Starting phenix.real_space_refine on Sat Oct 24 09:43:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wdo_65893/10_2026/9wdo_65893.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wdo_65893/10_2026/9wdo_65893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wdo_65893/10_2026/9wdo_65893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wdo_65893/10_2026/9wdo_65893.map" model { file = "/net/cci-nas-00/data/ceres_data/9wdo_65893/10_2026/9wdo_65893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wdo_65893/10_2026/9wdo_65893.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8080 2.51 5 N 2328 2.21 5 O 2388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12868 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3183 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "B" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3183 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "C" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3183 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "D" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3183 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'WV2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'WV2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'WV2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.26, per 1000 atoms: 0.25 Number of scatterers: 12868 At special positions: 0 Unit cell: (118.15, 85.85, 116.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2388 8.00 N 2328 7.00 C 8080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 667.0 milliseconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 6 sheets defined 53.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.589A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.704A pdb=" N TYR A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.786A pdb=" N ARG A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.939A pdb=" N VAL A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.777A pdb=" N HIS A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 316 through 322 removed outlier: 3.758A pdb=" N VAL A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 removed outlier: 3.532A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 364 removed outlier: 3.715A pdb=" N ALA A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.555A pdb=" N ILE A 378 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.860A pdb=" N GLY A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.836A pdb=" N ALA A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.521A pdb=" N ALA A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.646A pdb=" N LEU A 437 " --> pdb=" O TYR A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 467 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 524 through 543 Processing helix chain 'B' and resid 68 through 75 removed outlier: 3.596A pdb=" N LEU B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.710A pdb=" N TYR B 148 " --> pdb=" O PRO B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.643A pdb=" N ARG B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 302 removed outlier: 3.732A pdb=" N VAL B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 306 removed outlier: 3.809A pdb=" N HIS B 306 " --> pdb=" O PRO B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 306' Processing helix chain 'B' and resid 316 through 322 removed outlier: 3.751A pdb=" N VAL B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 330 removed outlier: 3.662A pdb=" N GLU B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 364 removed outlier: 3.844A pdb=" N ALA B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 353 " --> pdb=" O VAL B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.596A pdb=" N THR B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.869A pdb=" N GLY B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.853A pdb=" N ALA B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 410' Processing helix chain 'B' and resid 413 through 429 Processing helix chain 'B' and resid 433 through 444 removed outlier: 3.615A pdb=" N LEU B 437 " --> pdb=" O TYR B 433 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 Processing helix chain 'B' and resid 478 through 486 Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 524 through 543 removed outlier: 3.521A pdb=" N ASP B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.641A pdb=" N CYS C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 123 through 140 Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.716A pdb=" N TYR C 148 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 279 removed outlier: 3.920A pdb=" N ARG C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 302 removed outlier: 3.890A pdb=" N VAL C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 306 removed outlier: 3.799A pdb=" N HIS C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 306' Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 322 through 330 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 348 through 364 Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 384 through 398 removed outlier: 3.890A pdb=" N GLY C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.806A pdb=" N ALA C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.539A pdb=" N ALA C 417 " --> pdb=" O PHE C 413 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 444 removed outlier: 3.694A pdb=" N LEU C 437 " --> pdb=" O TYR C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 466 Processing helix chain 'C' and resid 478 through 487 removed outlier: 4.454A