Starting phenix.real_space_refine on Mon Jul 28 23:31:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ot0_20190/07_2025/6ot0_20190.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ot0_20190/07_2025/6ot0_20190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ot0_20190/07_2025/6ot0_20190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ot0_20190/07_2025/6ot0_20190.map" model { file = "/net/cci-nas-00/data/ceres_data/6ot0_20190/07_2025/6ot0_20190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ot0_20190/07_2025/6ot0_20190.cif" } resolution = 3.84 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= 0.003 sd= 0.067 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 71 5.16 5 C 6723 2.51 5 N 1792 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10572 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2887 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 13, 'TRANS': 350} Chain: "A" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2832 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 349} Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 995 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CO1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.86, per 1000 atoms: 0.65 Number of scatterers: 10572 At special positions: 0 Unit cell: (143.38, 131.61, 120.91, 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 71 16.00 O 1986 8.00 N 1792 7.00 C 6723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 193 " - pdb=" SG CYS R 213 " distance=2.03 Simple disulfide: pdb=" SG CYS R 490 " - pdb=" SG CYS R 507 " distance=2.02 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 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: 2.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 36.7% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'R' and resid 223 through 255 removed outlier: 3.704A pdb=" N HIS R 227 " --> pdb=" O THR R 223 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR R 251 " --> pdb=" O PHE R 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE R 252 " --> pdb=" O THR R 248 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA R 254 " --> pdb=" O ALA R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 273 removed outlier: 3.594A pdb=" N LEU R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 281 removed outlier: 3.705A pdb=" N GLY R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 309 removed outlier: 3.919A pdb=" N SER R 308 " --> pdb=" O GLU R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 345 removed outlier: 3.682A pdb=" N PHE R 318 " --> pdb=" O CYS R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 376 removed outlier: 3.585A pdb=" N PHE R 360 " --> pdb=" O LYS R 356 " (cutoff:3.500A) Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 397 through 426 removed outlier: 4.676A pdb=" N GLY R 402 " --> pdb=" O ARG R 398 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE R 403 " --> pdb=" O TYR R 399 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL R 404 " --> pdb=" O ARG R 400 " (cutoff:3.500A) Proline residue: R 407 - end of helix Processing helix chain 'R' and resid 438 through 494 removed outlier: 3.682A pdb=" N LYS R 444 " --> pdb=" O LYS R 440 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL R 463 " --> pdb=" O ALA R 459 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU R 464 " --> pdb=" O PHE R 460 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR R 466 " --> pdb=" O PHE R 462 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE R 475 " --> pdb=" O PHE R 471 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN R 476 " --> pdb=" O TYR R 472 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA R 478 " --> pdb=" O PHE R 474 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU R 479 " --> pdb=" O PHE R 475 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA R 492 " --> pdb=" O VAL R 488 " (cutoff:3.500A) Processing helix chain 'R' and resid 517 through 532 removed outlier: 4.085A pdb=" N ASN R 521 " --> pdb=" O VAL R 517 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET R 532 " --> pdb=" O THR R 528 " (cutoff:3.500A) Processing helix chain 'R' and resid 540 through 551 removed outlier: 4.057A pdb=" N ILE R 544 " --> pdb=" O ALA R 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 25 removed outlier: 3.549A pdb=" N ALA A 7 " --> pdb=" O CYS A 3 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 65 through 91 Processing helix chain 'A' and resid 100 through 112 removed outlier: 3.904A pdb=" N LEU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 4.096A pdb=" N ARG A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 151 through 158 removed outlier: 4.662A pdb=" N TYR A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 164 removed outlier: 3.714A pdb=" N ILE A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 241 through 255 removed outlier: 4.268A pdb=" N ALA A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.807A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.593A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 352 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.048A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.650A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing sheet with id=AA1, first strand: chain 'R' and resid 197 through 199 Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 191 removed outlier: 6.893A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.369A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.413A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.611A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.403A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.163A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 233 through 234 removed outlier: 6.484A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 284 through 288 removed outlier: 3.878A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 7 through 9 Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.757A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 7 through 10 Processing sheet with id=AB4, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.347A pdb=" N