Starting phenix.real_space_refine on Fri Sep 27 08:53:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aye_7018/09_2024/6aye_7018.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aye_7018/09_2024/6aye_7018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aye_7018/09_2024/6aye_7018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aye_7018/09_2024/6aye_7018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aye_7018/09_2024/6aye_7018.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6aye_7018/09_2024/6aye_7018.cif" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 128 5.16 5 C 10288 2.51 5 N 2488 2.21 5 O 2760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15664 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3916 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 3 Chain: "B" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3916 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 3 Chain: "C" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3916 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 3 Chain: "D" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3916 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 3 Time building chain proxies: 8.86, per 1000 atoms: 0.57 Number of scatterers: 15664 At special positions: 0 Unit cell: (106.92, 106.92, 117.48, 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 128 16.00 O 2760 8.00 N 2488 7.00 C 10288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 66.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 33 through 47 Processing helix chain 'A' and resid 49 through 56 removed outlier: 3.771A pdb=" N PHE A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 103 removed outlier: 3.823A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 135 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.935A pdb=" N VAL A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 324 removed outlier: 4.147A pdb=" N PHE A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 338 removed outlier: 3.603A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.894A pdb=" N MET A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 395 removed outlier: 4.305A pdb=" N ILE A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 435 removed outlier: 4.336A pdb=" N LEU A 401 " --> pdb=" O LYS A 397 " (cutoff:3.500A) Proline residue: A 410 - end of helix removed outlier: 3.934A pdb=" N ARG A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.717A pdb=" N THR A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 492 Processing helix chain 'A' and resid 492 through 514 Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'B' and resid 34 through 47 Processing helix chain 'B' and resid 49 through 56 removed outlier: 3.771A pdb=" N PHE B 53 " --> pdb=" O PRO B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 103 removed outlier: 3.822A pdb=" N ALA B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 135 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.936A pdb=" N VAL B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 324 removed outlier: 4.150A pdb=" N PHE B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA B 290 " --> pdb=" O MET B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.603A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 366 removed outlier: 3.895A pdb=" N MET B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 395 removed outlier: 4.305A pdb=" N ILE B 389 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE B 395 " --> pdb=" O TYR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 435 removed outlier: 4.335A pdb=" N LEU B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Proline residue: B 410 - end of helix removed outlier: 3.934A pdb=" N ARG B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 422 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE B 432 " --> pdb=" O PHE B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 456 Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.717A pdb=" N THR B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 492 Processing helix chain 'B' and resid 492 through 514 Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'C' and resid 34 through 47 Processing helix chain 'C' and resid 49 through 56 removed outlier: 3.771A pdb=" N PHE C 53 " --> pdb=" O PRO C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 103 removed outlier: 3.823A pdb=" N ALA C 64 " --> pdb=" O PRO C 60 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 135 Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.935A pdb=" N VAL C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 324 removed outlier: 4.150A pdb=" N PHE C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA C 290 " --> pdb=" O MET C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 3.602A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 366 removed outlier: 3.894A pdb=" N MET C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 395 removed outlier: 4.305A pdb=" N ILE C 389 " --> pdb=" O TRP C 385 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE C 395 " --> pdb=" O TYR C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 435 removed outlier: 4.337A pdb=" N LEU C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Proline residue: C 410 - end of helix removed outlier: 3.934A pdb=" N ARG C 414 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE C 432 " --> pdb=" O PHE C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 456 Processing helix chain 'C' and resid 459 through 466 removed outlier: 3.717A pdb=" N THR C 463 " --> pdb=" O ASP C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 492 Processing helix chain 'C' and resid 492 through 514 Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'D' and resid 34 through 47 Processing helix chain 'D' and resid 49 through 56 removed outlier: 3.770A pdb=" N PHE D 53 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 103 removed outlier: 3.822A pdb=" N ALA D 64 " --> pdb=" O PRO D 60 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 135 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.935A pdb=" N VAL D 230 " --> pdb=" O ASN D 226 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 324 removed outlier: 4.150A pdb=" N PHE D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 290 " --> pdb=" O MET D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 338 removed outlier: 3.602A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 366 removed outlier: 3.894A pdb=" N MET D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 395 removed outlier: 4.304A pdb=" N ILE D 389 " --> pdb=" O TRP D 385 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG D 390 " --> pdb=" O LEU D 386 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE D 394 " --> pdb=" O ARG D 390 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE D 395 " --> pdb=" O TYR D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 435 removed outlier: 4.335A pdb=" N LEU D 401 " --> pdb=" O LYS D 397 " (cutoff:3.500A) Proline residue: D 410 - end of helix removed outlier: 3.934A pdb=" N ARG D 414 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 422 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 428 " --> pdb=" O LEU D 424 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 456 Processing helix chain 'D' and resid 459 through 466 removed outlier: 3.717A pdb=" N THR D 463 " --> pdb=" O ASP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 492 Processing helix chain 'D' and resid 492 through 514 Processing helix chain 'D' and resid 519 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 7.250A pdb=" N LEU A 213 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR A 163 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 215 " --> pdb=" O HIS A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.565A pdb=" N ASN A 167 