pdb=" N TYR C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 507 through 509 No H-bonds generated for 'chain 'C' and resid 507 through 509' Processing helix chain 'C' and resid 524 through 543 removed outlier: 3.623A pdb=" N ASP C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 75 removed outlier: 3.519A pdb=" N LEU D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 123 through 140 Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.717A pdb=" N TYR D 148 " --> pdb=" O PRO D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 279 removed outlier: 3.810A pdb=" N ARG D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 302 removed outlier: 3.956A pdb=" N VAL D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 306 removed outlier: 3.845A pdb=" N HIS D 306 " --> pdb=" O PRO D 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 306' Processing helix chain 'D' and resid 316 through 322 Processing helix chain 'D' and resid 322 through 330 removed outlier: 3.670A pdb=" N GLU D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 348 through 364 Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.520A pdb=" N ILE D 378 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 379 " --> pdb=" O SER D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 398 removed outlier: 3.876A pdb=" N GLY D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.889A pdb=" N ALA D 409 " --> pdb=" O SER D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 431 removed outlier: 3.542A pdb=" N ALA D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 418 " --> pdb=" O PRO D 414 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 430 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 444 removed outlier: 3.620A pdb=" N LEU D 437 " --> pdb=" O TYR D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 466 removed outlier: 3.678A pdb=" N CYS D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 486 Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 507 through 509 No H-bonds generated for 'chain 'D' and resid 507 through 509' Processing helix chain 'D' and resid 524 through 543 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 93 removed outlier: 6.602A pdb=" N ILE A 90 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ARG A 116 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 92 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASN A 118 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 115 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP A 156 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 117 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 153 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N PHE A 284 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 155 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 332 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 403 " --> pdb=" O CYS A 369 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER A 89 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU A 404 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 91 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 516 removed outlier: 6.872A pdb=" N VAL A 493 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU A 515 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA A 495 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 471 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL A 496 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 473 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA A 470 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 567 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 567 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 556 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA B 470 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 471 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL B 496 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 473 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 493 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU B 515 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 495 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 93 removed outlier: 6.619A pdb=" N ILE B 90 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ARG B 116 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 92 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA B 115 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ASP B 156 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 117 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 153 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N PHE B 284 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 155 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 332 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS B 401 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 403 " --> pdb=" O CYS B 369 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER B 89 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU B 404 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 91 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 89 through 93 removed outlier: 6.397A pdb=" N ALA C 115 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASP C 156 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 117 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE C 153 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE C 284 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 155 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY C 332 