GLY H 13 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER H 53 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER H 62 " --> pdb=" O SER H 53 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1272 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: 3.59 Time building geometry restraints manager: 3.27 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: 3036 1.34 - 1.45: 1735 1.45 - 1.57: 5923 1.57 - 1.69: 11 1.69 - 1.81: 101 Bond restraints: 10806 Sorted by residual: bond pdb=" C TYR R 262 " pdb=" O TYR R 262 " ideal model delta sigma weight residual 1.238 1.550 -0.312 1.28e-02 6.10e+03 5.95e+02 bond pdb=" C14 CO1 R 601 " pdb=" C7 CO1 R 601 " ideal model delta sigma weight residual 1.519 1.629 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C11 CO1 R 601 " pdb=" C5 CO1 R 601 " ideal model delta sigma weight residual 1.530 1.605 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" CA VAL R 195 " pdb=" CB VAL R 195 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.35e+01 bond pdb=" C12 CO1 R 601 " pdb=" C5 CO1 R 601 " ideal model delta sigma weight residual 1.532 1.605 -0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 10801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 14263 2.80 - 5.60: 369 5.60 - 8.41: 18 8.41 - 11.21: 2 11.21 - 14.01: 1 Bond angle restraints: 14653 Sorted by residual: angle pdb=" C TYR R 262 " pdb=" N PRO R 263 " pdb=" CA PRO R 263 " ideal model delta sigma weight residual 119.84 128.24 -8.40 1.25e+00 6.40e-01 4.51e+01 angle pdb=" C GLU R 305 " pdb=" N PRO R 306 " pdb=" CA PRO R 306 " ideal model delta sigma weight residual 119.19 125.75 -6.56 1.06e+00 8.90e-01 3.83e+01 angle pdb=" CA VAL R 195 " pdb=" C VAL R 195 " pdb=" N PRO R 196 " ideal model delta sigma weight residual 120.83 117.75 3.08 6.10e-01 2.69e+00 2.54e+01 angle pdb=" N GLY R 347 " pdb=" CA GLY R 347 " pdb=" C GLY R 347 " ideal model delta sigma weight residual 113.18 102.43 10.75 2.37e+00 1.78e-01 2.06e+01 angle pdb=" N ASP B 246 " pdb=" CA ASP B 246 " pdb=" C ASP B 246 " ideal model delta sigma weight residual 112.87 118.27 -5.40 1.20e+00 6.94e-01 2.03e+01 ... (remaining 14648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 5627 15.50 - 31.00: 598 31.00 - 46.49: 164 46.49 - 61.99: 29 61.99 - 77.49: 14 Dihedral angle restraints: 6432 sinusoidal: 2532 harmonic: 3900 Sorted by residual: dihedral pdb=" CA TYR R 262 " pdb=" C TYR R 262 " pdb=" N PRO R 263 " pdb=" CA PRO R 263 " ideal model delta harmonic sigma weight residual 180.00 -110.37 -69.63 0 5.00e+00 4.00e-02 1.94e+02 dihedral pdb=" CA GLY R 347 " pdb=" C GLY R 347 " pdb=" N THR R 348 " pdb=" CA THR R 348 " ideal model delta harmonic sigma weight residual -180.00 -145.34 -34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA LEU R 346 " pdb=" C LEU R 346 " pdb=" N GLY R 347 " pdb=" CA GLY R 347 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 6429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1322 0.085 - 0.171: 275 0.171 - 0.256: 30 0.256 - 0.341: 5 0.341 - 0.427: 3 Chirality restraints: 1635 Sorted by residual: chirality pdb=" C5 CO1 R 601 " pdb=" C10 CO1 R 601 " pdb=" C11 CO1 R 601 " pdb=" C2 CO1 R 601 " both_signs ideal model delta sigma weight residual False -2.93 -3.36 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" C7 CO1 R 601 " pdb=" C14 CO1 R 601 " pdb=" C15 CO1 R 601 " pdb=" C3 CO1 R 601 " both_signs ideal model delta sigma weight residual False 2.86 3.27 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C2 CO1 R 601 " pdb=" C1 CO1 R 601 " pdb=" C5 CO1 R 601 " pdb=" C6 CO1 R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 1632 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 262 " -0.055 2.00e-02 2.50e+03 1.01e-01 1.02e+02 pdb=" C TYR R 262 " 0.175 2.00e-02 2.50e+03 pdb=" O TYR R 262 " -0.056 2.00e-02 2.50e+03 pdb=" N PRO R 263 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 262 " 0.088 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO R 263 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO R 263 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO R 263 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS R 433 " -0.045 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO R 434 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 434 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 434 " -0.038 5.00e-02 4.00e+02 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3100 2.84 - 3.35: 9933 3.35 - 3.87: 17327 3.87 - 4.38: 18362 4.38 - 4.90: 31332 Nonbonded interactions: 80054 Sorted by model distance: nonbonded pdb=" OD2 ASP A 231 " pdb=" NZ LYS A 277 " model vdw 2.324 3.120 nonbonded pdb=" ND2 ASN A 311 " pdb=" O LYS A 314 " model vdw 2.365 3.120 nonbonded pdb=" O VAL R 333 " pdb=" OG1 THR R 336 " model vdw 2.389 3.040 nonbonded pdb=" O THR R 245 " pdb=" OG1 THR R 248 " model vdw 2.405 3.040 nonbonded pdb=" NH2 ARG R 451 " pdb=" O THR R 534 " model vdw 2.421 3.120 ... (remaining 80049 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.730 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.009 0.312 10809 Z= 0.622 Angle : 1.131 14.010 14659 Z= 0.726 Chirality : 0.070 0.427 1635 Planarity : 0.006 0.132 1857 Dihedral : 14.443 77.489 3917 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.79 % Allowed : 7.67 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % 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: -3.15 (0.20), residues: 1333 helix: -1.55 (0.20), residues: 439 sheet: -1.21 (0.32), residues: 254 loop : -2.89 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 206 HIS 0.007 0.002 HIS R 433 PHE 0.016 0.002 PHE B 151 TYR 0.015 0.002 TYR A 302 ARG 0.009 0.001 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.15548 ( 442) hydrogen bonds : angle 6.93709 ( 1272) SS BOND : bond 0.00441 ( 3) SS BOND : angle 1.36951 ( 6) covalent geometry : bond 0.00896 (10806) covalent geometry : angle 1.13045 (14653) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 432 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8475 (mt0) cc_final: 0.8171 (mp10) REVERT: R 255 ASP cc_start: 0.8055 (t0) cc_final: 0.7718 (t0) REVERT: R 257 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7758 (mtt-85) REVERT: R 269 TYR cc_start: 0.9103 (m-80) cc_final: 0.8860 (m-10) REVERT: R 271 ASN cc_start: 0.8814 (p0) cc_final: 0.8606 (p0) REVERT: R 281 TRP cc_start: 0.8442 (m-10) cc_final: 0.7854 (m-10) REVERT: R 325 LEU cc_start: 0.8967 (pp) cc_final: 0.8679 (pp) REVERT: R 326 MET cc_start: 0.9046 (tpp) cc_final: 0.8763 (mmt) REVERT: R 343 PHE cc_start: 0.9212 (m-10) cc_final: 0.8375 (m-80) REVERT: R 344 LYS cc_start: 0.8491 (ttmt) cc_final: 0.7721 (mttp) REVERT: R 351 GLN cc_start: 0.8650 (tt0) cc_final: 0.8051 (tp-100) REVERT: R 400 ARG cc_start: 0.9277 (ttp80) cc_final: 0.9028 (ttp80) REVERT: R 485 ARG cc_start: 0.6033 (ttt180) cc_final: 0.4728 (tpp80) REVERT: R 491 GLN cc_start: 0.8927 (tt0) cc_final: 0.8632 (mm-40) REVERT: R 510 LYS cc_start: 0.8040 (tptm) cc_final: 0.6984 (ttpp) REVERT: A 18 MET cc_start: 0.7521 (mmm) cc_final: 0.6865 (tpp) REVERT: A 22 ASN cc_start: 0.8816 (m-40) cc_final: 0.8432 (m110) REVERT: A 36 LEU cc_start: 0.9106 (mp) cc_final: 0.8892 (mp) REVERT: A 47 ASN cc_start: 0.9253 (m-40) cc_final: 0.8965 (p0) REVERT: A 74 TYR cc_start: 0.8196 (m-10) cc_final: 0.7929 (m-80) REVERT: A 79 GLN cc_start: 0.9203 (tp-100) cc_final: 0.8683 (mt0) REVERT: A 147 GLN cc_start: 0.9143 (tp-100) cc_final: 0.8892 (tm-30) REVERT: A 188 HIS cc_start: 0.8250 (p-80) cc_final: 0.7890 (p-80) REVERT: A 195 HIS cc_start: 0.8805 (m-70) cc_final: 0.8399 (m90) REVERT: A 211 TRP cc_start: 0.8902 (p-90) cc_final: 0.8550 (p-90) REVERT: A 243 MET cc_start: 0.8824 (ptt) cc_final: 0.8362 (ptt) REVERT: A 244 HIS cc_start: 0.9241 (m170) cc_final: 0.8931 (m170) REVERT: A 269 ASN cc_start: 0.7581 (p0) cc_final: 0.7262 (p0) REVERT: A 320 TYR cc_start: 0.8823 (m-10) cc_final: 0.8619 (m-10) REVERT: B 3 GLU cc_start: 0.8883 (pt0) cc_final: 0.8593 (tp30) REVERT: B 23 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7545 (ptpp) REVERT: B 80 ILE cc_start: 0.8523 (tt) cc_final: 0.8186 (tt) REVERT: B 82 TRP cc_start: 0.8946 (m100) cc_final: 0.8469 (m100) REVERT: B 127 LYS cc_start: 0.9258 (mmmm) cc_final: 0.8638 (mttt) REVERT: B 171 ILE cc_start: 0.9401 (pt) cc_final: 0.9142 (pt) REVERT: B 183 HIS cc_start: 0.7937 (m-70) cc_final: 0.7430 (m170) REVERT: B 211 TRP cc_start: 0.8798 (m100) cc_final: 0.8299 (m100) REVERT: B 212 ASP cc_start: 0.7020 (p0) cc_final: 0.5568 (p0) REVERT: B 215 GLU cc_start: 0.9183 (tp30) cc_final: 0.8809 (tp30) REVERT: B 289 TYR cc_start: 0.8824 (m-80) cc_final: 0.7956 (m-80) REVERT: B 295 ASN cc_start: 0.8392 (p0) cc_final: 0.8148 (p0) REVERT: B 301 LYS cc_start: 0.7830 (mtmt) cc_final: 0.7080 (mmtt) REVERT: G 14 LYS cc_start: 0.9045 (mttm) cc_final: 0.8792 (mttm) REVERT: G 17 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8858 (mt-10) REVERT: L 37 TYR cc_start: 0.8607 (m-80) cc_final: 0.7363 (m-80) REVERT: L 59 VAL cc_start: 0.9373 (t) cc_final: 0.9119 (p) REVERT: L 97 ILE cc_start: 0.9480 (mm) cc_final: 0.8907 (mp) REVERT: L 104 LYS cc_start: 0.8983 (pttp) cc_final: 0.8758 (ptpt) REVERT: H 39 TRP cc_start: 0.9106 (m100) cc_final: 0.8891 (m100) REVERT: H 54 ILE cc_start: 0.8461 (tp) cc_final: 0.8017 (tt) REVERT: H 68 LYS cc_start: 0.9262 (pttt) cc_final: 0.9026 (ptpt) REVERT: H 103 PRO cc_start: 0.9106 (Cg_endo) cc_final: 0.8855 (Cg_exo) REVERT: H 128 THR cc_start: 0.9010 (p) cc_final: 0.8789 (t) outliers start: 9 outliers final: 3 residues processed: 436 average time/residue: 0.3277 time to fit residues: 196.1109 Evaluate side-chains 309 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain A residue 221 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 258 ASN R 309 ASN R 446 ASN A 68 GLN A 256 ASN A 294 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 16 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 340 ASN G 44 HIS L 80 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.106892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.087934 restraints weight = 35013.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090526 restraints weight = 19688.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092278 restraints weight = 13165.424| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10809 Z= 0.154 Angle : 0.676 11.345 14659 Z= 0.351 Chirality : 0.043 0.168 1635 Planarity : 0.005 0.100 1857 Dihedral : 5.935 48.158 1537 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.57 % Rotamer: Outliers : 3.52 % Allowed : 16.39 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % 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: -2.37 (0.21), residues: 1333 helix: -0.60 (0.22), residues: 447 sheet: -0.90 (0.31), residues: 269 loop : -2.65 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.024 0.002 PHE B 235 TYR 0.019 0.001 TYR H 120 ARG 0.006 0.001 ARG R 261 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 442) hydrogen bonds : angle 5.07390 ( 1272) SS BOND : bond 0.00623 ( 3) SS BOND : angle 1.57406 ( 6) covalent geometry : bond 0.00338 (10806) covalent geometry : angle 0.67505 (14653) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8440 (mt0) cc_final: 0.8011 (mp10) REVERT: R 228 GLN cc_start: 0.9221 (mt0) cc_final: 0.8914 (tp40) REVERT: R 257 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7704 (mmt90) REVERT: R 301 MET cc_start: 0.7429 (pmm) cc_final: 0.6740 (pmm) REVERT: R 340 HIS cc_start: 0.7182 (p-80) cc_final: 0.6676 (p-80) REVERT: R 351 GLN cc_start: 0.8410 (tt0) cc_final: 0.7703 (tp-100) REVERT: R 400 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8404 (ttp80) REVERT: R 485 ARG cc_start: 0.6169 (ttt180) cc_final: 0.4772 (tpp80) REVERT: A 18 MET cc_start: 0.7646 (mmm) cc_final: 0.7214 (mmm) REVERT: A 79 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8740 (mt0) REVERT: A 106 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8436 (tp40) REVERT: A 147 GLN cc_start: 0.9130 (tp-100) cc_final: 0.8922 (tm-30) REVERT: A 175 LEU cc_start: 0.8639 (mm) cc_final: 0.8350 (pp) REVERT: A 188 HIS cc_start: 0.8159 (p-80) cc_final: 0.7950 (p-80) REVERT: A 243 MET cc_start: 0.8438 (ptt) cc_final: 0.8001 (ptt) REVERT: A 266 LEU cc_start: 0.9270 (tt) cc_final: 0.9061 (tt) REVERT: B 61 MET cc_start: 0.7882 (ppp) cc_final: 0.7489 (ppp) REVERT: B 82 TRP cc_start: 