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE A 175 " --> pdb=" O HIS D 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 274 removed outlier: 3.607A pdb=" N PHE B 175 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 167 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 116 removed outlier: 7.251A pdb=" N LEU B 213 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR B 163 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 215 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 271 through 274 removed outlier: 3.589A pdb=" N PHE C 175 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN C 167 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 115 through 116 removed outlier: 7.250A pdb=" N LEU C 213 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR C 163 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 215 " --> pdb=" O HIS C 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 271 through 274 removed outlier: 3.594A pdb=" N PHE D 175 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN D 167 " --> pdb=" O ASP D 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 115 through 116 removed outlier: 7.250A pdb=" N LEU D 213 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR D 163 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR D 215 " --> pdb=" O HIS D 161 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 3141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4725 1.34 - 1.47: 4182 1.47 - 1.59: 6913 1.59 - 1.72: 8 1.72 - 1.85: 200 Bond restraints: 16028 Sorted by residual: bond pdb=" C THR C 519 " pdb=" N GLU C 520 " ideal model delta sigma weight residual 1.334 1.253 0.081 1.27e-02 6.20e+03 4.11e+01 bond pdb=" C THR D 519 " pdb=" N GLU D 520 " ideal model delta sigma weight residual 1.334 1.253 0.081 1.27e-02 6.20e+03 4.11e+01 bond pdb=" C THR A 519 " pdb=" N GLU A 520 " ideal model delta sigma weight residual 1.334 1.253 0.081 1.27e-02 6.20e+03 4.10e+01 bond pdb=" C THR B 519 " pdb=" N GLU B 520 " ideal model delta sigma weight residual 1.334 1.254 0.080 1.27e-02 6.20e+03 4.02e+01 bond pdb=" CB ASP C 36 " pdb=" CG ASP C 36 " ideal model delta sigma weight residual 1.516 1.597 -0.081 2.50e-02 1.60e+03 1.04e+01 ... (remaining 16023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 21203 3.63 - 7.25: 413 7.25 - 10.88: 40 10.88 - 14.51: 8 14.51 - 18.13: 4 Bond angle restraints: 21668 Sorted by residual: angle pdb=" N ARG B 58 " pdb=" CA ARG B 58 " pdb=" C ARG B 58 " ideal model delta sigma weight residual 112.94 120.27 -7.33 1.41e+00 5.03e-01 2.70e+01 angle pdb=" N ARG A 58 " pdb=" CA ARG A 58 " pdb=" C ARG A 58 " ideal model delta sigma weight residual 112.94 120.25 -7.31 1.41e+00 5.03e-01 2.69e+01 angle pdb=" CA LEU B 401 " pdb=" CB LEU B 401 " pdb=" CG LEU B 401 " ideal model delta sigma weight residual 116.30 134.43 -18.13 3.50e+00 8.16e-02 2.68e+01 angle pdb=" CA LEU D 401 " pdb=" CB LEU D 401 " pdb=" CG LEU D 401 " ideal model delta sigma weight residual 116.30 134.42 -18.12 3.50e+00 8.16e-02 2.68e+01 angle pdb=" CA LEU A 401 " pdb=" CB LEU A 401 " pdb=" CG LEU A 401 " ideal model delta sigma weight residual 116.30 134.42 -18.12 3.50e+00 8.16e-02 2.68e+01 ... (remaining 21663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 8160 16.02 - 32.03: 992 32.03 - 48.05: 208 48.05 - 64.07: 60 64.07 - 80.09: 20 Dihedral angle restraints: 9440 sinusoidal: 3796 harmonic: 5644 Sorted by residual: dihedral pdb=" CA GLY C 166 " pdb=" C GLY C 166 " pdb=" N ASN C 167 " pdb=" CA ASN C 167 " ideal model delta harmonic sigma weight residual 180.00 144.84 35.16 0 5.00e+00 4.00e-02 4.94e+01 dihedral pdb=" CA GLY A 166 " pdb=" C GLY A 166 " pdb=" N ASN A 167 " pdb=" CA ASN A 167 " ideal model delta harmonic sigma weight residual 180.00 144.84 35.16 0 5.00e+00 4.00e-02 4.94e+01 dihedral pdb=" CA GLY D 166 " pdb=" C GLY D 166 " pdb=" N ASN D 167 " pdb=" CA ASN D 167 " ideal model delta harmonic sigma weight residual 180.00 144.86 35.14 0 5.00e+00 4.00e-02 4.94e+01 ... (remaining 9437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2152 0.086 - 0.173: 276 0.173 - 0.259: 20 0.259 - 0.345: 0 0.345 - 0.432: 4 Chirality restraints: 2452 Sorted by residual: chirality pdb=" CA ARG A 58 " pdb=" N ARG A 58 " pdb=" C ARG A 58 " pdb=" CB ARG A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA ARG B 58 " pdb=" N ARG B 58 " pdb=" C ARG B 58 " pdb=" CB ARG B 58 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA ARG C 58 " pdb=" N ARG C 58 " pdb=" C ARG C 58 " pdb=" CB ARG C 58 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.59e+00 ... (remaining 2449 not shown) Planarity restraints: 2668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 45 " 0.028 2.00e-02 2.50e+03 2.17e-02 8.24e+00 pdb=" CG PHE C 45 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 45 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 45 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 45 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 45 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 45 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 45 " 0.028 2.00e-02 2.50e+03 2.17e-02 8.23e+00 pdb=" CG PHE D 45 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE D 45 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 45 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 45 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 45 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 45 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 45 " -0.028 2.00e-02 2.50e+03 2.16e-02 8.13e+00 pdb=" CG PHE A 45 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 45 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 45 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 45 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 45 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 45 " -0.005 2.00e-02 2.50e+03 ... (remaining 2665 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 903 2.72 - 3.27: 16526 3.27 - 3.81: 24602 3.81 - 4.36: 30260 4.36 - 4.90: 50586 Nonbonded interactions: 122877 Sorted by model distance: nonbonded pdb=" O ASP A 176 " pdb=" OD1 ASP A 176 " model vdw 2.180 3.040 nonbonded pdb=" O ASP B 176 " pdb=" OD1 ASP B 176 " model vdw 2.180 3.040 nonbonded pdb=" O ASP C 176 " pdb=" OD1 ASP C 176 " model vdw 2.180 3.040 nonbonded pdb=" O ASP D 176 " pdb=" OD1 ASP D 176 " model vdw 2.181 3.040 nonbonded pdb=" O SER A 330 " pdb=" CB GLN A 334 " model vdw 2.221 2.752 ... (remaining 122872 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.250 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.590 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.008 0.103 16028 Z= 0.535 Angle : 1.233 18.135 21668 Z= 0.669 Chirality : 0.060 0.432 2452 Planarity : 0.006 0.048 2668 Dihedral : 15.258 80.085 5784 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.56 % Favored : 93.80 % Rotamer: Outliers : 0.69 % Allowed : 16.44 % Favored : 82.87 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.16), residues: 1872 helix: -2.45 (0.12), residues: 1112 sheet: -0.16 (0.31), residues: 260 loop : -2.61 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP C 341 HIS 0.005 0.001 HIS C 252 PHE 0.049 0.004 PHE C 45 TYR 0.041 0.004 TYR B 117 ARG 0.028 0.005 ARG D 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 664 time to evaluate : 1.814 Fit side-chains revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9440 (t80) cc_final: 0.8828 (t80) REVERT: A 47 MET cc_start: 0.8892 (mtm) cc_final: 0.8502 (mtp) REVERT: A 52 LYS cc_start: 0.8780 (mttt) cc_final: 0.8105 (mmtt) REVERT: A 54 TRP cc_start: 0.7720 (t60) cc_final: 0.6853 (t-100) REVERT: A 66 GLN cc_start: 0.8965 (mm110) cc_final: 0.7754 (mm110) REVERT: A 69 LYS cc_start: 0.9104 (ttpt) cc_final: 0.8617 (ttpp) REVERT: A 124 ASP cc_start: 0.9020 (t0) cc_final: 0.8698 (t0) REVERT: A 137 