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS C 401 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET C 403 " --> pdb=" O CYS C 369 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER C 89 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU C 404 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE C 91 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 512 through 516 removed outlier: 6.895A pdb=" N VAL C 493 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU C 515 " --> pdb=" O VAL C 493 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA C 495 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE C 471 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL C 496 " --> pdb=" O ILE C 471 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 473 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA C 470 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 567 " --> pdb=" O THR C 556 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA D 470 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE D 471 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL D 496 " --> pdb=" O ILE D 471 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL D 473 " --> pdb=" O VAL D 496 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL D 493 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU D 515 " --> pdb=" O VAL D 493 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA D 495 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 89 through 93 removed outlier: 6.617A pdb=" N ILE D 90 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ARG D 116 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA D 92 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASN D 118 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA D 115 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP D 156 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 117 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE D 153 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE D 284 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU D 155 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE D 310 " --> pdb=" O GLY D 332 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N MET D 334 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER D 312 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS D 401 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET D 403 " --> pdb=" O CYS D 369 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N SER D 89 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU D 404 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE D 91 " --> pdb=" O LEU D 404 " (cutoff:3.500A) 591 hydrogen bonds defined for protein. 1731 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: 1.90 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2180 1.26 - 1.40: 2984 1.40 - 1.54: 7765 1.54 - 1.69: 39 1.69 - 1.83: 116 Bond restraints: 13084 Sorted by residual: bond pdb=" C20 WV2 D 602 " pdb=" N3 WV2 D 602 " ideal model delta sigma weight residual 1.451 1.119 0.332 2.00e-02 2.50e+03 2.76e+02 bond pdb=" C20 WV2 C 601 " pdb=" N3 WV2 C 601 " ideal model delta sigma weight residual 1.451 1.119 0.332 2.00e-02 2.50e+03 2.76e+02 bond pdb=" C20 WV2 A 601 " pdb=" N3 WV2 A 601 " ideal model delta sigma weight residual 1.451 1.119 0.332 2.00e-02 2.50e+03 2.75e+02 bond pdb=" C20 WV2 D 601 " pdb=" N3 WV2 D 601 " ideal model delta sigma weight residual 1.451 1.122 0.329 2.00e-02 2.50e+03 2.71e+02 bond pdb=" C15 WV2 D 601 " pdb=" N3 WV2 D 601 " ideal model delta sigma weight residual 1.450 1.128 0.322 2.00e-02 2.50e+03 2.58e+02 ... (remaining 13079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 17573 3.38 - 6.75: 123 6.75 - 10.13: 12 10.13 - 13.51: 3 13.51 - 16.89: 13 Bond angle restraints: 17724 Sorted by residual: angle pdb=" C15 WV2 D 602 " pdb=" N3 WV2 D 602 " pdb=" C20 WV2 D 602 " ideal model delta sigma weight residual 110.57 127.46 -16.89 3.00e+00 1.11e-01 3.17e+01 angle pdb=" C15 WV2 A 601 " pdb=" N3 WV2 A 601 " pdb=" C20 WV2 A 601 " ideal model delta sigma weight residual 110.57 127.36 -16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" C15 WV2 D 601 " pdb=" N3 WV2 D 601 " pdb=" C20 WV2 D 601 " ideal model delta sigma weight residual 110.57 127.34 -16.77 3.00e+00 1.11e-01 3.13e+01 angle pdb=" C15 WV2 C 601 " pdb=" N3 WV2 C 601 " pdb=" C20 WV2 C 601 " ideal model delta sigma weight residual 110.57 127.12 -16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O WV2 D 601 " pdb=" S WV2 D 601 " pdb=" O2 WV2 D 601 " ideal model delta sigma weight residual 118.67 102.24 16.43 3.00e+00 1.11e-01 3.00e+01 ... (remaining 17719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.59: 7394 30.59 - 61.18: 603 61.18 - 91.77: 32 91.77 - 122.36: 3 122.36 - 152.95: 8 Dihedral angle restraints: 8040 sinusoidal: 3240 harmonic: 4800 Sorted by residual: dihedral pdb=" C15 WV2 A 601 " pdb=" C16 WV2 A 601 " pdb=" N3 WV2 A 601 " pdb=" C17 WV2 A 601 " ideal model delta sinusoidal sigma weight residual 65.11 -87.84 152.95 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C15 WV2 D 602 " pdb=" C16 WV2 D 602 " pdb=" N3 WV2 D 602 " pdb=" C17 WV2 D 602 " ideal model delta sinusoidal sigma weight residual 65.11 -83.86 148.97 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" C15 WV2 D 601 " pdb=" C16 WV2 D 601 " pdb=" N3 WV2 D 601 " pdb=" C17 WV2 D 601 " ideal model delta sinusoidal sigma weight residual 65.11 -80.36 145.47 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 8037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1757 0.066 - 0.133: 