0.8890 (m100) cc_final: 0.8453 (m100) REVERT: B 127 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8693 (mttt) REVERT: B 175 GLN cc_start: 0.8850 (tp40) cc_final: 0.8337 (tm-30) REVERT: B 237 ASN cc_start: 0.9335 (p0) cc_final: 0.9051 (p0) REVERT: B 289 TYR cc_start: 0.8871 (m-80) cc_final: 0.8215 (m-80) REVERT: B 295 ASN cc_start: 0.8365 (p0) cc_final: 0.8033 (p0) REVERT: B 301 LYS cc_start: 0.7574 (mtmt) cc_final: 0.6682 (mmtt) REVERT: B 325 MET cc_start: 0.7147 (mtm) cc_final: 0.6858 (ttp) REVERT: B 333 ASP cc_start: 0.8374 (p0) cc_final: 0.8082 (p0) REVERT: G 17 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8889 (mt-10) REVERT: G 21 MET cc_start: 0.7876 (mmt) cc_final: 0.7649 (mmt) REVERT: L 59 VAL cc_start: 0.9413 (t) cc_final: 0.9164 (p) REVERT: L 97 ILE cc_start: 0.9403 (mm) cc_final: 0.8981 (mm) REVERT: H 108 MET cc_start: 0.8834 (mtp) cc_final: 0.8378 (mtp) REVERT: H 118 MET cc_start: 0.8263 (mpp) cc_final: 0.7897 (mpp) REVERT: H 120 TYR cc_start: 0.8033 (m-10) cc_final: 0.7816 (m-80) REVERT: H 128 THR cc_start: 0.8720 (p) cc_final: 0.8510 (t) outliers start: 40 outliers final: 27 residues processed: 325 average time/residue: 0.2069 time to fit residues: 97.0989 Evaluate side-chains 301 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 274 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 466 THR Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 112 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 0.0050 overall best weight: 2.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.105330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.086393 restraints weight = 36273.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.088946 restraints weight = 20331.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.090676 restraints weight = 13606.205| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10809 Z= 0.157 Angle : 0.667 12.710 14659 Z= 0.343 Chirality : 0.043 0.192 1635 Planarity : 0.005 0.102 1857 Dihedral : 5.809 53.096 1536 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.93 % Allowed : 18.06 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % 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: -2.01 (0.22), residues: 1333 helix: -0.23 (0.23), residues: 450 sheet: -0.65 (0.31), residues: 269 loop : -2.54 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 PHE 0.021 0.002 PHE H 32 TYR 0.018 0.001 TYR A 69 ARG 0.006 0.001 ARG R 400 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 442) hydrogen bonds : angle 4.96615 ( 1272) SS BOND : bond 0.00664 ( 3) SS BOND : angle 2.55639 ( 6) covalent geometry : bond 0.00351 (10806) covalent geometry : angle 0.66474 (14653) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 271 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8237 (m) cc_final: 0.7928 (p) REVERT: R 218 GLN cc_start: 0.8416 (mt0) cc_final: 0.7915 (mp10) REVERT: R 228 GLN cc_start: 0.9263 (mt0) cc_final: 0.8991 (tp40) REVERT: R 257 ARG cc_start: 0.8125 (mtp180) cc_final: 0.7734 (mmt90) REVERT: R 271 ASN cc_start: 0.8442 (p0) cc_final: 0.8165 (p0) REVERT: R 301 MET cc_start: 0.7548 (pmm) cc_final: 0.6663 (pmm) REVERT: R 351 GLN cc_start: 0.8297 (tt0) cc_final: 0.7666 (tp-100) REVERT: R 400 ARG cc_start: 0.8823 (ttp80) cc_final: 0.8564 (ttp80) REVERT: R 485 ARG cc_start: 0.6353 (ttt180) cc_final: 0.4994 (tpp80) REVERT: A 74 TYR cc_start: 0.8326 (m-10) cc_final: 0.8071 (m-80) REVERT: A 79 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8722 (mt0) REVERT: A 147 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8915 (tm-30) REVERT: A 164 GLN cc_start: 0.8878 (pt0) cc_final: 0.8617 (tm-30) REVERT: B 3 GLU cc_start: 0.8905 (tp30) cc_final: 0.8582 (pt0) REVERT: B 46 ARG cc_start: 0.7838 (mtt-85) cc_final: 0.7614 (mtt-85) REVERT: B 59 TYR cc_start: 0.8273 (m-80) cc_final: 0.7995 (m-80) REVERT: B 61 MET cc_start: 0.7904 (ppp) cc_final: 0.7367 (ppp) REVERT: B 127 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8668 (mttt) REVERT: B 209 LYS cc_start: 0.7977 (mmtp) cc_final: 0.7723 (mttp) REVERT: B 289 TYR cc_start: 0.8870 (m-80) cc_final: 0.8269 (m-80) REVERT: B 292 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: B 295 ASN cc_start: 0.8368 (p0) cc_final: 0.8012 (p0) REVERT: B 301 LYS cc_start: 0.7653 (mtmt) cc_final: 0.6891 (mmtt) REVERT: B 325 MET cc_start: 0.7332 (mtm) cc_final: 0.7056 (ttp) REVERT: B 333 ASP cc_start: 0.8566 (p0) cc_final: 0.8249 (p0) REVERT: G 17 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8973 (mt-10) REVERT: G 21 MET cc_start: 0.7888 (mmt) cc_final: 0.7606 (mmm) REVERT: L 59 VAL cc_start: 0.9378 (t) cc_final: 0.9127 (p) REVERT: L 97 ILE cc_start: 0.9382 (mm) cc_final: 0.8971 (mp) REVERT: H 50 TRP cc_start: 0.7966 (t60) cc_final: 0.7656 (t60) outliers start: 56 outliers final: 42 residues processed: 303 average time/residue: 0.2449 time to fit residues: 107.4012 Evaluate side-chains 294 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 466 THR Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 491 GLN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 107 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 21 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN B 142 HIS B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.103489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.085020 restraints weight = 35656.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087435 restraints weight = 20130.