TYR cc_start: 0.8912 (m-80) cc_final: 0.8705 (m-80) REVERT: A 271 ASP cc_start: 0.7982 (m-30) cc_final: 0.7766 (p0) REVERT: A 286 MET cc_start: 0.8959 (mmm) cc_final: 0.8148 (ptm) REVERT: A 312 GLN cc_start: 0.7668 (mt0) cc_final: 0.7320 (pt0) REVERT: A 339 ASN cc_start: 0.8152 (t0) cc_final: 0.7916 (t0) REVERT: A 341 TRP cc_start: 0.8535 (m100) cc_final: 0.8133 (m100) REVERT: A 347 ILE cc_start: 0.9171 (mt) cc_final: 0.8886 (tp) REVERT: A 361 GLU cc_start: 0.8840 (tt0) cc_final: 0.8035 (tp30) REVERT: A 362 ILE cc_start: 0.9367 (mt) cc_final: 0.9133 (mm) REVERT: A 382 MET cc_start: 0.9061 (ttp) cc_final: 0.8631 (tmm) REVERT: A 409 LEU cc_start: 0.9081 (tp) cc_final: 0.8873 (tt) REVERT: A 415 PHE cc_start: 0.9029 (t80) cc_final: 0.8448 (t80) REVERT: A 443 SER cc_start: 0.9282 (p) cc_final: 0.9013 (t) REVERT: A 459 ASP cc_start: 0.9210 (m-30) cc_final: 0.9003 (t0) REVERT: A 512 GLN cc_start: 0.9328 (mm-40) cc_final: 0.8936 (tm-30) REVERT: B 44 PHE cc_start: 0.8410 (t80) cc_final: 0.8207 (t80) REVERT: B 45 PHE cc_start: 0.9388 (t80) cc_final: 0.8752 (t80) REVERT: B 47 MET cc_start: 0.9003 (mtm) cc_final: 0.8713 (mtp) REVERT: B 54 TRP cc_start: 0.7447 (t60) cc_final: 0.6102 (t60) REVERT: B 59 LYS cc_start: 0.6074 (ttmt) cc_final: 0.4809 (tppt) REVERT: B 69 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8703 (ttpt) REVERT: B 72 MET cc_start: 0.9399 (mmm) cc_final: 0.9171 (tpp) REVERT: B 124 ASP cc_start: 0.9014 (t0) cc_final: 0.8692 (t0) REVERT: B 186 PHE cc_start: 0.7658 (m-80) cc_final: 0.7364 (m-10) REVERT: B 271 ASP cc_start: 0.8075 (m-30) cc_final: 0.7772 (p0) REVERT: B 286 MET cc_start: 0.8965 (mmm) cc_final: 0.8234 (ptm) REVERT: B 333 ASP cc_start: 0.7309 (m-30) cc_final: 0.6976 (m-30) REVERT: B 347 ILE cc_start: 0.9210 (mt) cc_final: 0.8968 (tp) REVERT: B 361 GLU cc_start: 0.8930 (tt0) cc_final: 0.8266 (tp30) REVERT: B 382 MET cc_start: 0.9062 (ttp) cc_final: 0.8589 (tmm) REVERT: B 383 LEU cc_start: 0.9216 (mp) cc_final: 0.8834 (mt) REVERT: B 415 PHE cc_start: 0.9024 (t80) cc_final: 0.8381 (t80) REVERT: B 443 SER cc_start: 0.9340 (p) cc_final: 0.8990 (t) REVERT: B 454 LEU cc_start: 0.9386 (tp) cc_final: 0.9137 (tp) REVERT: B 459 ASP cc_start: 0.9129 (m-30) cc_final: 0.8908 (t0) REVERT: B 470 LYS cc_start: 0.8810 (mttt) cc_final: 0.8487 (mtmm) REVERT: C 45 PHE cc_start: 0.9384 (t80) cc_final: 0.8742 (t80) REVERT: C 47 MET cc_start: 0.9000 (mtm) cc_final: 0.8683 (mtp) REVERT: C 52 LYS cc_start: 0.8736 (mttt) cc_final: 0.8099 (mmtt) REVERT: C 54 TRP cc_start: 0.7524 (t60) cc_final: 0.6191 (t60) REVERT: C 59 LYS cc_start: 0.6057 (ttmt) cc_final: 0.4824 (tppt) REVERT: C 72 MET cc_start: 0.9375 (mmm) cc_final: 0.9108 (tpp) REVERT: C 75 ILE cc_start: 0.9218 (mt) cc_final: 0.8999 (tt) REVERT: C 124 ASP cc_start: 0.9007 (t0) cc_final: 0.8693 (t0) REVERT: C 271 ASP cc_start: 0.8076 (m-30) cc_final: 0.7801 (p0) REVERT: C 286 MET cc_start: 0.8965 (mmm) cc_final: 0.8244 (ptm) REVERT: C 333 ASP cc_start: 0.7419 (m-30) cc_final: 0.7134 (m-30) REVERT: C 347 ILE cc_start: 0.9208 (mt) cc_final: 0.8998 (tp) REVERT: C 361 GLU cc_start: 0.8933 (tt0) cc_final: 0.8170 (tp30) REVERT: C 362 ILE cc_start: 0.9382 (mt) cc_final: 0.9171 (mm) REVERT: C 382 MET cc_start: 0.9042 (ttp) cc_final: 0.8570 (tmm) REVERT: C 383 LEU cc_start: 0.9199 (mp) cc_final: 0.8820 (mt) REVERT: C 415 PHE cc_start: 0.9009 (t80) cc_final: 0.8341 (t80) REVERT: C 443 SER cc_start: 0.9341 (p) cc_final: 0.9001 (t) REVERT: C 454 LEU cc_start: 0.9380 (tp) cc_final: 0.9138 (tp) REVERT: C 459 ASP cc_start: 0.9081 (m-30) cc_final: 0.8877 (t0) REVERT: C 470 LYS cc_start: 0.8760 (mttt) cc_final: 0.8427 (mtmm) REVERT: D 45 PHE cc_start: 0.9419 (t80) cc_final: 0.8867 (t80) REVERT: D 47 MET cc_start: 0.9016 (mtm) cc_final: 0.8697 (mtp) REVERT: D 52 LYS cc_start: 0.8794 (mttt) cc_final: 0.7986 (mmtt) REVERT: D 54 TRP cc_start: 0.7766 (t60) cc_final: 0.6441 (t60) REVERT: D 59 LYS cc_start: 0.6194 (ttmt) cc_final: 0.4802 (tppt) REVERT: D 66 GLN cc_start: 0.8921 (mm110) cc_final: 0.8607 (mm-40) REVERT: D 72 MET cc_start: 0.9360 (mmm) cc_final: 0.9143 (tpp) REVERT: D 79 LEU cc_start: 0.9619 (tp) cc_final: 0.9399 (mt) REVERT: D 124 ASP cc_start: 0.9013 (t0) cc_final: 0.8689 (t0) REVERT: D 271 ASP cc_start: 0.8015 (m-30) cc_final: 0.7700 (p0) REVERT: D 286 MET cc_start: 0.8964 (mmm) cc_final: 0.8214 (ptm) REVERT: D 344 MET cc_start: 0.8830 (mmm) cc_final: 0.8612 (mmt) REVERT: D 347 ILE cc_start: 0.9225 (mt) cc_final: 0.8965 (tp) REVERT: D 361 GLU cc_start: 0.8890 (tt0) cc_final: 0.8050 (tp30) REVERT: D 362 ILE cc_start: 0.9403 (mt) cc_final: 0.9168 (mm) REVERT: D 382 MET cc_start: 0.9043 (ttp) cc_final: 0.8534 (tmm) REVERT: D 383 LEU cc_start: 0.9206 (mp) cc_final: 0.8845 (mt) REVERT: D 415 PHE cc_start: 0.9043 (t80) cc_final: 0.8402 (t80) REVERT: D 443 SER cc_start: 0.9381 (p) cc_final: 0.9062 (t) REVERT: D 454 LEU cc_start: 0.9380 (tp) cc_final: 0.9155 (tp) outliers start: 12 outliers final: 8 residues processed: 664 average time/residue: 0.2457 time to fit residues: 243.7019 Evaluate side-chains 418 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 410 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 5.9990 chunk 142 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 125 GLN A 219 GLN A 262 ASN A 456 ASN A 468 GLN B 125 GLN B 219 GLN B 456 ASN C 219 GLN ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN D 219 GLN D 262 ASN D 456 ASN ** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16028 Z= 0.253 Angle : 0.694 10.944 21668 Z= 0.370 Chirality : 0.045 0.228 2452 Planarity : 0.004 0.042 2668 Dihedral : 5.433 26.302 2056 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.62 % Favored : 97.17 % Rotamer: Outliers : 0.75 % Allowed : 3.79 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 1872 helix: 0.18 (0.14), residues: 1132 sheet: 0.83 (0.33), residues: 220 loop : -2.09 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 272 HIS 0.006 0.001 HIS D 144 PHE 0.022 0.002 PHE D 485 TYR 0.021 0.002 TYR D 391 ARG 0.007 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 606 time to evaluate : 1.817 Fit side-chains REVERT: A 39 ARG cc_start: 0.6904 (ttp80) cc_final: 0.6586 (mtt90) REVERT: A 45 PHE cc_start: 0.9296 (t80) cc_final: 0.8982 (t80) REVERT: A 47 MET cc_start: 0.8604 (mtm) cc_final: 0.7899 (mtp) REVERT: A 52 LYS cc_start: 0.8806 (mttt) cc_final: 0.8139 (mmtt) REVERT: A 53 PHE cc_start: 0.8049 (m-80) cc_final: 0.7415 (m-80) REVERT: A 93 GLU cc_start: 0.8804 (tp30) cc_final: 0.8545 (tp30) REVERT: A 107 MET cc_start: 0.7878 (mmm) cc_final: 0.7560 (mmm) REVERT: A 124 ASP cc_start: 0.9145 (t0) cc_final: 0.8832 (t0) REVERT: A 156 MET cc_start: 0.8931 (ttt) cc_final: 0.8395 (tmm) REVERT: A 186 PHE cc_start: 0.7305 (m-80) cc_final: 0.6760 (m-80) REVERT: A 241 PHE cc_start: 0.8695 (m-10) cc_final: 0.7572 (m-10) REVERT: A 271 ASP cc_start: 0.8149 (m-30) cc_final: 0.7743 (p0) REVERT: A 312 GLN cc_start: 0.7690 (mt0) cc_final: 0.7420 (pt0) REVERT: A 327 LYS cc_start: 0.8630 (mmmt) cc_final: 0.7912 (mmtt) REVERT: A 341 TRP cc_start: 0.8307 (m100) cc_final: 0.7786 (m100) REVERT: A 344 MET cc_start: 0.7476 (mmt) cc_final: 0.7232 (mmt) REVERT: A 361 GLU cc_start: 0.8854 (tt0) cc_final: 0.7781 (tp30) REVERT: A 375 ILE cc_start: 0.9395 (mt) cc_final: 0.9184 (mt) REVERT: A 382 MET cc_start: 0.8964 (ttp) cc_final: 0.8373 (tmm) REVERT: A 460 MET cc_start: 0.8234 (ttp) cc_final: 0.7855 (ttp) REVERT: A 492 MET cc_start: 0.8793 (tpp) cc_final: 0.8585 (tpp) REVERT: A 512 GLN cc_start: 0.9454 (mm-40) cc_final: 0.8850 (tm-30) REVERT: A 524 PHE cc_start: 0.8212 (t80) cc_final: 0.7430 (t80) REVERT: B 45 PHE cc_start: 0.9233 (t80) cc_final: 0.8919 (t80) REVERT: B 47 MET cc_start: 0.8529 (mtm) cc_final: 0.7996 (mtp) REVERT: B 52 LYS cc_start: 0.8614 (mttt) cc_final: 0.7929 (mmtt) REVERT: B 53 PHE cc_start: 0.8218 (m-80) cc_final: 0.7506 (m-80) REVERT: B 