246 0.133 - 0.199: 25 0.199 - 0.265: 0 0.265 - 0.332: 4 Chirality restraints: 2032 Sorted by residual: chirality pdb=" C17 WV2 C 601 " pdb=" C16 WV2 C 601 " pdb=" C18 WV2 C 601 " pdb=" C19 WV2 C 601 " both_signs ideal model delta sigma weight residual True 2.39 -2.72 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C17 WV2 D 602 " pdb=" C16 WV2 D 602 " pdb=" C18 WV2 D 602 " pdb=" C19 WV2 D 602 " both_signs ideal model delta sigma weight residual True 2.39 -2.72 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C17 WV2 D 601 " pdb=" C16 WV2 D 601 " pdb=" C18 WV2 D 601 " pdb=" C19 WV2 D 601 " both_signs ideal model delta sigma weight residual True 2.39 -2.71 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 2029 not shown) Planarity restraints: 2312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 344 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO D 345 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 345 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 345 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 344 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO C 345 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 345 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 345 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 519 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO D 520 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 520 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 520 " 0.031 5.00e-02 4.00e+02 ... (remaining 2309 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2546 2.79 - 3.32: 11046 3.32 - 3.84: 20494 3.84 - 4.37: 23075 4.37 - 4.90: 41495 Nonbonded interactions: 98656 Sorted by model distance: nonbonded pdb=" OG SER C 100 " pdb=" OE1 GLU C 102 " model vdw 2.259 3.040 nonbonded pdb=" OG SER B 100 " pdb=" OE1 GLU B 102 " model vdw 2.271 3.040 nonbonded pdb=" NH2 ARG C 99 " pdb=" OE1 GLU C 129 " model vdw 2.271 3.120 nonbonded pdb=" OG SER A 100 " pdb=" OE1 GLU A 102 " model vdw 2.272 3.040 nonbonded pdb=" O1 WV2 D 602 " pdb=" O HOH D 701 " model vdw 2.285 3.040 ... (remaining 98651 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 66 through 574) selection = chain 'B' selection = (chain 'C' and resid 66 through 574) selection = (chain 'D' and resid 66 through 574) } 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=1.00 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: 1.550 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.760 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.010 0.332 13084 Z= 0.513 Angle : 0.843 16.886 17724 Z= 0.387 Chirality : 0.048 0.332 2032 Planarity : 0.006 0.061 2312 Dihedral : 20.603 152.949 4936 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 31.59 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 1664 helix: 0.92 (0.17), residues: 756 sheet: 1.14 (0.28), residues: 336 loop : -1.03 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 559 TYR 0.007 0.001 TYR A 126 PHE 0.016 0.001 PHE B 274 TRP 0.012 0.002 TRP B 558 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.01024 / 0.51 (13084) covalent geometry : angle 0.84262 / 0.39 (17724) hydrogen bonds : bond 0.19240 / 12.60 ( 591) hydrogen bonds : angle 4.99844 / 3.54 ( 1731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.422 Fit side-chains REVERT: B 440 GLU cc_start: 0.7331 (mp0) cc_final: 0.7089 (mp0) REVERT: B 573 ILE cc_start: 0.7417 (mm) cc_final: 0.7033 (mm) REVERT: D 564 TYR cc_start: 0.5098 (m-10) cc_final: 0.4852 (m-10) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.7297 time to fit residues: 143.5222 Evaluate side-chains 173 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 278 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.191523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139992 restraints weight = 12316.621| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.57 r_work: 0.3641 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13084 Z= 0.158 Angle : 0.567 5.370 17724 Z= 0.295 Chirality : 0.045 0.154 2032 Planarity : 0.005 0.047 2312 Dihedral : 12.695 138.426 1948 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.74 % Allowed : 26.12 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1664 helix: 1.68 (0.18), residues: 780 sheet: 0.83 (0.27), residues: 336 loop : -0.93 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 337 TYR 0.007 0.001 TYR C 126 PHE 0.014 0.002 PHE C 274 TRP 0.008 0.002 TRP A 558 HIS 0.006 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (13084) covalent geometry : angle 0.56690 / 0.30 (17724) hydrogen bonds : bond 0.06655 / 4.52 ( 591) hydrogen bonds : angle 3.65245 / 2.55 ( 1731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 0.440 Fit side-chains REVERT: A 287 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7164 (t80) REVERT: A 564 TYR cc_start: 0.6296 (m-80) cc_final: 0.5657 (m-80) REVERT: B 287 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6995 (t80) REVERT: B 325 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: B 439 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.5818 (mp0) REVERT: B 440 GLU cc_start: 0.7302 (mp0) cc_final: 0.7079 (mp0) REVERT: B 464 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.6859 (t80) REVERT: B 479 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7309 (ttm170) REVERT: C 129 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: D 564 TYR cc_start: 0.5876 (m-10) cc_final: 0.5589 (m-10) outliers start: 50 outliers final: 21 residues processed: 210 average time/residue: 0.7769 time to fit residues: 173.9875 Evaluate side-chains 187 