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.089086 restraints weight = 13527.215| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10809 Z= 0.184 Angle : 0.673 13.588 14659 Z= 0.346 Chirality : 0.042 0.178 1635 Planarity : 0.005 0.105 1857 Dihedral : 5.873 65.178 1536 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.85 % Rotamer: Outliers : 6.08 % Allowed : 19.47 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % 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: -1.88 (0.22), residues: 1333 helix: -0.12 (0.23), residues: 452 sheet: -0.64 (0.31), residues: 273 loop : -2.46 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 PHE 0.021 0.002 PHE H 32 TYR 0.019 0.001 TYR H 102 ARG 0.006 0.001 ARG R 400 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 442) hydrogen bonds : angle 4.98910 ( 1272) SS BOND : bond 0.00295 ( 3) SS BOND : angle 2.10290 ( 6) covalent geometry : bond 0.00408 (10806) covalent geometry : angle 0.67147 (14653) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 263 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8311 (m) cc_final: 0.7978 (p) REVERT: R 218 GLN cc_start: 0.8477 (mt0) cc_final: 0.7938 (mp10) REVERT: R 257 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7677 (mmt90) REVERT: R 301 MET cc_start: 0.7555 (pmm) cc_final: 0.6593 (pmm) REVERT: R 351 GLN cc_start: 0.8037 (tt0) cc_final: 0.7527 (tp-100) REVERT: R 400 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8563 (ttp80) REVERT: R 433 HIS cc_start: 0.6279 (OUTLIER) cc_final: 0.5802 (p-80) REVERT: R 449 MET cc_start: 0.9207 (ttt) cc_final: 0.8638 (tpp) REVERT: R 485 ARG cc_start: 0.6426 (ttt180) cc_final: 0.5121 (tpp80) REVERT: A 74 TYR cc_start: 0.8321 (m-10) cc_final: 0.8060 (m-80) REVERT: A 79 GLN cc_start: 0.9034 (tp40) cc_final: 0.8719 (mt0) REVERT: A 283 LEU cc_start: 0.8517 (tt) cc_final: 0.8247 (tp) REVERT: B 46 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7560 (mtt-85) REVERT: B 61 MET cc_start: 0.7919 (ppp) cc_final: 0.7366 (ppp) REVERT: B 82 TRP cc_start: 0.8850 (m100) cc_final: 0.8629 (m100) REVERT: B 127 LYS cc_start: 0.9176 (mmmm) cc_final: 0.8625 (mttt) REVERT: B 175 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8333 (tm-30) REVERT: B 289 TYR cc_start: 0.8911 (m-80) cc_final: 0.8327 (m-80) REVERT: B 292 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: B 295 ASN cc_start: 0.8389 (p0) cc_final: 0.7996 (p0) REVERT: B 301 LYS cc_start: 0.7770 (mtmt) cc_final: 0.7012 (mmtt) REVERT: B 325 MET cc_start: 0.7390 (mtm) cc_final: 0.7152 (ttp) REVERT: B 333 ASP cc_start: 0.8641 (p0) cc_final: 0.8344 (p0) REVERT: G 17 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8865 (mt-10) REVERT: G 21 MET cc_start: 0.7944 (mmt) cc_final: 0.7703 (mmm) REVERT: G 36 ASP cc_start: 0.8780 (t0) cc_final: 0.8422 (m-30) REVERT: L 59 VAL cc_start: 0.9340 (t) cc_final: 0.9074 (p) REVERT: L 97 ILE cc_start: 0.9445 (mm) cc_final: 0.8988 (mm) REVERT: H 30 PHE cc_start: 0.7471 (p90) cc_final: 0.7219 (p90) outliers start: 69 outliers final: 53 residues processed: 302 average time/residue: 0.2348 time to fit residues: 104.6444 Evaluate side-chains 299 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 466 THR Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 116 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 0.1980 chunk 52 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 ASN R 340 HIS R 361 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.107197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.088446 restraints weight = 34927.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.090976 restraints weight = 19579.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.092675 restraints weight = 13087.911| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10809 Z= 0.114 Angle : 0.659 11.717 14659 Z= 0.330 Chirality : 0.042 0.189 1635 Planarity : 0.004 0.099 1857 Dihedral : 5.612 72.746 1536 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.02 % Allowed : 22.38 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.68 (0.22), residues: 1333 helix: 0.08 (0.23), residues: 453 sheet: -0.49 (0.31), residues: 276 loop : -2.39 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 PHE 0.023 0.001 PHE H 71 TYR 0.019 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 442) hydrogen bonds : angle 4.72308 ( 1272) SS BOND : bond 0.00321 ( 3) SS BOND : angle 1.31757 ( 6) covalent geometry : bond 0.00255 (10806) covalent geometry : angle 0.65857 (14653) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8349 (m) cc_final: 0.8109 (p) REVERT: R 218 GLN cc_start: 0.8359 (mt0) cc_final: 0.7773 (mp10) REVERT: R 228 GLN cc_start: 0.9259 (mt0) cc_final: 0.9010 (tp40) REVERT: R 252 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8055 (t80) REVERT: R 257 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7719 (mmt90) REVERT: R 301 MET cc_start: 0.7447 (pmm) cc_final: 0.6534 (pmm) REVERT: R 351 GLN cc_start: 0.7978 (tt0) cc_final: 0.7429 (tp-100) REVERT: R 433 HIS cc_start: 0.6205 (OUTLIER) cc_final: 0.5722 (p-80) REVERT: R 447 GLU cc_start: 0.7964 (tp30) cc_final: 0.7402 (tm-30) REVERT: R 485 ARG cc_start: 0.6250 (ttt180) cc_final: 0.4987 (tpp80) REVERT: A 18 MET cc_start: 0.7204 (mmm) cc_final: 0.6587 (tpp) REVERT: A 74 TYR cc_start: 0.8171 (m-10) cc_final: 0.7890 (m-80) REVERT: A 79 GLN cc_start: 0.9070 (tp40) cc_final: 0.8677 (mt0) REVERT: A 132 LYS cc_start: 0.9354 (mttt) cc_final: 0.8853 (mttm) REVERT: A 175 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8496 (pp) REVERT: A 232 LEU cc_start: 0.8622 (mp) cc_final: 0.7748 (tt) REVERT: A 283 LEU cc_start: 0.8537 (tt) cc_final: 0.8304 (tp) REVERT: B 3 GLU cc_start: 0.8764 (tp30) cc_final: 0.8381 (pt0) REVERT: B 46 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7545 (mtt-85) REVERT: B 61 MET cc_start: 0.7881 (ppp) cc_final: 0.7021 (ppp) REVERT: B 175 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8295 (tm-30) REVERT: B 209 LYS cc_start: 0.7994 (mmtp) cc_final: 0.7686 (mttt) REVERT: B 289 TYR cc_start: 0.8813 (m-80) cc_final: 0.8276 (m-80) REVERT: B 292 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: B 325 MET cc_start: 0.6971 (mtm) cc_final: 0.6758 (ttm) REVERT: B 333 ASP cc_start: 0.8561 (p0) cc_final: 0.8218 (p0) REVERT: G 17 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8833 (mt-10) REVERT: L 59 VAL cc_start: 0.9298 (t) cc_final: 0.9047 (p) REVERT: L 97 ILE cc_start: 0.9291 (mm) cc_final: 0.9056 (mp) REVERT: H 30 PHE cc_start: 0.7428 (p90) cc_final: 0.7066 (p90) REVERT: H 32 PHE cc_start: 0.8641 (t80) cc_final: 0.8357 (t80) REVERT: H 120 TYR cc_start: 0.8005 (m-10) cc_final: 0.7645 (m-80) outliers start: 57 outliers final: 42 residues processed: 312 average time/residue: 0.2708 time to fit residues: 123.5388 Evaluate side-chains 299 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 56 optimal weight: 0.0570 chunk 27 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 85 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.105048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.086461 restraints weight = 35402.