54 TRP cc_start: 0.7466 (t60) cc_final: 0.6447 (t-100) REVERT: B 72 MET cc_start: 0.9288 (mmm) cc_final: 0.9002 (mmp) REVERT: B 93 GLU cc_start: 0.8769 (tp30) cc_final: 0.8507 (tp30) REVERT: B 119 GLN cc_start: 0.9114 (mt0) cc_final: 0.8764 (mt0) REVERT: B 124 ASP cc_start: 0.9140 (t0) cc_final: 0.8835 (t0) REVERT: B 156 MET cc_start: 0.8942 (ttt) cc_final: 0.8377 (tmm) REVERT: B 186 PHE cc_start: 0.7186 (m-80) cc_final: 0.6666 (m-80) REVERT: B 241 PHE cc_start: 0.8731 (m-10) cc_final: 0.7603 (m-10) REVERT: B 271 ASP cc_start: 0.8128 (m-30) cc_final: 0.7682 (p0) REVERT: B 288 PHE cc_start: 0.9041 (t80) cc_final: 0.8631 (t80) REVERT: B 333 ASP cc_start: 0.6983 (m-30) cc_final: 0.6482 (m-30) REVERT: B 336 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7734 (tt0) REVERT: B 361 GLU cc_start: 0.8879 (tt0) cc_final: 0.8126 (tp30) REVERT: B 375 ILE cc_start: 0.9357 (mt) cc_final: 0.9148 (mt) REVERT: B 382 MET cc_start: 0.8936 (ttp) cc_final: 0.8343 (tmm) REVERT: B 383 LEU cc_start: 0.9246 (mp) cc_final: 0.8953 (mt) REVERT: B 391 TYR cc_start: 0.8447 (m-80) cc_final: 0.8090 (m-80) REVERT: B 415 PHE cc_start: 0.8977 (t80) cc_final: 0.8528 (t80) REVERT: B 418 CYS cc_start: 0.9155 (m) cc_final: 0.8775 (t) REVERT: B 458 ASP cc_start: 0.9398 (t70) cc_final: 0.9197 (t70) REVERT: B 491 TYR cc_start: 0.9272 (m-10) cc_final: 0.9039 (m-10) REVERT: B 524 PHE cc_start: 0.8113 (t80) cc_final: 0.7908 (t80) REVERT: C 38 MET cc_start: 0.8676 (mmt) cc_final: 0.8005 (mmm) REVERT: C 45 PHE cc_start: 0.9145 (t80) cc_final: 0.8806 (t80) REVERT: C 47 MET cc_start: 0.8546 (mtm) cc_final: 0.7986 (mtp) REVERT: C 52 LYS cc_start: 0.8549 (mttt) cc_final: 0.7869 (mmtt) REVERT: C 53 PHE cc_start: 0.8086 (m-80) cc_final: 0.7318 (m-80) REVERT: C 54 TRP cc_start: 0.7456 (t60) cc_final: 0.6436 (t-100) REVERT: C 72 MET cc_start: 0.9276 (mmm) cc_final: 0.8997 (tpp) REVERT: C 119 GLN cc_start: 0.9097 (mt0) cc_final: 0.8763 (mt0) REVERT: C 124 ASP cc_start: 0.9163 (t0) cc_final: 0.8846 (t0) REVERT: C 156 MET cc_start: 0.8984 (ttt) cc_final: 0.8348 (tmm) REVERT: C 186 PHE cc_start: 0.7262 (m-10) cc_final: 0.7052 (m-80) REVERT: C 241 PHE cc_start: 0.8756 (m-10) cc_final: 0.7624 (m-10) REVERT: C 270 LYS cc_start: 0.8435 (pttt) cc_final: 0.8146 (pttt) REVERT: C 271 ASP cc_start: 0.8154 (m-30) cc_final: 0.7670 (p0) REVERT: C 316 GLU cc_start: 0.8672 (tt0) cc_final: 0.8417 (tt0) REVERT: C 320 PHE cc_start: 0.6945 (t80) cc_final: 0.6469 (m-80) REVERT: C 333 ASP cc_start: 0.7044 (m-30) cc_final: 0.6533 (m-30) REVERT: C 336 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7633 (tt0) REVERT: C 361 GLU cc_start: 0.8901 (tt0) cc_final: 0.8414 (tp30) REVERT: C 375 ILE cc_start: 0.9338 (mt) cc_final: 0.9122 (mt) REVERT: C 382 MET cc_start: 0.9045 (ttp) cc_final: 0.8378 (tmm) REVERT: C 383 LEU cc_start: 0.9226 (mp) cc_final: 0.8947 (mt) REVERT: C 415 PHE cc_start: 0.8994 (t80) cc_final: 0.8548 (t80) REVERT: C 481 TYR cc_start: 0.9492 (t80) cc_final: 0.9284 (t80) REVERT: C 491 TYR cc_start: 0.9270 (m-10) cc_final: 0.9019 (m-10) REVERT: D 44 PHE cc_start: 0.8692 (t80) cc_final: 0.7772 (t80) REVERT: D 45 PHE cc_start: 0.9245 (t80) cc_final: 0.8865 (t80) REVERT: D 47 MET cc_start: 0.8643 (mtm) cc_final: 0.8042 (mtp) REVERT: D 52 LYS cc_start: 0.8623 (mttt) cc_final: 0.7896 (mmtt) REVERT: D 53 PHE cc_start: 0.8134 (m-80) cc_final: 0.7463 (m-80) REVERT: D 54 TRP cc_start: 0.7500 (t60) cc_final: 0.6646 (t-100) REVERT: D 72 MET cc_start: 0.9217 (mmm) cc_final: 0.8939 (mmp) REVERT: D 107 MET cc_start: 0.7949 (mmm) cc_final: 0.7686 (mmm) REVERT: D 119 GLN cc_start: 0.9107 (mt0) cc_final: 0.8810 (mt0) REVERT: D 124 ASP cc_start: 0.9156 (t0) cc_final: 0.8860 (t0) REVERT: D 186 PHE cc_start: 0.6892 (m-80) cc_final: 0.6433 (m-80) REVERT: D 241 PHE cc_start: 0.8720 (m-10) cc_final: 0.7607 (m-10) REVERT: D 271 ASP cc_start: 0.8277 (m-30) cc_final: 0.8031 (p0) REVERT: D 288 PHE cc_start: 0.9032 (t80) cc_final: 0.8705 (t80) REVERT: D 353 ILE cc_start: 0.8578 (mm) cc_final: 0.8308 (mm) REVERT: D 361 GLU cc_start: 0.8901 (tt0) cc_final: 0.8114 (tp30) REVERT: D 375 ILE cc_start: 0.9318 (mt) cc_final: 0.9090 (mt) REVERT: D 382 MET cc_start: 0.9069 (ttp) cc_final: 0.8545 (tmm) REVERT: D 383 LEU cc_start: 0.9263 (mp) cc_final: 0.8976 (mt) REVERT: D 415 PHE cc_start: 0.9009 (t80) cc_final: 0.8490 (t80) REVERT: D 491 TYR cc_start: 0.9230 (m-10) cc_final: 0.8983 (m-10) REVERT: D 524 PHE cc_start: 0.8225 (t80) cc_final: 0.8011 (t80) outliers start: 13 outliers final: 0 residues processed: 607 average time/residue: 0.2291 time to fit residues: 213.3194 Evaluate side-chains 402 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 171 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 152 optimal weight: 9.9990 chunk 169 optimal weight: 0.0770 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN A 406 GLN B 468 GLN C 262 ASN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 GLN D 262 ASN D 468 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16028 Z= 0.213 Angle : 0.610 9.384 21668 Z= 0.325 Chirality : 0.043 0.189 2452 Planarity : 0.003 0.022 2668 Dihedral : 4.793 25.878 2056 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 0.57 % Allowed : 2.76 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 1872 helix: 1.38 (0.15), residues: 1128 sheet: 1.20 (0.32), residues: 216 loop : -1.77 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 341 HIS 0.008 0.001 HIS D 100 PHE 0.023 0.002 PHE C 497 TYR 0.019 0.002 TYR B 391 ARG 0.004 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 502 time to evaluate : 1.929 Fit side-chains REVERT: A 39 ARG cc_start: 0.7446 (ttp80) cc_final: 0.6689 (ttm110) REVERT: A 45 PHE cc_start: 0.9131 (t80) cc_final: 0.8786 (t80) REVERT: A 47 MET cc_start: 0.8709 (mtm) cc_final: 0.7716 (mtp) REVERT: A 52 LYS cc_start: 0.8634 (mttt) cc_final: 0.7901 (mmtt) REVERT: A 53 PHE cc_start: 0.7936 (m-80) cc_final: 0.7387 (m-80) REVERT: A 86 MET cc_start: 0.8458 (mmm) cc_final: 0.8132 (tpp) REVERT: A 124 ASP cc_start: 0.9191 (t0) cc_final: 0.8947 (t0) REVERT: A 156 MET cc_start: 0.9025 (ttt) cc_final: 0.8428 (tmm) REVERT: A 241 PHE cc_start: 0.8712 (m-10) cc_final: 0.8312 (m-10) REVERT: A 312 GLN cc_start: 0.7823 (mt0) cc_final: 0.7348 (pt0) REVERT: A 327 LYS cc_start: 0.8620 (mmmt) cc_final: 0.7964 (mmtt) REVERT: A 336 GLU cc_start: 0.7934 (tp30) cc_final: 0.7656 (tp30) REVERT: A 341 TRP cc_start: 0.8224 (m100) cc_final: 0.7889 (m100) REVERT: A 415 PHE cc_start: 0.9063 (t80) cc_final: 0.8693 (t80) REVERT: A 423 TYR cc_start: 0.8773 (t80) cc_final: 0.8525 (t80) REVERT: A 439 ASP cc_start: 0.9061 (p0) cc_final: 0.8783 (p0) REVERT: A 449 GLU cc_start: 0.8572 (pt0) cc_final: 0.8263 (pt0) REVERT: A 458 ASP cc_start: 0.9502 (t70) cc_final: 0.9243 (t0) REVERT: A 492 MET cc_start: 0.8705 (tpp) cc_final: 0.8461 (tpp) REVERT: A 512 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8644 (tm-30) REVERT: A 524 PHE cc_start: 0.8116 (t80) cc_final: 0.7545 (t80) REVERT: B 45 PHE cc_start: 0.9039 (t80) cc_final: 0.8746 (t80) REVERT: B 47 MET cc_start: 0.8667 (mtm) cc_final: 0.7781 (mtp) REVERT: B 52 LYS cc_start: 0.8547 (mttt) cc_final: 0.7761 (mmtt) REVERT: B 53 PHE cc_start: 0.8008 (m-80) cc_final: 0.7403 (m-80) REVERT: B 63 LEU cc_start: 0.8077 (tt) cc_final: 0.7810 (tt) REVERT: B 72 MET cc_start: 0.9109 (mmm) cc_final: 0.8793 (mmp) REVERT: B 119 GLN cc_start: 0.8912 (mt0) cc_final: 0.8551 (mt0) REVERT: B 124 ASP cc_start: 0.9194 (t0) cc_final: 0.8927 (t0) REVERT: B 165 ARG cc_start: 0.6011 (ttp80) cc_final: 0.5784 (ttp80) REVERT: B 241 PHE cc_start: 0.8745 (m-10) cc_final: 0.8505 (m-80) REVERT: B 288 PHE cc_start: 0.9038 (t80) cc_final: 0.8396 (t80) REVERT: B 295 THR cc_start: 0.9000 (t) cc_final: 0.8759 (t) REVERT: B 327 LYS cc_start: 0.8597 (mmmt) cc_final: 0.7942 (mmtt) REVERT: B 415 PHE cc_start: 0.9082 (t80) cc_final: 0.8397 (t80) REVERT: B 439 ASP cc_start: 0.9108 (p0) cc_final: 0.8856 (p0) REVERT: C 38 MET cc_start: 0.8769 (mmt) cc_final: 0.7922 (mmm) REVERT: C 44 PHE cc_start: 0.8830 (t80) cc_final: 0.7738 (t80) REVERT: C 45 PHE cc_start: 0.8987 (t80) cc_final: 0.8676 (t80) REVERT: C 47 MET cc_start: 0.8691 (mtm) cc_final: 0.7822 (mtp) REVERT: C 52 LYS cc_start: 0.8523 (mttt) cc_final: 0.7732 (mmtt) REVERT: C 53 PHE cc_start: 0.7835 (m-80) cc_final: 0.7120 (m-80) REVERT: C 63 LEU cc_start: 0.8068 (tt) cc_final: 0.7825 (tt) REVERT: C 72 MET cc_start: 0.9149 (mmm) cc_final: 0.8925 (tpp) REVERT: C 93 GLU cc_start: 0.8846 (tp30) cc_final: 0.8644 (tp30) REVERT: C 119 GLN cc_start: 0.8940 (mt0) cc_final: 0.8680 (mt0) REVERT: C 124 ASP cc_start: 0.9202 (t0) cc_final: 0.8934 (t0) REVERT: C 156 MET cc_start: 0.9087 (ttt) cc_final: 0.8505 (tmm) REVERT: C 241 PHE cc_start: 0.8799 (m-10) cc_final: 0.8481 (m-80) REVERT: C 294 LEU cc_start: 0.9280 (mp) cc_final: 0.9039 (mp) REVERT: C 320 PHE cc_start: 0.7097 (t80) cc_final: 0.6486 (m-80) REVERT: C 327 LYS cc_start: 0.8599 (mmmt) cc_final: 0.7878 (mmtt) REVERT: C 335 MET cc_start: 0.6315 (mmm) cc_final: 0.5636 (mtm) REVERT: C 361 GLU cc_start: 0.8834 (tt0) cc_final: 0.8360 (tp30) REVERT: C 415 PHE cc_start: 0.9009 (t80) cc_final: 0.8668 (t80) REVERT: C 439 ASP cc_start: 0.8984 (p0) cc_final: 0.8712 (p0) REVERT: C 512 GLN cc_start: 0.8353 (tt0) cc_final: 0.8142 (mm-40) REVERT: D 44 PHE cc_start: 0.8641 (t80) cc_final: 0.7483 (t80) REVERT: D 45 PHE cc_start: 0.9051 (t80) cc_final: 0.8692 (t80) REVERT: D 47 MET cc_start: 0.8715 (mtm) cc_final: 0.7756 (mtp) REVERT: D 52 LYS cc_start: 0.8558 (mttt) cc_final: 0.7714 (mmtt) REVERT: D 53 PHE cc_start: 0.8025 (m-80) cc_final: 0.7508 (m-80) REVERT: D 63 LEU cc_start: 0.8142 (tt) cc_final: 0.7845 (tt) REVERT: D 72 MET cc_start: 0.9063 (mmm) cc_final: 0.8763 (mmp) REVERT: D 107 MET cc_start: 0.8188 (mmm) cc_final: 0.7954 (mmm) REVERT: D 124 ASP cc_start: 0.9206 (t0) cc_final: 0.8944 (t0) REVERT: D 165 ARG cc_start: 0.6069 (ttp80) cc_final: 0.5757 (ttp80) REVERT: D 241 PHE cc_start: 0.8746 (m-10) cc_final: 0.8346 (m-80) REVERT: D 271 ASP cc_start: 0.8234 (m-30) cc_final: 0.7923 (p0) REVERT: D 288 PHE cc_start: 0.8897 (t80) cc_final: 0.8254 (t80) REVERT: D 313 LEU cc_start: 0.8069 (mp) cc_final: 0.7857 (tt) REVERT: D 317 PHE cc_start: 0.8038 (t80) cc_final: 0.7814 (t80) REVERT: D 327 LYS cc_start: 0.8545 (mmmt) cc_final: 0.7891 (mmtt) REVERT: D 335 MET cc_start: 0.6300 (mmm) cc_final: 0.5864 (mtm) REVERT: D 415 PHE cc_start: 0.9020 (t80) cc_final: 0.8401 (t80) REVERT: D 439 ASP cc_start: 0.8970 (p0) cc_final: 0.8708 (p0) REVERT: D 449 GLU cc_start: 0.8478 (pt0) cc_final: 0.8274 (pt0) outliers start: 10 outliers final: 0 residues processed: 503 average time/residue: 0.2317 time to fit residues: 178.7970 Evaluate side-chains 371 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN B 262 ASN B 406 GLN C 262 ASN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN D 262 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 16028 Z= 0.397 Angle : 0.689 11.020 21668 Z= 0.372 Chirality : 0.045 0.192 2452 Planarity : 0.003 0.027 2668 Dihedral : 4.772 26.753 2056 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.23 % Allowed : 4.71 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1872 helix: 1.46 (0.15), residues: 1140 sheet: 1.25 (0.33), residues: 224 loop : -1.89 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 431 HIS 0.008 0.002 HIS A 144 PHE 0.036 0.003 PHE A 489 TYR 0.018 0.002 TYR B 481 ARG 0.004 0.000 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 466 time to evaluate : 1.732 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7529 (ttp80) cc_final: 0.6715 (ttm110) REVERT: A 44 PHE cc_start: 0.8761 (t80) cc_final: 0.7396 (t80) REVERT: A 45 PHE cc_start: 0.9211 (t80) cc_final: 0.8779 (t80) REVERT: A 47 MET cc_start: 0.8794 (mtm) cc_final: 0.7176 (mtp) REVERT: A 52 LYS cc_start: 0.8709 (mttt) cc_final: 0.7864 (mmtt) REVERT: A 53 PHE cc_start: 0.8149 (m-80) cc_final: 0.7524 (m-80) REVERT: A 86 MET cc_start: 0.8572 (mmm) cc_final: 0.8221 (tpp) REVERT: A 124 ASP cc_start: 0.9205 (t0) cc_final: 0.8941 (t0) REVERT: A 136 LEU cc_start: 0.9319 (tt) cc_final: 0.9107 (tt) REVERT: A 165 ARG cc_start: 0.5631 (ttp80) cc_final: 0.5303 (ttp80) REVERT: A 312 GLN cc_start: 0.7853 (mt0) cc_final: 0.7364 (pt0) REVERT: A 313 LEU cc_start: 0.8086 (mp) cc_final: 0.7770 (tt) REVERT: A 327 LYS cc_start: 0.8507 (mmmt) cc_final: 0.7846 (mmtt) REVERT: A 335 MET cc_start: 0.6357 (mmm) cc_final: 0.5124 (ptp) REVERT: A 341 TRP cc_start: 0.8448 (m100) cc_final: 0.8213 (m100) REVERT: A 415 PHE cc_start: 0.9098 (t80) cc_final: 0.8454 (t80) REVERT: A 439 ASP cc_start: 0.9138 (p0) cc_final: 0.8904 (p0) REVERT: A 492 MET cc_start: 0.8851 (tpp) cc_final: 0.8645 (tpp) REVERT: A 512 GLN cc_start: 0.9368 (mm-40) cc_final: 0.8744 (tm-30) REVERT: A 524 PHE cc_start: 0.8029 (t80) cc_final: 0.7472 (t80) REVERT: B 44 PHE cc_start: 0.8764 (t80) cc_final: 0.7244 (t80) REVERT: B 45 PHE cc_start: 0.9094 (t80) cc_final: 0.8749 (t80) REVERT: B 47 MET cc_start: 0.8909 (mtm) cc_final: 0.7168 (mtp) REVERT: B 52 LYS cc_start: 0.8520 (mttt) cc_final: 0.7793 (mmtt) REVERT: B 53 PHE cc_start: 0.8089 (m-80) cc_final: 0.7325 (m-80) REVERT: B 124 ASP cc_start: 0.9210 (t0) cc_final: 0.8926 (t0) REVERT: B 327 LYS cc_start: 0.8585 (mmmt) cc_final: 0.7861 (mmtt) REVERT: B 335 MET cc_start: 0.6222 (mmm) cc_final: 0.5282 (ptp) REVERT: B 414 ARG cc_start: 0.9166 (mtt-85) cc_final: 0.8942 (mtm-85) REVERT: B 439 ASP cc_start: 0.9170 (p0) cc_final: 0.8961 (p0) REVERT: B 492 MET cc_start: 0.8930 (tpp) cc_final: 0.8427 (tpp) REVERT: C 38 MET cc_start: 0.8568 (mmm) cc_final: 0.8326 (mmm) REVERT: C 45 PHE cc_start: 0.9131 (t80) cc_final: 0.8808 (t80) REVERT: C 47 MET cc_start: 0.8880 (mtm) cc_final: 0.8484 (mtp) REVERT: C 52 LYS cc_start: 0.8571 (mttt) cc_final: 0.7729 (mmtt) REVERT: C 53 PHE cc_start: 0.7999 (m-80) cc_final: 0.7409 (m-80) REVERT: C 72 MET cc_start: 0.9110 (mmm) cc_final: 0.8862 (tpp) REVERT: C 93 GLU cc_start: 0.9030 (tp30) cc_final: 0.8778 (tp30) REVERT: C 124 ASP cc_start: 0.9212 (t0) cc_final: 0.8937 (t0) REVERT: C 136 LEU cc_start: 0.9347 (tt) cc_final: 0.9038 (tt) REVERT: C 262 ASN cc_start: 0.9250 (OUTLIER) cc_final: 0.9014 (t0) REVERT: C 294 LEU cc_start: 0.9261 (mp) cc_final: 0.9043 (mp) REVERT: C 320 PHE cc_start: 0.7071 (t80) cc_final: 0.6442 (m-10) REVERT: C 327 LYS cc_start: 0.8361 (mmmt) cc_final: 0.7706 (mmtt) REVERT: C 335 MET cc_start: 0.6153 (mmm) cc_final: 0.5549 (mtm) REVERT: C 361 GLU cc_start: 0.8816 (tt0) cc_final: 0.8424 (tp30) REVERT: C 415 PHE cc_start: 0.9103 (t80) cc_final: 0.8459 (t80) REVERT: C 481 TYR cc_start: 0.9535 (t80) cc_final: 0.9287 (t80) REVERT: C 492 MET cc_start: 0.8870 (tpp) cc_final: 0.8487 (tpp) REVERT: C 512 GLN cc_start: 0.8640 (tt0) cc_final: 0.8339 (tm-30) REVERT: D 39 ARG cc_start: 0.7446 (ttp80) cc_final: 0.6606 (ttm110) REVERT: D 44 PHE cc_start: 0.8712 (t80) cc_final: 0.7323 (t80) REVERT: D 45 PHE cc_start: 0.9224 (t80) cc_final: 0.8771 (t80) REVERT: D 47 MET cc_start: 0.8911 (mtm) cc_final: 0.7256 (mtp) REVERT: D 52 LYS cc_start: 0.8506 (mttt) cc_final: 0.7763 (mmtt) REVERT: D 53 PHE cc_start: 0.7946 (m-80) cc_final: 0.7273 (m-80) REVERT: D 72 MET cc_start: 0.9023 (mmm) cc_final: 0.8689 (mmp) REVERT: D 124 ASP cc_start: 0.9220 (t0) cc_final: 0.8941 (t0) REVERT: D 136 LEU cc_start: 0.9333 (tt) cc_final: 0.9025 (tt) REVERT: D 165 ARG cc_start: 0.5873 (ttp80) cc_final: 0.5622 (ttp80) REVERT: D 262 ASN cc_start: 0.9240 (OUTLIER) cc_final: 0.9040 (t0) REVERT: D 288 PHE cc_start: 0.8778 (t80) cc_final: 0.8055 (t80) REVERT: D 313 LEU cc_start: 0.8177 (mp) cc_final: 0.7899 (tt) REVERT: D 327 LYS cc_start: 0.8427 (mmmt) cc_final: 0.7687 (mmtt) REVERT: D 335 MET cc_start: 0.6521 (mmm) cc_final: 0.5956 (mtm) REVERT: D 481 TYR cc_start: 