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 572 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [128, 92, 166, 60, 11, 157, 77, 79, 153, 125, 137] chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 153 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.192909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141481 restraints weight = 12388.170| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.56 r_work: 0.3658 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13084 Z= 0.117 Angle : 0.487 5.016 17724 Z= 0.257 Chirality : 0.043 0.142 2032 Planarity : 0.004 0.042 2312 Dihedral : 12.887 143.968 1948 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.27 % Allowed : 25.67 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1664 helix: 2.10 (0.18), residues: 784 sheet: 0.72 (0.27), residues: 336 loop : -0.76 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 559 TYR 0.009 0.001 TYR D 126 PHE 0.012 0.001 PHE C 274 TRP 0.006 0.001 TRP C 525 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (13084) covalent geometry : angle 0.48743 / 0.26 (17724) hydrogen bonds : bond 0.05128 / 3.50 ( 591) hydrogen bonds : angle 3.42783 / 2.39 ( 1731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 177 time to evaluate : 0.486 Fit side-chains REVERT: A 287 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7172 (t80) REVERT: B 293 ASP cc_start: 0.6506 (m-30) cc_final: 0.6290 (m-30) REVERT: B 325 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: B 439 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.5808 (mp0) REVERT: B 440 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: B 464 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7000 (t80) REVERT: B 479 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7080 (ttm170) REVERT: B 573 ILE cc_start: 0.7580 (mm) cc_final: 0.7226 (mm) REVERT: C 77 ASP cc_start: 0.7188 (t0) cc_final: 0.6746 (p0) REVERT: C 501 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: D 287 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7157 (t80) REVERT: D 443 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.5877 (mtp180) REVERT: D 564 TYR cc_start: 0.5912 (m-10) cc_final: 0.5579 (m-10) outliers start: 57 outliers final: 19 residues processed: 212 average time/residue: 0.7447 time to fit residues: 168.7647 Evaluate side-chains 205 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 564 TYR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 564 TYR Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 443 ARG Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [87, 20, 28, 61, 51, 99, 45, 1, 144, 4, 155] chunk 87 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 144 optimal weight: 0.6980 chunk 4 optimal weight: 0.0000 chunk 155 optimal weight: 0.0980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.200161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153053 restraints weight = 12562.479| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.33 r_work: 0.3759 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13084 Z= 0.078 Angle : 0.420 4.590 17724 Z= 0.219 Chirality : 0.041 0.132 2032 Planarity : 0.003 0.040 2312 Dihedral : 12.518 139.602 1948 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.07 % Allowed : 26.65 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.21), residues: 1664 helix: 2.49 (0.19), residues: 784 sheet: 0.84 (0.28), residues: 336 loop : -0.62 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 559 TYR 0.013 0.001 TYR C 126 PHE 0.011 0.001 PHE C 274 TRP 0.006 0.001 TRP C 525 HIS 0.004 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00168 / 0.08 (13084) covalent geometry : angle 0.41996 / 0.22 (17724) hydrogen bonds : bond 0.03368 / 2.30 ( 591) hydrogen bonds : angle 3.23262 / 2.26 ( 1731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.416 Fit side-chains REVERT: A 287 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7203 (t80) REVERT: A 464 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6807 (t80) REVERT: B 287 PHE cc_start: 0.6781 (OUTLIER) cc_final: 0.6281 (t80) REVERT: B 382 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7018 (mtp85) REVERT: B 439 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.5845 (mp0) REVERT: B 440 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 464 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6865 (t80) REVERT: B 479 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7042 (ttm170) REVERT: B 573 ILE cc_start: 0.7502 (mm) cc_final: 0.7174 (mm) REVERT: C 77 ASP cc_start: 0.7315 (t0) cc_final: 0.6836 (p0) REVERT: C 328 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6201 (mp0) REVERT: C 382 ARG cc_start: 0.7936 (mtp180) cc_final: 0.6966 (mtp85) REVERT: D 287 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7168 (t80) REVERT: D 439 GLU cc_start: 0.6481 (mt-10) cc_final: 0.6018 (mp0) REVERT: D 443 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.5810 (mtp180) REVERT: D 479 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7009 (ttm170) REVERT: D 564 TYR cc_start: 0.5774 (m-10) cc_final: 0.5459 (m-10) outliers start: 41 outliers final: 13 residues processed: 204 average time/residue: 0.7442 time to fit residues: 162.0694 Evaluate side-chains 197 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 564 TYR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 564 TYR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 443 ARG Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [28, 122, 23, 80, 109, 55, 108, 142, 104, 49, 105] chunk 28 optimal weight: 0.2980 chunk 