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088935 restraints weight = 20003.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.090584 restraints weight = 13406.479| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10809 Z= 0.160 Angle : 0.675 11.192 14659 Z= 0.347 Chirality : 0.043 0.215 1635 Planarity : 0.005 0.100 1857 Dihedral : 5.731 79.914 1536 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 6.52 % Allowed : 22.91 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.76 (0.22), residues: 1333 helix: 0.07 (0.23), residues: 452 sheet: -0.58 (0.32), residues: 262 loop : -2.43 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.018 0.002 PHE A 95 TYR 0.018 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 442) hydrogen bonds : angle 4.78951 ( 1272) SS BOND : bond 0.00286 ( 3) SS BOND : angle 1.63945 ( 6) covalent geometry : bond 0.00362 (10806) covalent geometry : angle 0.67390 (14653) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 263 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8464 (mt0) cc_final: 0.7924 (mp10) REVERT: R 228 GLN cc_start: 0.9365 (mt0) cc_final: 0.9058 (tp40) REVERT: R 257 ARG cc_start: 0.8116 (mtp180) cc_final: 0.7710 (mmt180) REVERT: R 301 MET cc_start: 0.7537 (pmm) cc_final: 0.6693 (pmm) REVERT: R 339 TRP cc_start: 0.9237 (OUTLIER) cc_final: 0.9034 (m-90) REVERT: R 351 GLN cc_start: 0.7930 (tt0) cc_final: 0.7419 (tp-100) REVERT: R 433 HIS cc_start: 0.6252 (OUTLIER) cc_final: 0.5715 (p-80) REVERT: R 447 GLU cc_start: 0.8016 (tp30) cc_final: 0.7432 (tm-30) REVERT: R 485 ARG cc_start: 0.6383 (ttt180) cc_final: 0.5183 (tpp80) REVERT: R 491 GLN cc_start: 0.8545 (tp40) cc_final: 0.8126 (tp40) REVERT: R 523 PHE cc_start: 0.8737 (t80) cc_final: 0.8397 (t80) REVERT: A 79 GLN cc_start: 0.9090 (tp40) cc_final: 0.8708 (mt0) REVERT: A 132 LYS cc_start: 0.9362 (mttt) cc_final: 0.8851 (mttm) REVERT: A 175 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8514 (pp) REVERT: A 178 ARG cc_start: 0.7230 (mtt180) cc_final: 0.6959 (mtt180) REVERT: A 283 LEU cc_start: 0.8583 (tt) cc_final: 0.8371 (tp) REVERT: B 3 GLU cc_start: 0.8745 (tp30) cc_final: 0.8477 (tp30) REVERT: B 61 MET cc_start: 0.8032 (ppp) cc_final: 0.7604 (ppp) REVERT: B 82 TRP cc_start: 0.9001 (OUTLIER) cc_final: 0.8730 (m100) REVERT: B 127 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8642 (mttt) REVERT: B 175 GLN cc_start: 0.8891 (tp-100) cc_final: 0.8503 (tm-30) REVERT: B 289 TYR cc_start: 0.8927 (m-80) cc_final: 0.8377 (m-80) REVERT: B 292 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 295 ASN cc_start: 0.8324 (p0) cc_final: 0.8117 (p0) REVERT: B 325 MET cc_start: 0.7254 (mtm) cc_final: 0.6999 (ttm) REVERT: B 333 ASP cc_start: 0.8693 (p0) cc_final: 0.8362 (p0) REVERT: G 14 LYS cc_start: 0.9331 (mtpp) cc_final: 0.9080 (mtmm) REVERT: G 17 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8886 (mt-10) REVERT: L 59 VAL cc_start: 0.9267 (t) cc_final: 0.9010 (p) REVERT: H 32 PHE cc_start: 0.8615 (t80) cc_final: 0.8343 (t80) REVERT: H 68 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8430 (ptpp) REVERT: H 112 TYR cc_start: 0.8553 (m-10) cc_final: 0.8125 (m-10) REVERT: H 120 TYR cc_start: 0.8121 (m-10) cc_final: 0.7735 (m-80) outliers start: 74 outliers final: 53 residues processed: 307 average time/residue: 0.1989 time to fit residues: 89.6814 Evaluate side-chains 307 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 271 ASN Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain R residue 545 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 95 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.104695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.086156 restraints weight = 35870.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.088628 restraints weight = 20186.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.090314 restraints weight = 13510.741| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10809 Z= 0.156 Angle : 0.682 11.835 14659 Z= 0.347 Chirality : 0.043 0.206 1635 Planarity : 0.005 0.100 1857 Dihedral : 5.799 86.197 1536 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 6.17 % Allowed : 22.91 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % 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: -1.75 (0.22), residues: 1333 helix: 0.06 (0.23), residues: 455 sheet: -0.56 (0.32), residues: 262 loop : -2.43 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 PHE 0.021 0.002 PHE A 95 TYR 0.018 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 442) hydrogen bonds : angle 4.79644 ( 1272) SS BOND : bond 0.00262 ( 3) SS BOND : angle 1.01060 ( 6) covalent geometry : bond 0.00354 (10806) covalent geometry : angle 0.68150 (14653) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 258 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8434 (mt0) cc_final: 0.7847 (mp10) REVERT: R 228 GLN cc_start: 0.9391 (mt0) cc_final: 0.9056 (tp40) REVERT: R 257 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7734 (mmt180) REVERT: R 301 MET cc_start: 0.7527 (pmm) cc_final: 0.6715 (pmm) REVERT: R 351 GLN cc_start: 0.7910 (tt0) cc_final: 0.7397 (tp-100) REVERT: R 433 HIS cc_start: 0.6267 (OUTLIER) cc_final: 0.5722 (p-80) REVERT: R 447 GLU cc_start: 0.8055 (tp30) cc_final: 0.7508 (tm-30) REVERT: R 485 ARG cc_start: 0.6587 (ttt180) cc_final: 0.5384 (tpp80) REVERT: R 491 GLN cc_start: 0.8509 (tp40) cc_final: 0.8058 (tp40) REVERT: R 523 PHE cc_start: 0.8738 (t80) cc_final: 0.8397 (t80) REVERT: A 79 GLN cc_start: 0.9055 (tp40) cc_final: 0.8679 (mt0) REVERT: A 198 MET cc_start: 0.8326 (tpt) cc_final: 0.8086 (tpt) REVERT: A 268 LEU cc_start: 0.8913 (mt) cc_final: 0.8678 (mt) REVERT: B 3 GLU cc_start: 0.8698 (tp30) cc_final: 0.8474 (tp30) REVERT: B 61 MET cc_start: 0.8017 (ppp) cc_final: 0.7735 (ppp) REVERT: B 127 LYS cc_start: 0.9152 (mmmm) cc_final: 0.8677 (mttt) REVERT: B 136 SER cc_start: 0.8753 (m) cc_final: 0.8537 (t) REVERT: B 175 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8207 (tm-30) REVERT: B 235 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.5682 (t80) REVERT: B 289 TYR cc_start: 0.8907 (m-80) cc_final: 0.8385 (m-80) REVERT: B 292 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: B 295 ASN cc_start: 0.8348 (p0) cc_final: 0.8123 (p0) REVERT: B 325 MET cc_start: 0.7271 (mtm) cc_final: 0.7008 (ttm) REVERT: B 333 ASP cc_start: 0.8675 (p0) cc_final: 0.8333 (p0) REVERT: L 59 VAL cc_start: 0.9284 (t) cc_final: 0.9010 (p) REVERT: H 32 PHE cc_start: 0.8594 (t80) cc_final: 0.8335 (t80) REVERT: H 68 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8398 (ptpp) outliers start: 70 outliers final: 58 residues processed: 299 average time/residue: 0.2033 time to fit residues: 88.9470 Evaluate side-chains 303 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 241 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain R residue 545 TRP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 89 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 108 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.107527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.088680 restraints weight = 34848.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.091198 restraints weight = 19761.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092888 restraints weight = 13283.924| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10809 Z= 0.119 Angle : 0.689 12.520 14659 Z= 0.344 Chirality : 0.042 0.198 1635 Planarity : 0.004 0.096 1857 Dihedral : 5.663 89.652 1536 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.29 % Allowed : 24.41 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.61 (0.23), residues: 1333 helix: 0.05 (0.24), residues: 453 sheet: -0.28 (0.33), residues: 266 loop : -2.34 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP R 339 HIS 0.006 0.001 HIS R 227 PHE 0.021 0.001 PHE A 95 TYR 0.020 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 442) hydrogen bonds : angle 4.70677 ( 1272) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.65501 ( 6) covalent geometry : bond 0.00269 (10806) covalent geometry : angle 0.68942 (14653) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 268 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8113 (m) cc_final: 0.7866 (p) REVERT: R 218 GLN cc_start: 0.8406 (mt0) cc_final: 0.7832 (mp10) REVERT: R 228 GLN cc_start: 0.9375 (mt0) cc_final: 0.9048 (tp40) REVERT: R 257 ARG cc_start: 0.8116 (mtp180) cc_final: 0.7663 (mmt180) REVERT: R 301 MET cc_start: 0.7486 (pmm) cc_final: 0.6648 (pmm) REVERT: R 351 GLN cc_start: 0.7865 (tt0) cc_final: 0.7265 (tp-100) REVERT: R 433 HIS cc_start: 0.6330 (OUTLIER) cc_final: 0.5832 (p-80) REVERT: R 447 GLU cc_start: 0.8242 (tp30) cc_final: 0.7735 (tm-30) REVERT: R 485 ARG cc_start: 0.6599 (ttt180) cc_final: 0.5472 (tpp80) REVERT: R 491 GLN cc_start: 0.8574 (tp40) cc_final: 0.8096 (tp40) REVERT: R 523 PHE cc_start: 0.8646 (t80) cc_final: 0.8334 (t80) REVERT: A 9 ASP cc_start: 0.8509 (m-30) cc_final: 0.8267 (m-30) REVERT: A 18 MET cc_start: 0.7245 (mmm) cc_final: 0.6646 (tpp) REVERT: A 74 TYR cc_start: 0.8145 (m-10) cc_final: 0.7865 (m-80) REVERT: A 79 GLN cc_start: 0.9075 (tp40) cc_final: 0.8696 (mt0) REVERT: A 132 LYS cc_start: 0.9371 (mttt) cc_final: 0.8822 (mttm) REVERT: A 175 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8481 (pp) REVERT: A 283 LEU cc_start: 0.8584 (tt) cc_final: 0.8380 (tp) REVERT: B 3 GLU cc_start: 0.8634 (tp30) cc_final: 0.8423 (tp30) REVERT: B 45 MET cc_start: 0.8868 (tpp) cc_final: 0.8563 (mmt) REVERT: B 61 MET cc_start: 0.7938 (ppp) cc_final: 0.7718 (ppp) REVERT: B 110 ASN cc_start: 0.8534 (p0) cc_final: 0.8121 (p0) REVERT: B 169 TRP cc_start: 0.8470 (OUTLIER) cc_final: 0.8242 (m-10) REVERT: B 175 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8249 (tm-30) REVERT: B 289 TYR cc_start: 0.8868 (m-80) cc_final: 0.8232 (m-80) REVERT: B 292 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: B 333 ASP cc_start: 0.8579 (p0) cc_final: 0.8209 (p0) REVERT: L 59 VAL cc_start: 0.9247 (t) cc_final: 0.8978 (p) REVERT: H 32 PHE cc_start: 0.8601 (t80) cc_final: 0.8332 (t80) REVERT: H 120 TYR cc_start: 0.8029 (m-10) cc_final: 0.7777 (m-80) outliers start: 60 outliers final: 48 residues processed: 304 average time/residue: 0.2022 time to fit residues: 89.4533 Evaluate side-chains 305 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 253 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.104832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.086181 restraints weight = 35780.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.088670 restraints weight = 20285.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.090372 restraints weight = 13550.135| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10809 Z= 0.164 Angle : 0.706 12.088 14659 Z= 0.359 Chirality : 0.043 0.187 1635 Planarity : 0.005 0.095 1857 Dihedral : 5.813 88.896 1536 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 5.55 % Allowed : 24.41 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % 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: -1.67 (0.22), residues: 1333 helix: 0.10 (0.24), residues: 452 sheet: -0.43 (0.33), residues: 257 loop : -2.38 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.025 0.002 PHE R 484 TYR 0.018 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 442) hydrogen bonds : angle 4.85597 ( 1272) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.93608 ( 6) covalent geometry : bond 0.00373 (10806) covalent geometry : angle 0.70555 (14653) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 254 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8454 (mt0) cc_final: 0.7850 (mp10) REVERT: R 228 GLN cc_start: 0.9425 (mt0) cc_final: 0.9077 (tp40) REVERT: R 257 ARG cc_start: 0.8222 (mtp180) cc_final: 0.7718 (mmt180) REVERT: R 301 MET cc_start: 0.7525 (pmm) cc_final: 0.6760 (pmm) REVERT: R 339 TRP cc_start: 0.9233 (m-90) cc_final: 0.8757 (m-90) REVERT: R 418 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8435 (t80) REVERT: R 433 HIS cc_start: 0.6320 (OUTLIER) cc_final: 0.5759 (p-80) REVERT: R 447 GLU cc_start: 0.8286 (tp30) cc_final: 0.7760 (tm-30) REVERT: R 449 MET cc_start: 