0.9462 (t80) cc_final: 0.9181 (t80) REVERT: D 492 MET cc_start: 0.8870 (tpp) cc_final: 0.8466 (tpp) REVERT: D 512 GLN cc_start: 0.8713 (tt0) cc_final: 0.8295 (tm-30) REVERT: D 524 PHE cc_start: 0.7840 (t80) cc_final: 0.7255 (t80) outliers start: 4 outliers final: 0 residues processed: 470 average time/residue: 0.2420 time to fit residues: 173.3228 Evaluate side-chains 365 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 363 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 135 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 92 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 76 GLN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16028 Z= 0.319 Angle : 0.642 10.054 21668 Z= 0.346 Chirality : 0.044 0.199 2452 Planarity : 0.003 0.036 2668 Dihedral : 4.692 26.791 2056 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.23 % Allowed : 1.78 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 1872 helix: 1.66 (0.15), residues: 1140 sheet: 1.33 (0.34), residues: 224 loop : -1.89 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 431 HIS 0.011 0.002 HIS C 100 PHE 0.027 0.002 PHE C 394 TYR 0.021 0.002 TYR A 481 ARG 0.005 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 481 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.8838 (t80) cc_final: 0.7278 (t80) REVERT: A 45 PHE cc_start: 0.9153 (t80) cc_final: 0.8768 (t80) REVERT: A 47 MET cc_start: 0.8917 (mtm) cc_final: 0.8186 (mtp) REVERT: A 53 PHE cc_start: 0.8105 (m-80) cc_final: 0.7485 (m-80) REVERT: A 86 MET cc_start: 0.8567 (mmm) cc_final: 0.8190 (tpp) REVERT: A 124 ASP cc_start: 0.9164 (t0) cc_final: 0.8903 (t0) REVERT: A 136 LEU cc_start: 0.9416 (tt) cc_final: 0.9124 (tt) REVERT: A 165 ARG cc_start: 0.5814 (ttp80) cc_final: 0.5581 (ttp80) REVERT: A 217 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8756 (tt0) REVERT: A 312 GLN cc_start: 0.7828 (mt0) cc_final: 0.7380 (pt0) REVERT: A 313 LEU cc_start: 0.8072 (mp) cc_final: 0.7805 (tt) REVERT: A 317 PHE cc_start: 0.7944 (t80) cc_final: 0.7703 (t80) REVERT: A 327 LYS cc_start: 0.8420 (mmmt) cc_final: 0.7761 (mmtt) REVERT: A 336 GLU cc_start: 0.8519 (tp30) cc_final: 0.8272 (tp30) REVERT: A 341 TRP cc_start: 0.8522 (m100) cc_final: 0.8288 (m100) REVERT: A 406 GLN cc_start: 0.9150 (mt0) cc_final: 0.8864 (mt0) REVERT: A 415 PHE cc_start: 0.9196 (t80) cc_final: 0.8381 (t80) REVERT: A 423 TYR cc_start: 0.8854 (t80) cc_final: 0.8132 (t80) REVERT: A 492 MET cc_start: 0.8905 (tpp) cc_final: 0.8567 (tpp) REVERT: A 512 GLN cc_start: 0.9357 (mm-40) cc_final: 0.8900 (tm-30) REVERT: B 45 PHE cc_start: 0.9056 (t80) cc_final: 0.8749 (t80) REVERT: B 47 MET cc_start: 0.8930 (mtm) cc_final: 0.7088 (mtp) REVERT: B 52 LYS cc_start: 0.8443 (mttt) cc_final: 0.7784 (mmtt) REVERT: B 53 PHE cc_start: 0.8042 (m-80) cc_final: 0.7277 (m-80) REVERT: B 72 MET cc_start: 0.8762 (mmp) cc_final: 0.8422 (tpp) REVERT: B 124 ASP cc_start: 0.9218 (t0) cc_final: 0.8934 (t0) REVERT: B 165 ARG cc_start: 0.5795 (ttp80) cc_final: 0.5571 (ttp80) REVERT: B 294 LEU cc_start: 0.9247 (mp) cc_final: 0.9044 (mp) REVERT: B 327 LYS cc_start: 0.8499 (mmmt) cc_final: 0.7789 (mmtt) REVERT: B 382 MET cc_start: 0.9131 (tpt) cc_final: 0.8687 (tpp) REVERT: B 492 MET cc_start: 0.8903 (tpp) cc_final: 0.8412 (tpp) REVERT: C 45 PHE cc_start: 0.9044 (t80) cc_final: 0.8736 (t80) REVERT: C 47 MET cc_start: 0.8962 (mtm) cc_final: 0.7992 (mtp) REVERT: C 52 LYS cc_start: 0.8483 (mttt) cc_final: 0.8032 (mtpp) REVERT: C 53 PHE cc_start: 0.8064 (m-80) cc_final: 0.7316 (m-80) REVERT: C 72 MET cc_start: 0.9057 (mmm) cc_final: 0.8785 (tpp) REVERT: C 93 GLU cc_start: 0.8956 (tp30) cc_final: 0.8655 (tp30) REVERT: C 124 ASP cc_start: 0.9098 (t0) cc_final: 0.8827 (t0) REVERT: C 136 LEU cc_start: 0.9371 (tt) cc_final: 0.9058 (tt) REVERT: C 165 ARG cc_start: 0.5793 (ttp80) cc_final: 0.5572 (ttp80) REVERT: C 294 LEU cc_start: 0.9358 (mp) cc_final: 0.9154 (mp) REVERT: C 320 PHE cc_start: 0.7206 (t80) cc_final: 0.6418 (m-10) REVERT: C 327 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7642 (mmtt) REVERT: C 335 MET cc_start: 0.6220 (mmm) cc_final: 0.5724 (mtm) REVERT: C 361 GLU cc_start: 0.8819 (tt0) cc_final: 0.8307 (tp30) REVERT: C 382 MET cc_start: 0.9114 (tpt) cc_final: 0.8663 (tpp) REVERT: C 415 PHE cc_start: 0.9165 (t80) cc_final: 0.8400 (t80) REVERT: C 481 TYR cc_start: 0.9507 (t80) cc_final: 0.9260 (t80) REVERT: C 492 MET cc_start: 0.8833 (tpp) cc_final: 0.8477 (tpp) REVERT: C 512 GLN cc_start: 0.8587 (tt0) cc_final: 0.8326 (tm-30) REVERT: D 39 ARG cc_start: 0.7503 (ttp80) cc_final: 0.6425 (ttm110) REVERT: D 44 PHE cc_start: 0.8737 (t80) cc_final: 0.7211 (t80) REVERT: D 45 PHE cc_start: 0.9206 (t80) cc_final: 0.8737 (t80) REVERT: D 47 MET cc_start: 0.8922 (mtm) cc_final: 0.8172 (mtp) REVERT: D 53 PHE cc_start: 0.7868 (m-80) cc_final: 0.7169 (m-80) REVERT: D 65 ILE cc_start: 0.9454 (tp) cc_final: 0.9248 (tp) REVERT: D 124 ASP cc_start: 0.9227 (t0) cc_final: 0.8940 (t0) REVERT: D 136 LEU cc_start: 0.9292 (tt) cc_final: 0.8977 (tt) REVERT: D 327 LYS cc_start: 0.8409 (mmmt) cc_final: 0.7718 (mmtt) REVERT: D 335 MET cc_start: 0.6244 (mmm) cc_final: 0.5631 (mtm) REVERT: D 382 MET cc_start: 0.9157 (tpt) cc_final: 0.8745 (tpp) REVERT: D 481 TYR cc_start: 0.9480 (t80) cc_final: 0.9213 (t80) REVERT: D 492 MET cc_start: 0.8840 (tpp) cc_final: 0.8473 (tpp) REVERT: D 524 PHE cc_start: 0.7669 (t80) cc_final: 0.7279 (t80) outliers start: 4 outliers final: 0 residues processed: 481 average time/residue: 0.2473 time to fit residues: 181.5540 Evaluate side-chains 365 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 15 optimal weight: 0.0010 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN C 228 GLN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16028 Z= 0.179 Angle : 0.576 10.887 21668 Z= 0.306 Chirality : 0.041 0.221 2452 Planarity : 0.003 0.017 2668 Dihedral : 4.491 26.408 2056 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.19), residues: 1872 helix: 1.98 (0.15), residues: 1140 sheet: 1.54 (0.33), residues: 216 loop : -1.89 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 341 HIS 0.007 0.001 HIS B 100 PHE 0.022 0.002 PHE A 524 TYR 0.021 0.001 TYR A 481 ARG 0.006 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9082 (t80) cc_final: 0.8776 (t80) REVERT: A 86 MET cc_start: 0.8539 (mmm) cc_final: 0.8194 (tpp) REVERT: A 124 ASP cc_start: 0.9172 (t0) cc_final: 0.8962 (t0) REVERT: A 165 ARG cc_start: 0.5737 (ttp80) cc_final: 0.5497 (ttp80) REVERT: A 217 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 312 GLN cc_start: 0.7800 (mt0) cc_final: 0.7353 (pt0) REVERT: A 313 LEU cc_start: 0.8093 (mp) cc_final: 0.7839 (tt) REVERT: A 327 LYS cc_start: 0.8434 (mmmt) cc_final: 0.7769 (mmtt) REVERT: A 382 MET cc_start: 0.8288 (tpt) cc_final: 0.8064 (tpt) REVERT: A 415 PHE cc_start: 0.9136 (t80) cc_final: 0.8226 (t80) REVERT: A 458 ASP cc_start: 0.9568 (t70) cc_final: 0.9353 (t0) REVERT: A 512 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8704 (tm-30) REVERT: B 45 PHE cc_start: 0.8975 (t80) cc_final: 0.8731 (t80) REVERT: B 47 MET cc_start: 0.8855 (mtm) cc_final: 0.8108 (mtp) REVERT: B 53 PHE cc_start: 0.7899 (m-80) cc_final: 0.7180 (m-80) REVERT: B 72 MET cc_start: 0.8786 (mmp) cc_final: 0.8469 (mmp) REVERT: B 124 ASP cc_start: 0.9171 (t0) cc_final: 0.8937 (t0) REVERT: B 165 ARG cc_start: 0.5701 (ttp80) cc_final: 0.5460 (ttp80) REVERT: B 327 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7709 (mmtt) REVERT: B 382 MET cc_start: 0.8118 (tpt) cc_final: 0.7873 (tpt) REVERT: B 406 GLN cc_start: 0.9099 (mt0) cc_final: 0.8892 (mt0) REVERT: C 44 PHE cc_start: 0.8901 (t80) cc_final: 0.7393 (t80) REVERT: C 45 PHE cc_start: 0.8953 (t80) cc_final: 0.8648 (t80) REVERT: C 47 MET cc_start: 0.8878 (mtm) cc_final: 0.8099 (mtp) REVERT: C 72 MET cc_start: 0.8994 (mmm) cc_final: 0.8748 (tpp) REVERT: C 93 GLU cc_start: 0.8904 (tp30) cc_final: 0.8559 (tp30) REVERT: C 124 ASP cc_start: 0.9186 (t0) cc_final: 0.8934 (t0) REVERT: C 165 ARG cc_start: 0.5704 (ttp80) cc_final: 0.5475 (ttp80) REVERT: C 327 LYS cc_start: 0.8324 (mmmt) cc_final: 0.7621 (mmtt) REVERT: C 335 MET cc_start: 0.6288 (mmm) cc_final: 0.5651 (mtm) REVERT: C 388 VAL cc_start: 0.9285 (t) cc_final: 0.9067 (t) REVERT: C 415 PHE cc_start: 0.9161 (t80) cc_final: 0.8230 (t80) REVERT: C 492 MET cc_start: 0.8718 (tpp) cc_final: 0.8317 (tpp) REVERT: D 45 PHE cc_start: 0.9220 (t80) cc_final: 0.8814 (t80) REVERT: D 72 MET cc_start: 0.8613 (mmp) cc_final: 0.8274 (tpp) REVERT: D 124 ASP cc_start: 0.9184 (t0) cc_final: 0.8941 (t0) REVERT: D 165 ARG cc_start: 0.5848 (ttp80) cc_final: 0.5632 (ttp80) REVERT: D 327 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7675 (mmtt) REVERT: D 335 MET cc_start: 0.6333 (mmm) cc_final: 0.5723 (mtm) REVERT: D 459 ASP cc_start: 0.8887 (t70) cc_final: 0.8477 (t70) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.2524 time to fit residues: 181.1916 Evaluate side-chains 367 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN C 76 GLN ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16028 Z= 0.208 Angle : 0.587 8.605 21668 Z= 0.314 Chirality : 0.041 0.162 2452 Planarity : 0.003 0.024 2668 Dihedral : 4.435 25.708 2056 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 1872 helix: 2.02 (0.15), residues: 1140 sheet: 1.50 (0.34), residues: 224 loop : -1.83 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 341 HIS 0.005 0.001 HIS C 100 PHE 0.024 0.002 PHE A 337 TYR 0.028 0.002 TYR D 426 ARG 0.006 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9142 (t80) cc_final: 0.8695 (t80) REVERT: A 86 MET cc_start: 0.8445 (mmm) cc_final: 0.8124 (tpp) REVERT: A 124 ASP cc_start: 0.9158 (t0) cc_final: 0.8889 (t0) REVERT: A 165 ARG cc_start: 0.5707 (ttp80) cc_final: 0.5454 (ttp80) REVERT: A 217 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8707 (mt-10) REVERT: A 312 GLN cc_start: 0.7574 (mt0) cc_final: 0.7335 (pt0) REVERT: A 327 LYS cc_start: 0.8430 (mmmt) cc_final: 0.7707 (mmtt) REVERT: A 335 MET cc_start: 0.6115 (mmm) cc_final: 0.5207 (mtm) REVERT: A 388 VAL cc_start: 0.9255 (t) cc_final: 0.9036 (t) REVERT: A 415 PHE cc_start: 0.9208 (t80) cc_final: 0.8192 (t80) REVERT: A 458 ASP cc_start: 0.9563 (t70) cc_final: 0.9335 (t0) REVERT: A 512 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8789 (mm110) REVERT: B 45 PHE cc_start: 0.9089 (t80) cc_final: 0.8707 (t80) REVERT: B 47 MET cc_start: 0.9225 (mtm) cc_final: 0.8663 (mtp) REVERT: B 72 MET cc_start: 0.8801 (mmp) cc_final: 0.8479 (mmp) REVERT: B 124 ASP cc_start: 0.9153 (t0) cc_final: 0.8896 (t0) REVERT: B 165 ARG cc_start: 0.5675 (ttp80) cc_final: 0.5421 (ttp80) REVERT: B 327 LYS cc_start: 0.8437 (mmmt) cc_final: 0.7723 (mmtt) REVERT: B 335 MET cc_start: 0.6216 (mmm) cc_final: 0.5424 (mtm) REVERT: C 45 PHE cc_start: 0.9046 (t80) cc_final: 0.8741 (t80) REVERT: C 72 MET cc_start: 0.8992 (mmm) cc_final: 0.8742 (tpp) REVERT: C 93 GLU cc_start: 0.8931 (tp30) cc_final: 0.8567 (tp30) REVERT: C 124 ASP cc_start: 0.9168 (t0) cc_final: 0.8886 (t0) REVERT: C 165 ARG cc_start: 0.5687 (ttp80) cc_final: 0.5472 (ttp80) REVERT: C 327 LYS cc_start: 0.8344 (mmmt) cc_final: 0.7601 (mmtt) REVERT: C 335 MET cc_start: 0.6179 (mmm) cc_final: 0.5671 (mtm) REVERT: C 361 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8362 (tp30) REVERT: C 415 PHE cc_start: 0.9176 (t80) cc_final: 0.8251 (t80) REVERT: C 492 MET cc_start: 0.8795 (tpp) cc_final: 0.8398 (tpp) REVERT: C 524 PHE cc_start: 0.7302 (t80) cc_final: 0.6997 (t80) REVERT: D 45 PHE cc_start: 0.9175 (t80) cc_final: 0.8721 (t80) REVERT: D 72 MET cc_start: 0.8676 (mmp) cc_final: 0.8392 (mmp) REVERT: D 124 ASP cc_start: 0.9170 (t0) cc_final: 0.8907 (t0) REVERT: D 165 ARG cc_start: 0.5787 (ttp80) cc_final: 0.5536 (ttp80) REVERT: D 327 LYS cc_start: 0.8432 (mmmt) cc_final: 0.7674 (mmtt) REVERT: D 335 MET cc_start: 0.6313 (mmm) cc_final: 0.5790 (mtm) REVERT: D 361 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8879 (mt-10) REVERT: D 388 VAL cc_start: 0.9219 (t) cc_final: 0.9010 (t) REVERT: D 459 ASP cc_start: 0.8883 (t70) cc_final: 0.8481 (t70) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.2373 time to fit residues: 166.8466 Evaluate side-chains 372 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 115 optimal weight: 7.9990 chunk 123 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 228 GLN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN D 406 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16028 Z= 0.189 Angle : 0.576 10.125 21668 Z= 0.303 Chirality : 0.041 0.189 2452 Planarity : 0.003 0.019 2668 Dihedral : 4.367 24.329 2056 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 1872 helix: 2.05 (0.15), residues: 1144 sheet: 1.58 (0.34), residues: 224 loop : -1.91 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 341 HIS 0.004 0.001 HIS C 100 PHE 0.027 0.002 PHE A 524 TYR 0.012 0.001 TYR C 423 ARG 0.005 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9102 (t80) cc_final: 0.8684 (t80) REVERT: A 86 MET cc_start: 0.8420 (mmm) cc_final: 0.8097 (tpp) REVERT: A 124 ASP cc_start: 0.9125 (t0) cc_final: 0.8877 (t0) REVERT: A 217 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8673 (mt-10) REVERT: A 312 GLN cc_start: 0.7648 (mt0) cc_final: 0.7355 (pt0) REVERT: A 327 LYS cc_start: 0.8369 (mmmt) cc_final: 0.7725 (mmtt) REVERT: A 335 MET cc_start: 0.5963 (mmm) cc_final: 0.5356 (mtm) REVERT: A 415 PHE cc_start: 0.9220 (t80) cc_final: 0.8243 (t80) REVERT: A 458 ASP cc_start: 0.9548 (t70) cc_final: 0.9339 (t0) REVERT: A 512 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8711 (tm-30) REVERT: B 45 PHE cc_start: 0.9100 (t80) cc_final: 0.8761 (t80) REVERT: B 47 MET cc_start: 0.9251 (mtm) cc_final: 0.8618 (mtp) REVERT: B 72 MET cc_start: 0.8796 (mmp) cc_final: 0.8469 (mmp) REVERT: B 124 ASP cc_start: 0.9145 (t0) cc_final: 0.8874 (t0) REVERT: B 165 ARG cc_start: 0.5616 (ttp80) cc_final: 0.5395 (ttp80) REVERT: B 291 PHE cc_start: 0.9147 (m-80) cc_final: 0.8865 (m-80) REVERT: B 327 LYS cc_start: 0.8291 (mmmt) cc_final: 0.7625 (mmtt) REVERT: B 335 MET cc_start: 0.6317 (mmm) cc_final: 0.5779 (mtm) REVERT: C 45 PHE cc_start: 0.9106 (t80) cc_final: 0.8833 (t80) REVERT: C 93 GLU cc_start: 0.8921 (tp30) cc_final: 0.8553 (tp30) REVERT: C 124 ASP cc_start: 0.9134 (t0) cc_final: 0.8893 (t0) REVERT: C 165 ARG cc_start: 0.5645 (ttp80) cc_final: 0.5423 (ttp80) REVERT: C 327 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7654 (mmtt) REVERT: C 335 MET cc_start: 0.6204 (mmm) cc_final: 0.5791 (mtm) REVERT: C 361 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8407 (tp30) REVERT: C 415 PHE cc_start: 0.9149 (t80) cc_final: 0.8106 (t80) REVERT: C 492 MET cc_start: 0.8754 (tpp) cc_final: 0.8391 (tpp) REVERT: D 45 PHE cc_start: 0.9208 (t80) cc_final: 0.8733 (t80) REVERT: D 72 MET cc_start: 0.8650 (mmp) cc_final: 0.8206 (mmp) REVERT: D 124 ASP cc_start: 0.9173 (t0) cc_final: 0.8900 (t0) REVERT: D 327 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7678 (mmtt) REVERT: D 335 MET cc_start: 0.6157 (mmm) cc_final: 0.5679 (mtm) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2251 time to fit residues: 158.2943 Evaluate side-chains 371 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 76 GLN ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16028 Z= 0.265 Angle : 0.625 10.515 21668 Z= 0.332 Chirality : 0.043 0.227 2452 Planarity : 0.003 0.024 2668 Dihedral : 4.430 24.406 2056 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 1872 helix: 1.90 (0.15), residues: 1144 sheet: 1.55 (0.33), residues: 224 loop : -1.84 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 341 HIS 0.004 0.001 HIS B 100 PHE 0.030 0.002 PHE B 394 TYR 0.021 0.002 TYR B 426 ARG 0.005 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9105 (t80) cc_final: 0.8579 (t80) REVERT: A 86 MET cc_start: 0.8431 (mmm) cc_final: 0.8093 (tpp) REVERT: A 124 ASP cc_start: 0.9153 (t0) cc_final: 0.8925 (t0) REVERT: A 217 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8800 (mt-10) REVERT: A 312 GLN cc_start: 0.7531 (mt0) cc_final: 0.7208 (pt0) REVERT: A 327 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7516 (mmtt) REVERT: A 335 MET cc_start: 0.5942 (mmm) cc_final: 0.5518 (mtm) REVERT: A 382 MET cc_start: 0.8620 (tpt) cc_final: 0.8114 (tpt) REVERT: A 406 GLN cc_start: 0.9109 (mt0) cc_final: 0.8844 (mt0) REVERT: A 415 PHE cc_start: 0.9277 (t80) cc_final: 0.8322 (t80) REVERT: A 432 ILE cc_start: 0.9220 (tp) cc_final: 0.9017 (tp) REVERT: A 512 GLN cc_start: 0.9251 (mm-40) cc_final: 0.8733 (tm-30) REVERT: B 45 PHE cc_start: 0.9200 (t80) cc_final: 0.8858 (t80) REVERT: B 47 MET cc_start: 0.9262 (mtm) cc_final: 0.8689 (ttp) REVERT: B 124 ASP cc_start: 0.9173 (t0) cc_final: 0.8903 (t0) REVERT: B 165 ARG cc_start: 0.5712 (ttp80) cc_final: 0.5472 (ttp80) REVERT: B 284 TYR cc_start: 0.8068 (p90) cc_final: 0.7856 (p90) REVERT: B 291 PHE cc_start: 0.9132 (m-80) cc_final: 0.8890 (m-80) REVERT: B 327 LYS cc_start: 0.8281 (mmmt) cc_final: 0.7689 (mmtt) REVERT: B 335 MET cc_start: 0.5998 (mmm) cc_final: 0.5587 (mtm) REVERT: B 382 MET cc_start: 0.8522 (tpt) cc_final: 0.8242 (tpp) REVERT: B 492 MET cc_start: 0.8810 (tpp) cc_final: 0.8312 (tpp) REVERT: C 45 PHE cc_start: 0.9121 (t80) cc_final: 0.8797 (t80) REVERT: C 93 GLU cc_start: 0.8972 (tp30) cc_final: 0.8578 (tp30) REVERT: C 124 ASP cc_start: 0.9202 (t0) cc_final: 0.8939 (t0) REVERT: C 165 ARG cc_start: 0.5637 (ttp80) cc_final: 0.5429 (ttp80) REVERT: C 327 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7769 (mmtt) REVERT: C 335 MET cc_start: 0.6154 (mmm) cc_final: 0.5714 (mtm) REVERT: C 361 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8497 (tp30) REVERT: C 382 MET cc_start: 0.8519 (tpt) cc_final: 0.8162 (tpp) REVERT: C 415 PHE cc_start: 0.9272 (t80) cc_final: 0.8121 (t80) REVERT: D 45 PHE cc_start: 0.9237 (t80) cc_final: 0.8736 (t80) REVERT: D 65 ILE cc_start: 0.9441 (tp) cc_final: 0.9224 (tp) REVERT: D 72 MET cc_start: 0.8654 (mmp) cc_final: 0.8216 (mmp) REVERT: D 124 ASP cc_start: 0.9199 (t0) cc_final: 0.8941 (t0) REVERT: D 327 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7559 (mmtt) REVERT: D 335 MET cc_start: 0.6221 (mmm) cc_final: 0.5738 (mtm) REVERT: D 382 MET cc_start: 0.8245 (tpt) cc_final: 0.7954 (tpt) REVERT: D 388 VAL cc_start: 0.9194 (t) cc_final: 0.8976 (t) REVERT: D 492 MET cc_start: 0.8844 (tpp) cc_final: 0.8453 (tpp) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.2244 time to fit residues: 154.9293 Evaluate side-chains 372 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 158 optimal weight: 0.0050 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN C 228 GLN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16028 Z= 0.180 Angle : 0.585 9.441 21668 Z= 0.305 Chirality : 0.041 0.203 2452 Planarity : 0.003 0.021 2668 Dihedral : 4.352 23.907 2056 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.19), residues: 1872 helix: 1.92 (0.15), residues: 1144 sheet: 1.55 (0.33), residues: 224 loop : -1.83 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 341 HIS 0.004 0.001 HIS C 100 PHE 0.026 0.002 PHE A 524 TYR 0.012 0.001 TYR A 426 ARG 0.004 0.000 ARG A 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.9160 (t80) cc_final: 0.8514 (t80) REVERT: A 65 ILE cc_start: 0.9398 (tp) cc_final: 0.9158 (tp) REVERT: A 86 MET cc_start: 0.8429 (mmm) cc_final: 0.8134 (tpp) REVERT: A 124 ASP cc_start: 0.9187 (t0) cc_final: 0.8938 (t0) REVERT: A 217 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8701 (mt-10) REVERT: A 327 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7513 (mmtt) REVERT: A 335 MET cc_start: 0.6031 (mmm) cc_final: 0.5754 (mtm) REVERT: A 375 ILE cc_start: 0.9409 (mt) cc_final: 0.9179 (mt) REVERT: A 382 MET cc_start: 0.9047 (tpt) cc_final: 0.8692 (tpp) REVERT: A 415 PHE cc_start: 0.9214 (t80) cc_final: 0.8171 (t80) REVERT: A 432 ILE cc_start: 0.9062 (tp) cc_final: 0.8813 (tp) REVERT: A 491 TYR cc_start: 0.9124 (m-10) cc_final: 0.8738 (m-10) REVERT: A 512 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8678 (tm-30) REVERT: B 45 PHE cc_start: 0.9201 (t80) cc_final: 0.8862 (t80) REVERT: B 72 MET cc_start: 0.8688 (mmp) cc_final: 0.8418 (tpp) REVERT: B 120 SER cc_start: 0.9340 (m) cc_final: 0.9113 (p) REVERT: B 124 ASP cc_start: 0.9168 (t0) cc_final: 0.8909 (t0) REVERT: B 165 ARG cc_start: 0.5674 (ttp80) cc_final: 0.5451 (ttp80) REVERT: B 288 PHE cc_start: 0.8748 (t80) cc_final: 0.8516 (t80) REVERT: B 291 PHE cc_start: 0.9125 (m-80) cc_final: 0.8862 (m-80) REVERT: B 327 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7655 (mmtt) REVERT: B 335 MET cc_start: 0.5823 (mmm) cc_final: 0.5524 (mtm) REVERT: B 336 GLU cc_start: 0.8293 (tp30) cc_final: 0.7720 (tt0) REVERT: B 382 MET cc_start: 0.8733 (tpt) cc_final: 0.7996 (tpt) REVERT: B 439 ASP cc_start: 0.9032 (p0) cc_final: 0.8829 (p0) REVERT: B 492 MET cc_start: 0.8667 (tpp) cc_final: 0.8226 (tpp) REVERT: B 521 LEU cc_start: 0.8703 (mp) cc_final: 0.8475 (mp) REVERT: C 45 PHE cc_start: 0.9071 (t80) cc_final: 0.8770 (t80) REVERT: C 93 GLU cc_start: 0.8898 (tp30) cc_final: 0.8512 (tp30) REVERT: C 120 SER cc_start: 0.9336 (m) cc_final: 0.8994 (p) REVERT: C 124 ASP cc_start: 0.9164 (t0) cc_final: 0.8876 (t0) REVERT: C 165 ARG cc_start: 0.5713 (ttp80) cc_final: 0.5498 (ttp80) REVERT: C 284 TYR cc_start: 0.8021 (p90) cc_final: 0.7813 (p90) REVERT: C 327 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7724 (mmtt) REVERT: C 335 MET cc_start: 0.6163 (mmm) cc_final: 0.5808 (mtm) REVERT: C 361 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8485 (tp30) REVERT: C 382 MET cc_start: 0.8892 (tpt) cc_final: 0.8441 (tpp) REVERT: C 415 PHE cc_start: 0.9206 (t80) cc_final: 0.7921 (t80) REVERT: C 512 GLN cc_start: 0.8746 (tp40) cc_final: 0.8227 (tm-30) REVERT: D 45 PHE cc_start: 0.9267 (t80) cc_final: 0.8744 (t80) REVERT: D 65 ILE cc_start: 0.9438 (tp) cc_final: 0.9225 (tp) REVERT: D 72 MET cc_start: 0.8545 (mmp) cc_final: 0.8133 (mmp) REVERT: D 93 GLU cc_start: 0.9202 (tp30) cc_final: 0.8980 (tp30) REVERT: D 124 ASP cc_start: 0.9184 (t0) cc_final: 0.8887 (t0) REVERT: D 327 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7440 (mmtt) REVERT: D 335 MET cc_start: 0.6211 (mmm) cc_final: 0.5880 (mtm) REVERT: D 388 VAL cc_start: 0.9164 (t) cc_final: 0.8941 (t) REVERT: D 414 ARG cc_start: 0.8876 (mtt-85) cc_final: 0.8641 (mpt-90) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.2206 time to fit residues: 157.5273 Evaluate side-chains 385 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.6980 chunk 137 optimal weight: 0.1980 chunk 22 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 0.0970 chunk 62 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN C 228 GLN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.181827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142802 restraints weight = 20869.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.146429 restraints weight = 12699.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.148554 restraints weight = 9148.760| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16028 Z= 0.173 Angle : 0.595 9.506 21668 Z= 0.307 Chirality : 0.041 0.183 2452 Planarity : 0.003 0.024 2668 Dihedral : 4.314 21.366 2056 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 1872 helix: 1.86 (0.15), residues: 1148 sheet: 1.79 (0.34), residues: 216 loop : -1.81 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 341 HIS 0.004 0.001 HIS B 100 PHE 0.029 0.001 PHE D 524 TYR 0.018 0.001 TYR B 426 ARG 0.004 0.000 ARG B 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.66 seconds wall clock time: 65 minutes 5.40 seconds (3905.40 seconds total)