122 optimal weight: 9.9990 chunk 23 optimal weight: 0.0770 chunk 80 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.198036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151064 restraints weight = 12599.465| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.65 r_work: 0.3728 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13084 Z= 0.095 Angle : 0.444 4.606 17724 Z= 0.232 Chirality : 0.042 0.134 2032 Planarity : 0.003 0.040 2312 Dihedral : 12.560 138.390 1948 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.14 % Allowed : 26.50 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.21), residues: 1664 helix: 2.57 (0.19), residues: 784 sheet: 0.80 (0.28), residues: 336 loop : -0.55 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 103 TYR 0.010 0.001 TYR C 126 PHE 0.011 0.001 PHE C 274 TRP 0.005 0.001 TRP C 525 HIS 0.004 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 (13084) covalent geometry : angle 0.44435 / 0.23 (17724) hydrogen bonds : bond 0.04208 / 2.88 ( 591) hydrogen bonds : angle 3.20856 / 2.25 ( 1731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.484 Fit side-chains REVERT: A 287 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.7191 (t80) REVERT: A 464 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.6801 (t80) REVERT: A 527 ASP cc_start: 0.7666 (m-30) cc_final: 0.7385 (m-30) REVERT: B 287 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6247 (t80) REVERT: B 439 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.5823 (mp0) REVERT: B 464 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6776 (t80) REVERT: B 573 ILE cc_start: 0.7516 (mm) cc_final: 0.7182 (mm) REVERT: C 77 ASP cc_start: 0.7260 (t0) cc_final: 0.6775 (p0) REVERT: C 328 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6336 (mp0) REVERT: C 382 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7007 (mtp85) REVERT: C 464 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6616 (t80) REVERT: C 501 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: D 287 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7145 (t80) REVERT: D 439 GLU cc_start: 0.6491 (mt-10) cc_final: 0.6004 (mp0) REVERT: D 443 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.5783 (mtp180) REVERT: D 564 TYR cc_start: 0.5832 (m-10) cc_final: 0.5474 (m-10) outliers start: 42 outliers final: 19 residues processed: 203 average time/residue: 0.7210 time to fit residues: 156.8341 Evaluate side-chains 204 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 564 TYR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 564 TYR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 443 ARG Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [74, 19, 130, 94, 66, 72, 55, 122, 73, 2, 103] chunk 74 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.189113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137382 restraints weight = 12284.735| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.56 r_work: 0.3610 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13084 Z= 0.198 Angle : 0.596 5.925 17724 Z= 0.314 Chirality : 0.046 0.169 2032 Planarity : 0.005 0.040 2312 Dihedral : 13.522 150.972 1948 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.67 % Allowed : 25.60 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.21), residues: 1664 helix: 2.15 (0.18), residues: 780 sheet: 0.66 (0.27), residues: 328 loop : -0.79 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 337 TYR 0.006 0.001 TYR B 148 PHE 0.014 0.002 PHE C 141 TRP 0.008 0.002 TRP B 558 HIS 0.006 0.002 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.20 (13084) covalent geometry : angle 0.59585 / 0.31 (17724) hydrogen bonds : bond 0.07145 / 4.88 ( 591) hydrogen bonds : angle 3.51623 / 2.47 ( 1731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.388 Fit side-chains REVERT: A 287 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6987 (t80) REVERT: A 479 ARG cc_start: 0.7690 (ttt180) cc_final: 0.7402 (tmm160) REVERT: B 81 GLU cc_start: 0.5781 (tp30) cc_final: 0.4685 (pm20) REVERT: B 287 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6308 (t80) REVERT: B 293 ASP cc_start: 0.6514 (m-30) cc_final: 0.6235 (m-30) REVERT: B 439 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.5527 (mp0) REVERT: B 464 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6678 (t80) REVERT: B 479 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7103 (ttm170) REVERT: C 77 ASP cc_start: 0.7067 (t0) cc_final: 0.6596 (p0) REVERT: C 328 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6514 (mm-30) REVERT: C 479 ARG cc_start: 0.7729 (ttt180) cc_final: 0.7419 (tmm160) REVERT: D 77 ASP cc_start: 0.7216 (t0) cc_final: 0.6984 (OUTLIER) REVERT: D 287 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7007 (t80) REVERT: D 479 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7046 (ttm170) REVERT: D 559 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.6753 (mpt-90) REVERT: D 564 TYR cc_start: 0.5853 (m-10) cc_final: 0.5359 (m-10) outliers start: 49 outliers final: 18 residues processed: 204 average time/residue: 0.7571 time to fit residues: 165.0772 Evaluate side-chains 187 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 559 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [15, 49, 131, 50, 122, 80, 79, 132, 11, 67, 117] chunk 15 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.188630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137028 restraints weight = 12353.099| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.55 r_work: 0.3611 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13084 