0.9159 (ttt) cc_final: 0.8740 (tpp) REVERT: R 485 ARG cc_start: 0.6591 (ttt180) cc_final: 0.5405 (tpp80) REVERT: R 491 GLN cc_start: 0.8596 (tp40) cc_final: 0.8096 (tp40) REVERT: A 74 TYR cc_start: 0.8102 (m-10) cc_final: 0.7856 (m-80) REVERT: A 79 GLN cc_start: 0.9112 (tp40) cc_final: 0.8754 (mt0) REVERT: B 82 TRP cc_start: 0.8988 (OUTLIER) cc_final: 0.8755 (m100) REVERT: B 110 ASN cc_start: 0.8634 (p0) cc_final: 0.8117 (p0) REVERT: B 136 SER cc_start: 0.8833 (m) cc_final: 0.8606 (t) REVERT: B 289 TYR cc_start: 0.8897 (m-80) cc_final: 0.8221 (m-80) REVERT: B 292 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: B 333 ASP cc_start: 0.8696 (p0) cc_final: 0.8352 (p0) REVERT: G 32 LYS cc_start: 0.9337 (ptpt) cc_final: 0.9092 (ptpt) REVERT: G 36 ASP cc_start: 0.8911 (t0) cc_final: 0.8546 (m-30) REVERT: L 59 VAL cc_start: 0.9283 (t) cc_final: 0.9000 (p) REVERT: L 90 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8507 (tm-30) REVERT: H 32 PHE cc_start: 0.8531 (t80) cc_final: 0.8322 (t80) REVERT: H 86 MET cc_start: 0.8249 (pmm) cc_final: 0.7783 (mpp) REVERT: H 120 TYR cc_start: 0.8125 (m-10) cc_final: 0.7844 (m-80) outliers start: 63 outliers final: 54 residues processed: 291 average time/residue: 0.1964 time to fit residues: 83.5869 Evaluate side-chains 308 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 418 PHE Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain R residue 545 TRP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.107330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.088567 restraints weight = 35235.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.091109 restraints weight = 19967.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092846 restraints weight = 13342.169| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10809 Z= 0.127 Angle : 0.733 15.008 14659 Z= 0.364 Chirality : 0.043 0.191 1635 Planarity : 0.004 0.094 1857 Dihedral : 5.772 86.803 1536 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.58 % Allowed : 26.52 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.55 (0.23), residues: 1333 helix: 0.05 (0.24), residues: 454 sheet: -0.20 (0.33), residues: 266 loop : -2.29 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 PHE 0.017 0.001 PHE A 108 TYR 0.025 0.001 TYR H 112 ARG 0.006 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 442) hydrogen bonds : angle 4.77831 ( 1272) SS BOND : bond 0.00122 ( 3) SS BOND : angle 0.61965 ( 6) covalent geometry : bond 0.00289 (10806) covalent geometry : angle 0.73323 (14653) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8420 (mt0) cc_final: 0.7829 (mp10) REVERT: R 228 GLN cc_start: 0.9408 (mt0) cc_final: 0.9071 (tp40) REVERT: R 257 ARG cc_start: 0.8177 (mtp180) cc_final: 0.7697 (mmt180) REVERT: R 301 MET cc_start: 0.7484 (pmm) cc_final: 0.6704 (pmm) REVERT: R 339 TRP cc_start: 0.9163 (m-90) cc_final: 0.8709 (m-90) REVERT: R 418 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8468 (t80) REVERT: R 433 HIS cc_start: 0.6372 (OUTLIER) cc_final: 0.5869 (p-80) REVERT: R 447 GLU cc_start: 0.8252 (tp30) cc_final: 0.7750 (tm-30) REVERT: R 449 MET cc_start: 0.9197 (ttt) cc_final: 0.8766 (tpp) REVERT: R 485 ARG cc_start: 0.6659 (ttt180) cc_final: 0.5495 (tpp80) REVERT: R 491 GLN cc_start: 0.8601 (tp40) cc_final: 0.8103 (tp40) REVERT: A 9 ASP cc_start: 0.8530 (m-30) cc_final: 0.8311 (m-30) REVERT: A 18 MET cc_start: 0.7283 (mmm) cc_final: 0.6703 (tpp) REVERT: A 74 TYR cc_start: 0.8157 (m-10) cc_final: 0.7923 (m-80) REVERT: A 79 GLN cc_start: 0.9125 (tp40) cc_final: 0.8748 (mt0) REVERT: A 132 LYS cc_start: 0.9341 (mttt) cc_final: 0.8743 (mttm) REVERT: A 175 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8542 (pp) REVERT: A 283 LEU cc_start: 0.8528 (tt) cc_final: 0.8287 (tp) REVERT: A 296 TYR cc_start: 0.7712 (p90) cc_final: 0.7491 (p90) REVERT: A 322 HIS cc_start: 0.7920 (t-90) cc_final: 0.7601 (t-90) REVERT: B 110 ASN cc_start: 0.8565 (p0) cc_final: 0.8222 (p0) REVERT: B 136 SER cc_start: 0.8650 (m) cc_final: 0.8448 (t) REVERT: B 289 TYR cc_start: 0.8908 (m-80) cc_final: 0.8224 (m-80) REVERT: B 292 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: B 325 MET cc_start: 0.7177 (ttp) cc_final: 0.6905 (ttm) REVERT: B 333 ASP cc_start: 0.8667 (p0) cc_final: 0.8290 (p0) REVERT: G 32 LYS cc_start: 0.9280 (ptpt) cc_final: 0.8946 (ptpt) REVERT: G 36 ASP cc_start: 0.8906 (t0) cc_final: 0.8532 (m-30) REVERT: L 59 VAL cc_start: 0.9244 (t) cc_final: 0.8968 (p) REVERT: H 120 TYR cc_start: 0.8085 (m-10) cc_final: 0.7833 (m-80) outliers start: 52 outliers final: 46 residues processed: 295 average time/residue: 0.2373 time to fit residues: 102.5673 Evaluate side-chains 312 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 418 PHE Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 112 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 120 optimal weight: 0.0870 chunk 92 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 244 HIS B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.108068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089357 restraints weight = 34746.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.091924 restraints weight = 19835.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093656 restraints weight = 13254.204| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10809 Z= 0.123 Angle : 0.721 14.547 14659 Z= 0.358 Chirality : 0.044 0.216 1635 Planarity : 0.004 0.099 1857 Dihedral : 5.585 86.085 1535 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.67 % Allowed : 26.61 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 (0.23), residues: 1333 helix: 0.09 (0.24), residues: 449 sheet: -0.20 (0.32), residues: 271 loop : -2.23 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.028 0.001 PHE R 484 TYR 0.017 0.001 TYR A 69 ARG 0.006 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 442) hydrogen bonds : angle 4.68783 ( 1272) SS BOND : bond 0.00129 ( 3) SS BOND : angle 0.56916 ( 6) covalent geometry : bond 0.00284 (10806) covalent geometry : angle 0.72112 (14653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4925.57 seconds wall clock time: 90 minutes 59.97 seconds (5459.97 seconds total)