final: 0.6568 (ttm-80) REVERT: D 539 GLN cc_start: 0.7014 (mt0) cc_final: 0.6606 (mt0) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.3237 time to fit residues: 169.9989 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 : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.0010 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 81 optimal weight: 0.0270 chunk 100 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.6646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 517 HIS B 539 GLN C 367 ASN C 447 GLN C 548 GLN D 321 HIS D 571 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.183301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.158153 restraints weight = 28868.106| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.00 r_work: 0.3580 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 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 = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2871 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= 0.223 Angle : 0.611 7.970 19839 Z= 0.313 Chirality : 0.047 0.257 2121 Planarity : 0.004 0.064 2525 Dihedral : 10.812 164.725 2095 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.47 % Favored : 96.41 % Rotamer: Outliers : 2.09 % Allowed : 14.83 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1728 helix: 1.42 (0.18), residues: 862 sheet: 2.05 (0.58), residues: 84 loop : -0.72 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 285 HIS 0.007 0.001 HIS B 233 PHE 0.020 0.002 PHE D 141 TYR 0.031 0.002 TYR B 315 ARG 0.009 0.001 ARG D 470 *********************** 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 231 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 1.827 Fit side-chains REVERT: A 254 MET cc_start: 0.7537 (ttm) cc_final: 0.7223 (ttm) REVERT: A 330 ASP cc_start: 0.8105 (t0) cc_final: 0.7883 (t0) REVERT: A 367 ASN cc_start: 0.7904 (m-40) cc_final: 0.7666 (m-40) REVERT: A 435 ASP cc_start: 0.6921 (m-30) cc_final: 0.6715 (m-30) REVERT: B 396 TYR cc_start: 0.7833 (m-80) cc_final: 0.7423 (m-80) REVERT: B 469 LYS cc_start: 0.7484 (mttt) cc_final: 0.6802 (mmmt) REVERT: B 505 MET cc_start: 0.7838 (ttp) cc_final: 0.7520 (ttm) REVERT: B 547 GLU cc_start: 0.7318 (pm20) cc_final: 0.6001 (tp30) REVERT: C 287 TYR cc_start: 0.7447 (m-80) cc_final: 0.7112 (m-80) REVERT: C 374 TYR cc_start: 0.7554 (m-80) cc_final: 0.6374 (m-80) REVERT: D 239 MET cc_start: 0.9017 (mtm) cc_final: 0.8774 (mtp) REVERT: D 371 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.8004 (ttp80) REVERT: D 383 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: D 470 ARG cc_start: 0.7228 (tpt90) cc_final: 0.6943 (tpt170) outliers start: 30 outliers final: 17 residues processed: 220 average time/residue: 0.3274 time to fit residues: 100.6583 Evaluate side-chains 180 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 382 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 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 90 optimal weight: 0.0370 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 376 HIS B 210 HIS D 125 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.174153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.146944 restraints weight = 27330.352| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.51 r_work: 0.3439 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- 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 = 0.48 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 = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14630 Z= 0.231 Angle : 0.587 6.422 19839 Z= 0.299 Chirality : 0.046 0.158 2121 Planarity : 0.004 0.049 2525 Dihedral : 10.459 160.471 2095 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 2.63 % Allowed : 15.64 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1728 helix: 1.38 (0.18), residues: 875 sheet: 1.99 (0.49), residues: 114 loop : -0.92 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 313 HIS 0.009 0.001 HIS B 233 PHE 0.028 0.002 PHE D 141 TYR 0.028 0.002 TYR B 315 ARG 0.006 0.001 ARG B 134 *********************** 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 217 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 1.686 Fit side-chains revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7544 (mmtp) cc_final: 0.7153 (tmtt) REVERT: B 119 ASN cc_start: 0.8033 (t0) cc_final: 0.7760 (t0) REVERT: B 142 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.6944 (mp10) REVERT: B 396 TYR cc_start: 0.7806 (m-80) cc_final: 0.7526 (m-80) REVERT: B 469 LYS cc_start: 0.7615 (mttt) cc_final: 0.6940 (mmmt) REVERT: B 505 MET cc_start: 0.7850 (ttp) cc_final: 0.7592 (ttm) REVERT: B 547 GLU cc_start: 0.8055 (pm20) cc_final: 0.7635 (pt0) REVERT: C 287 TYR cc_start: 0.7690 (m-80) cc_final: 0.7409 (m-80) REVERT: C 374 TYR cc_start: 0.7738 (m-80) cc_final: 0.6544 (m-80) REVERT: C 424 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: C 555 LYS cc_start: 0.7704 (mmmm) cc_final: 0.7453 (mmtp) REVERT: D 239 MET cc_start: 0.8974 (mtm) cc_final: 0.8769 (mtp) REVERT: D 334 PHE cc_start: 0.8443 (t80) cc_final: 0.8177 (t80) REVERT: D 371 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.8021 (ttp80) outliers start: 38 outliers final: 24 residues processed: 208 average time/residue: 0.3293 time to fit residues: 96.6331 Evaluate side-chains 178 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 552 VAL Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 460 THR 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 549 LEU 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 387 THR Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 150 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 58 optimal weight: 0.0020 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 109 optimal weight: 7.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 GLN D 571 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.176274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.152432 restraints weight = 20853.802| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.57 r_work: 0.3547 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4494 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= 0.165 Angle : 0.525 6.280 19839 Z= 0.265 Chirality : 0.044 0.161 2121 Planarity : 0.004 0.051 2525 Dihedral : 10.023 157.872 2095 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.96 % Allowed : 17.40 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1728 helix: 1.59 (0.18), residues: 867 sheet: 2.18 (0.50), residues: 114 loop : -0.85 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 313 HIS 0.006 0.001 HIS B 233 PHE 0.014 0.001 PHE D 141 TYR 0.022 0.001 TYR B 315 ARG 0.005 0.000 ARG A 348 *********************** 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 196 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.554 Fit side-chains REVERT: A 288 LYS cc_start: 0.7189 (mmtp) cc_final: 0.6967 (tmtt) REVERT: A 314 ASP cc_start: 0.8086 (t0) cc_final: 0.7788 (t0) REVERT: A 433 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8279 (p) REVERT: B 119 ASN cc_start: 0.8010 (t0) cc_final: 0.7721 (t0) REVERT: B 271 GLN cc_start: 0.8508 (mt0) cc_final: 0.8252 (mt0) REVERT: B 469 LYS cc_start: 0.7423 (mttt) cc_final: 0.6887 (mmmt) REVERT: B 547 GLU cc_start: 0.7920 (pm20) cc_final: 0.7655 (pt0) REVERT: C 287 TYR cc_start: 0.7616 (m-80) cc_final: 0.7352 (m-80) REVERT: C 385 MET cc_start: 0.8172 (mtp) cc_final: 0.7879 (mtp) REVERT: C 424 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: D 334 PHE cc_start: 0.8396 (t80) cc_final: 0.8156 (t80) outliers start: 28 outliers final: 15 residues processed: 190 average time/residue: 0.3405 time to fit residues: 90.7627 Evaluate side-chains 164 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 433 SER 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 182 LEU Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 118 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 548 GLN C 370 HIS ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.170882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143170 restraints weight = 27397.511| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.09 r_work: 0.3376 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14630 Z= 0.252 Angle : 0.576 6.702 19839 Z= 0.293 Chirality : 0.046 0.157 2121 Planarity : 0.004 0.049 2525 Dihedral : 10.200 154.278 2095 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.90 % Allowed : 17.33 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1728 helix: 1.50 (0.18), residues: 865 sheet: 2.22 (0.51), residues: 114 loop : -0.90 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 313 HIS 0.008 0.001 HIS B 233 PHE 0.020 0.002 PHE D 141 TYR 0.025 0.002 TYR B 315 ARG 0.005 0.000 ARG A 348 *********************** 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 195 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.673 Fit side-chains REVERT: A 346 GLU cc_start: 0.3907 (OUTLIER) cc_final: 0.3328 (pm20) REVERT: A 417 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7808 (tm-30) REVERT: B 119 ASN cc_start: 0.8266 (t0) cc_final: 0.7998 (t0) REVERT: B 142 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.6951 (mp10) REVERT: B 271 GLN cc_start: 0.8546 (mt0) cc_final: 0.8245 (mt0) REVERT: B 352 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.8270 (mtp180) REVERT: B 469 LYS cc_start: 0.7574 (mttt) cc_final: 0.7362 (mmmt) REVERT: C 287 TYR cc_start: 0.7745 (m-80) cc_final: 0.7542 (m-80) REVERT: C 385 MET cc_start: 0.7983 (mtp) cc_final: 0.7673 (mtt) REVERT: C 424 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: D 326 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7153 (mt0) REVERT: D 334 PHE cc_start: 0.8517 (t80) cc_final: 0.8259 (t80) outliers start: 42 outliers final: 26 residues processed: 185 average time/residue: 0.3472 time to fit residues: 89.1439 Evaluate side-chains 174 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 385 MET Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 370 HIS Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 170 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN B 571 GLN C 370 HIS C 548 GLN 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 = 0.3884 r_free = 0.3884 target = 0.167947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139174 restraints weight = 27489.920| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.29 r_work: 0.3355 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14630 Z= 0.258 Angle : 0.581 8.813 19839 Z= 0.292 Chirality : 0.046 0.154 2121 Planarity : 0.004 0.050 2525 Dihedral : 10.265 151.153 2095 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.10 % Allowed : 18.00 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1728 helix: 1.41 (0.18), residues: 870 sheet: 2.26 (0.51), residues: 110 loop : -0.94 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 313 HIS 0.007 0.001 HIS B 233 PHE 0.021 0.002 PHE C 454 TYR 0.026 0.002 TYR B 315 ARG 0.006 0.001 ARG A 348 *********************** 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 198 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 1.629 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.3988 (OUTLIER) cc_final: 0.3389 (pm20) REVERT: A 433 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8560 (p) REVERT: A 442 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7920 (ttp80) REVERT: B 119 ASN cc_start: 0.8294 (t0) cc_final: 0.8030 (t0) REVERT: B 142 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: B 271 GLN cc_start: 0.8589 (mt0) cc_final: 0.8312 (mt0) REVERT: B 352 ARG cc_start: 0.8708 (mmm-85) cc_final: 0.8372 (mtp180) REVERT: B 385 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6586 (mtp) REVERT: B 448 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8268 (pt) REVERT: B 469 LYS cc_start: 0.7666 (mttt) cc_final: 0.7410 (mmmt) REVERT: C 369 LEU cc_start: 0.8386 (tt) cc_final: 0.8143 (tp) REVERT: C 380 ASN cc_start: 0.7092 (OUTLIER) cc_final: 0.6850 (m-40) REVERT: C 385 MET cc_start: 0.8112 (mtp) cc_final: 0.7720 (mtt) REVERT: C 424 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8008 (m-30) REVERT: D 326 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7218 (mt0) REVERT: D 334 PHE cc_start: 0.8519 (t80) cc_final: 0.8259 (t80) outliers start: 45 outliers final: 31 residues processed: 188 average time/residue: 0.3361 time to fit residues: 87.5044 Evaluate side-chains 182 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 433 SER 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 195 ASP Chi-restraints excluded: chain B residue 340 VAL 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 B residue 448 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 265 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 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 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 27 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 137 optimal weight: 0.0870 chunk 89 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 548 GLN C 364 HIS C 548 GLN D 125 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.168291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140741 restraints weight = 21679.815| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.21 r_work: 0.3379 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14630 Z= 0.272 Angle : 0.591 7.482 19839 Z= 0.299 Chirality : 0.047 0.162 2121 Planarity : 0.004 0.050 2525 Dihedral : 10.324 146.671 2095 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.30 % Allowed : 18.68 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1728 helix: 1.36 (0.18), residues: 871 sheet: 2.11 (0.51), residues: 114 loop : -0.94 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 285 HIS 0.011 0.001 HIS C 370 PHE 0.021 0.002 PHE D 267 TYR 0.026 0.002 TYR B 315 ARG 0.006 0.001 ARG B 470 *********************** 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 192 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 1.636 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.3985 (OUTLIER) cc_final: 0.3365 (pm20) REVERT: A 433 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8641 (p) REVERT: A 442 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8001 (ttp80) REVERT: A 551 ARG cc_start: 0.5886 (mtm180) cc_final: 0.5395 (ptp-170) REVERT: B 119 ASN cc_start: 0.8294 (t0) cc_final: 0.8021 (t0) REVERT: B 142 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.6971 (mp10) REVERT: B 271 GLN cc_start: 0.8577 (mt0) cc_final: 0.8292 (mt0) REVERT: B 352 ARG cc_start: 0.8727 (mmm-85) cc_final: 0.8370 (mtp180) REVERT: B 448 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8285 (pt) REVERT: B 469 LYS cc_start: 0.7726 (mttt) cc_final: 0.7043 (mmmt) REVERT: B 470 ARG cc_start: 0.7455 (tpt90) cc_final: 0.7043 (tpp-160) REVERT: C 254 MET cc_start: 0.7907 (mtm) cc_final: 0.7589 (mtm) REVERT: C 369 LEU cc_start: 0.8402 (tt) cc_final: 0.8175 (tp) REVERT: C 380 ASN cc_start: 0.7154 (OUTLIER) cc_final: 0.6909 (m-40) REVERT: C 385 MET cc_start: 0.8145 (mtp) cc_final: 0.7736 (mtt) REVERT: C 424 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: D 326 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7256 (mt0) REVERT: D 334 PHE cc_start: 0.8521 (t80) cc_final: 0.8257 (t80) REVERT: D 470 ARG cc_start: 0.7568 (tpt90) cc_final: 0.6847 (tpt170) outliers start: 48 outliers final: 32 residues processed: 182 average time/residue: 0.3228 time to fit residues: 82.8613 Evaluate side-chains 177 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 311 ASP 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 433 SER 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 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 B residue 428 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 311 ASP 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 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 511 GLU 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 34 optimal weight: 10.0000 chunk 153 optimal weight: 0.5980 chunk 120 optimal weight: 0.0020 chunk 102 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 548 GLN C 370 HIS C 548 GLN 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 = 0.3910 r_free = 0.3910 target = 0.170375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142132 restraints weight = 29215.864| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.45 r_work: 0.3436 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- 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 = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14630 Z= 0.163 Angle : 0.522 6.268 19839 Z= 0.263 Chirality : 0.044 0.157 2121 Planarity : 0.004 0.051 2525 Dihedral : 10.000 141.893 2095 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.83 % Allowed : 19.29 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1728 helix: 1.65 (0.18), residues: 864 sheet: 2.20 (0.51), residues: 110 loop : -0.86 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 285 HIS 0.006 0.001 HIS B 233 PHE 0.013 0.001 PHE C 454 TYR 0.024 0.001 TYR D 456 ARG 0.006 0.000 ARG A 348 *********************** 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 183 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 2.100 Fit side-chains revert: symmetry clash REVERT: A 551 ARG cc_start: 0.5889 (mtm180) cc_final: 0.5559 (ptp-170) REVERT: B 119 ASN cc_start: 0.8244 (t0) cc_final: 0.7982 (t0) REVERT: B 142 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.6983 (mp10) REVERT: B 271 GLN cc_start: 0.8461 (mt0) cc_final: 0.8252 (mt0) REVERT: B 352 ARG cc_start: 0.8666 (mmm-85) cc_final: 0.8327 (mtp180) REVERT: B 469 LYS cc_start: 0.7751 (mttt) cc_final: 0.7536 (mmtt) REVERT: B 470 ARG cc_start: 0.7449 (tpt90) cc_final: 0.7087 (tpp-160) REVERT: C 369 LEU cc_start: 0.8142 (tt) cc_final: 0.7668 (tp) REVERT: C 385 MET cc_start: 0.7987 (mtp) cc_final: 0.7714 (mtt) REVERT: C 424 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: C 503 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6574 (tp) REVERT: D 149 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: D 326 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7104 (mt0) REVERT: D 470 ARG cc_start: 0.7488 (tpt90) cc_final: 0.6855 (tpt170) outliers start: 41 outliers final: 25 residues processed: 177 average time/residue: 0.3310 time to fit residues: 83.9818 Evaluate side-chains 165 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 265 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 503 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 137 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 HIS D 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.169907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.142385 restraints weight = 23050.219| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.11 r_work: 0.3398 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5678 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= 0.192 Angle : 0.540 6.998 19839 Z= 0.272 Chirality : 0.045 0.165 2121 Planarity : 0.004 0.049 2525 Dihedral : 10.046 136.483 2095 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.63 % Allowed : 19.15 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1728 helix: 1.65 (0.18), residues: 865 sheet: 2.15 (0.50), residues: 110 loop : -0.85 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 285 HIS 0.009 0.001 HIS C 370 PHE 0.015 0.001 PHE C 454 TYR 0.026 0.001 TYR D 456 ARG 0.006 0.000 ARG A 348 *********************** 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 178 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: A 442 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7912 (ttp80) REVERT: B 119 ASN cc_start: 0.8242 (t0) cc_final: 0.7957 (t0) REVERT: B 142 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.6987 (mp10) REVERT: B 271 GLN cc_start: 0.8490 (mt0) cc_final: 0.8260 (mt0) REVERT: B 352 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8306 (mtp180) REVERT: B 470 ARG cc_start: 0.7447 (tpt90) cc_final: 0.7078 (tpp-160) REVERT: C 371 ARG cc_start: 0.7389 (ptp-170) cc_final: 0.7166 (ptp-110) REVERT: C 385 MET cc_start: 0.8038 (mtp) cc_final: 0.7711 (mtt) REVERT: C 424 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: C 503 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6557 (tp) REVERT: D 149 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: D 334 PHE cc_start: 0.8457 (t80) cc_final: 0.8216 (t80) REVERT: D 497 ASP cc_start: 0.7158 (m-30) cc_final: 0.6512 (t0) outliers start: 38 outliers final: 27 residues processed: 172 average time/residue: 0.3564 time to fit residues: 86.5306 Evaluate side-chains 163 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 503 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 119 optimal weight: 0.0370 chunk 112 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 HIS D 125 HIS D 571 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.144346 restraints weight = 27232.033| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.23 r_work: 0.3377 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14630 Z= 0.155 Angle : 0.522 7.175 19839 Z= 0.264 Chirality : 0.044 0.159 2121 Planarity : 0.004 0.049 2525 Dihedral : 9.809 130.714 2095 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.23 % Allowed : 19.82 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.21), residues: 1728 helix: 1.73 (0.18), residues: 864 sheet: 2.28 (0.50), residues: 110 loop : -0.72 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 285 HIS 0.006 0.001 HIS B 233 PHE 0.012 0.001 PHE C 454 TYR 0.025 0.001 TYR D 456 ARG 0.004 0.000 ARG D 134 ********************** 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 169 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.442 Fit side-chains revert: symmetry clash REVERT: A 442 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7904 (ttp80) REVERT: B 119 ASN cc_start: 0.8258 (t0) cc_final: 0.7976 (t0) REVERT: B 142 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.6978 (mp10) REVERT: B 271 GLN cc_start: 0.8418 (mt0) cc_final: 0.8204 (mt0) REVERT: B 352 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8265 (mtp180) REVERT: B 470 ARG cc_start: 0.7410 (tpt90) cc_final: 0.7118 (tpp-160) REVERT: C 380 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6374 (m-40) REVERT: C 385 MET cc_start: 0.7990 (mtp) cc_final: 0.7685 (mtt) REVERT: C 416 MET cc_start: 0.6735 (mmm) cc_final: 0.5993 (mmm) REVERT: C 424 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: C 503 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6512 (tp) REVERT: D 149 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: D 470 ARG cc_start: 0.7554 (tpt90) cc_final: 0.7046 (tpp-160) REVERT: D 497 ASP cc_start: 0.7199 (m-30) cc_final: 0.6533 (t0) outliers start: 32 outliers final: 25 residues processed: 166 average time/residue: 0.3218 time to fit residues: 74.7272 Evaluate side-chains 163 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 442 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 311 ASP 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 503 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 89 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 57 optimal weight: 0.0970 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 138 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 HIS D 125 HIS D 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.172038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144601 restraints weight = 21713.878| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.02 r_work: 0.3418 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5792 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= 0.165 Angle : 0.523 7.176 19839 Z= 0.265 Chirality : 0.044 0.148 2121 Planarity : 0.004 0.049 2525 Dihedral : 9.633 129.632 2095 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.43 % Allowed : 19.76 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1728 helix: 1.75 (0.18), residues: 864 sheet: 2.21 (0.49), residues: 110 loop : -0.70 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 285 HIS 0.007 0.001 HIS B 233 PHE 0.013 0.001 PHE C 454 TYR 0.025 0.001 TYR D 456 ARG 0.006 0.000 ARG A 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6054.56 seconds wall clock time: 110 minutes 27.43 seconds (6627.43 seconds total)