Z= 0.194 Angle : 0.598 6.036 17724 Z= 0.316 Chirality : 0.046 0.164 2032 Planarity : 0.005 0.040 2312 Dihedral : 13.784 152.789 1948 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.74 % Allowed : 25.30 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.21), residues: 1664 helix: 1.98 (0.18), residues: 780 sheet: 0.46 (0.27), residues: 328 loop : -0.91 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 103 TYR 0.006 0.002 TYR D 148 PHE 0.011 0.002 PHE C 141 TRP 0.007 0.002 TRP B 558 HIS 0.006 0.002 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.19 (13084) covalent geometry : angle 0.59814 / 0.32 (17724) hydrogen bonds : bond 0.06956 / 4.76 ( 591) hydrogen bonds : angle 3.53994 / 2.48 ( 1731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.472 Fit side-chains REVERT: A 287 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.7077 (t80) REVERT: A 479 ARG cc_start: 0.8056 (ttt180) cc_final: 0.7772 (tmm160) REVERT: B 77 ASP cc_start: 0.7283 (t0) cc_final: 0.6989 (OUTLIER) REVERT: B 81 GLU cc_start: 0.6020 (tp30) cc_final: 0.5042 (pm20) REVERT: B 287 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6540 (t80) REVERT: B 290 LYS cc_start: 0.6261 (OUTLIER) cc_final: 0.5953 (pttm) REVERT: B 293 ASP cc_start: 0.6723 (m-30) cc_final: 0.6418 (m-30) REVERT: B 439 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.5915 (mp0) REVERT: B 464 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6840 (t80) REVERT: B 479 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7833 (tmm160) REVERT: C 77 ASP cc_start: 0.7241 (t0) cc_final: 0.6826 (p0) REVERT: C 328 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6811 (mm-30) REVERT: C 479 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7774 (tmm160) REVERT: D 77 ASP cc_start: 0.7360 (t0) cc_final: 0.7011 (p0) REVERT: D 287 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7205 (t80) REVERT: D 347 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6551 (pt0) REVERT: D 479 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7413 (ttm170) REVERT: D 559 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7032 (mpt-90) REVERT: D 564 TYR cc_start: 0.6366 (m-10) cc_final: 0.5986 (m-80) outliers start: 50 outliers final: 20 residues processed: 203 average time/residue: 0.7415 time to fit residues: 160.9737 Evaluate side-chains 189 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 564 TYR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 559 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [114, 112, 40, 0, 97, 54, 128, 110, 8, 17, 12] chunk 114 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.193170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142096 restraints weight = 12188.363| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.54 r_work: 0.3668 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13084 Z= 0.095 Angle : 0.455 4.671 17724 Z= 0.240 Chirality : 0.042 0.136 2032 Planarity : 0.004 0.039 2312 Dihedral : 13.214 145.081 1948 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.99 % Allowed : 25.90 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.21), residues: 1664 helix: 2.40 (0.19), residues: 784 sheet: 0.49 (0.27), residues: 336 loop : -0.68 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 103 TYR 0.011 0.001 TYR D 126 PHE 0.009 0.001 PHE B 274 TRP 0.009 0.001 TRP A 525 HIS 0.003 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (13084) covalent geometry : angle 0.45511 / 0.24 (17724) hydrogen bonds : bond 0.04114 / 2.82 ( 591) hydrogen bonds : angle 3.26470 / 2.28 ( 1731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.478 Fit side-chains REVERT: A 287 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.7113 (t80) REVERT: B 77 ASP cc_start: 0.7344 (t0) cc_final: 0.7062 (OUTLIER) REVERT: B 287 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6523 (t80) REVERT: B 293 ASP cc_start: 0.6839 (m-30) cc_final: 0.6604 (m-30) REVERT: B 439 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.5956 (mp0) REVERT: B 464 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6739 (t80) REVERT: B 573 ILE cc_start: 0.7601 (mm) cc_final: 0.7300 (mm) REVERT: C 328 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6653 (mm-30) REVERT: C 479 ARG cc_start: 0.7856 (ttt180) cc_final: 0.7583 (tmm160) REVERT: D 77 ASP cc_start: 0.7309 (t0) cc_final: 0.7041 (p0) REVERT: D 287 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7211 (t80) REVERT: D 479 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7147 (ttm170) REVERT: D 564 TYR cc_start: 0.6140 (m-10) cc_final: 0.5762 (m-80) outliers start: 40 outliers final: 20 residues processed: 203 average time/residue: 0.7348 time to fit residues: 159.8201 Evaluate side-chains 193 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 564 TYR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 564 TYR Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [154, 118, 58, 29, 52, 64, 1, 15, 125, 82, 126] chunk 154 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 0.0770 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.192176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140966 restraints weight = 12240.444| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.54 r_work: 0.3653 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13084 Z= 0.111 Angle : 0.480 5.006 17724 Z= 0.252 Chirality : 0.043 0.136 2032 Planarity : 0.004 0.040 2312 Dihedral : 13.202 144.910 1948 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.25 % Allowed : 26.80 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.21), residues: 1664 helix: 2.43 (0.19), residues: 784 sheet: 0.49 (0.27), residues: 336 loop : -0.69 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 103 TYR 0.009 0.001 TYR D 126 PHE 0.009 0.001 PHE B 274 TRP 0.007 0.001 TRP C 525 HIS 0.004 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (13084) covalent geometry : angle 0.47987 / 0.25 (17724) hydrogen bonds : bond 0.04775 / 3.27 ( 591) hydrogen bonds : angle 3.25958 / 2.29 ( 1731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.397 Fit side-chains REVERT: A 287 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7130 (t80) REVERT: A 464 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6925 (t80) REVERT: A 479 ARG cc_start: 0.7915 (ttt180) cc_final: 0.7645 (tmm160) REVERT: B 77 ASP cc_start: 0.7361 (t0) cc_final: 0.7042 (OUTLIER) REVERT: B 287 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6538 (t80) REVERT: B 293 ASP cc_start: 0.6665 (m-30) cc_final: 0.6450 (m-30) REVERT: B 439 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.5977 (mp0) REVERT: C 328 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6614 (mm-30) REVERT: C 479 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7601 (tmm160) REVERT: D 77 ASP cc_start: 0.7343 (t0) cc_final: 0.7046 (p0) REVERT: D 287 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7275 (t80) REVERT: D 329 VAL cc_start: 0.7333 (t) cc_final: 0.7067 (p) REVERT: D 564 TYR cc_start: 0.6166 (m-10) cc_final: 0.5781 (m-80) outliers start: 30 outliers final: 21 residues processed: 183 average time/residue: 0.7202 time to fit residues: 141.5754 Evaluate side-chains 187 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 564 TYR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [1, 137, 98, 72, 59, 125, 43, 71, 19, 55, 82] chunk 1 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 19 optimal weight: 0.0370 chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.190042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138583 restraints weight = 12323.056| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.54 r_work: 0.3626 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13084 Z= 0.155 Angle : 0.543 5.548 17724 Z= 0.286 Chirality : 0.044 0.143 2032 Planarity : 0.004 0.040 2312 Dihedral : 13.515 149.207 1948 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.17 % Allowed : 27.02 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.21), residues: 1664 helix: 2.27 (0.18), residues: 780 sheet: 0.50 (0.27), residues: 328 loop : -0.81 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 103 TYR 0.008 0.001 TYR D 433 PHE 0.010 0.002 PHE C 141 TRP 0.007 0.001 TRP B 558 HIS 0.004 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (13084) covalent geometry : angle 0.54349 / 0.29 (17724) hydrogen bonds : bond 0.06067 / 4.15 ( 591) hydrogen bonds : angle 3.39922 / 2.38 ( 1731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.467 Fit side-chains REVERT: A 287 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7176 (t80) REVERT: A 464 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6932 (t80) REVERT: A 479 ARG cc_start: 0.7985 (ttt180) cc_final: 0.7700 (tmm160) REVERT: B 81 GLU cc_start: 0.6055 (tp30) cc_final: 0.4814 (pm20) REVERT: B 287 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6563 (t80) REVERT: B 293 ASP cc_start: 0.6723 (m-30) cc_final: 0.6459 (m-30) REVERT: B 439 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.5998 (mp0) REVERT: B 464 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.6998 (t80) REVERT: C 328 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6721 (mm-30) REVERT: C 479 ARG cc_start: 0.7971 (ttt180) cc_final: 0.7697 (tmm160) REVERT: D 77 ASP cc_start: 0.7359 (t0) cc_final: 0.7042 (p0) REVERT: D 287 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7250 (t80) REVERT: D 329 VAL cc_start: 0.7386 (t) cc_final: 0.7117 (p) REVERT: D 479 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7405 (ttm170) REVERT: D 564 TYR cc_start: 0.6235 (m-10) cc_final: 0.5834 (m-80) outliers start: 29 outliers final: 18 residues processed: 187 average time/residue: 0.7267 time to fit residues: 145.5540 Evaluate side-chains 187 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [122, 163, 0, 139, 92, 100, 27, 79, 160, 123, 60] chunk 122 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 79 optimal weight: 0.0970 chunk 160 optimal weight: 0.9990 chunk 123 optimal weight: 0.0870 chunk 60 optimal weight: 1.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.192225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140922 restraints weight = 12275.845| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.54 r_work: 0.3643 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13084 Z= 0.108 Angle : 0.477 5.037 17724 Z= 0.251 Chirality : 0.042 0.136 2032 Planarity : 0.004 0.040 2312 Dihedral : 13.267 146.264 1948 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.32 % Allowed : 26.72 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.21), residues: 1664 helix: 2.42 (0.19), residues: 784 sheet: 0.56 (0.28), residues: 328 loop : -0.66 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 103 TYR 0.009 0.001 TYR D 126 PHE 0.009 0.001 PHE B 274 TRP 0.008 0.001 TRP C 525 HIS 0.003 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (13084) covalent geometry : angle 0.47678 / 0.25 (17724) hydrogen bonds : bond 0.04625 / 3.16 ( 591) hydrogen bonds : angle 3.27236 / 2.29 ( 1731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5174.17 seconds wall clock time: 88 minutes 25.21 seconds (5305.21 seconds total)