Starting phenix.real_space_refine on Fri Feb 14 23:54:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ot0_20190/02_2025/6ot0_20190.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ot0_20190/02_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_20190/02_2025/6ot0_20190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ot0_20190/02_2025/6ot0_20190.map" model { file = "/net/cci-nas-00/data/ceres_data/6ot0_20190/02_2025/6ot0_20190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ot0_20190/02_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-5592/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: 6.45, per 1000 atoms: 0.61 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: 2.63 Conformation dependent library (CDL) restraints added in 1.5 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: 1.09 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: 3.01 Time building geometry restraints manager: 3.05 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: 1.650 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.810 Find NCS groups from input model: 0.160 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.870 ------------------------------------------------------------------------------- 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 10806 Z= 0.605 Angle : 1.130 14.010 14653 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 *********************** 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 : 1.252 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: 0.2481 time to fit residues: 147.6163 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 : 1.152 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090524 restraints weight = 19688.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092273 restraints weight = 13170.357| |-----------------------------------------------------------------------------| 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 10806 Z= 0.221 Angle : 0.675 11.345 14653 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 *********************** 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 : 1.179 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: 0.8040 (mtp180) cc_final: 0.7704 (mmt90) REVERT: R 301 MET cc_start: 0.7428 (pmm) cc_final: 0.6741 (pmm) REVERT: R 340 HIS cc_start: 0.7184 (p-80) cc_final: 0.6678 (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: 0.8405 (ttp80) REVERT: R 485 ARG cc_start: 0.6168 (ttt180) cc_final: 0.4772 (tpp80) REVERT: A 18 MET cc_start: 0.7644 (mmm) cc_final: 0.7212 (mmm) REVERT: A 79 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8738 (mt0) REVERT: A 106 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8433 (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: 0.8158 (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: 0.7488 (ppp) REVERT: B 82 TRP cc_start: 0.8891 (m100) cc_final: 0.8453 (m100) REVERT: B 127 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8694 (mttt) REVERT: B 175 GLN cc_start: 0.8851 (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: 0.8870 (m-80) cc_final: 0.8215 (m-80) REVERT: B 295 ASN cc_start: 0.8366 (p0) cc_final: 0.8034 (p0) REVERT: B 301 LYS cc_start: 0.7573 (mtmt) cc_final: 0.6681 (mmtt) REVERT: B 325 MET cc_start: 0.7147 (mtm) cc_final: 0.6858 (ttp) REVERT: B 333 ASP cc_start: 0.8373 (p0) cc_final: 0.8080 (p0) REVERT: G 17 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8889 (mt-10) REVERT: G 21 MET cc_start: 0.7876 (mmt) cc_final: 0.7650 (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: 0.8836 (mtp) cc_final: 0.8379 (mtp) REVERT: H 118 MET cc_start: 0.8265 (mpp) cc_final: 0.7897 (mpp) REVERT: H 120 TYR cc_start: 0.8032 (m-10) cc_final: 0.7816 (m-80) REVERT: H 128 THR cc_start: 0.8719 (p) cc_final: 0.8510 (t) outliers start: 40 outliers final: 27 residues processed: 325 average time/residue: 0.2096 time to fit residues: 97.3436 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 : 1.144 ------------------------------------------------------------------------------- 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: 6.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.105820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.086846 restraints weight = 36189.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.089404 restraints weight = 20289.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.091157 restraints weight = 13592.778| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10806 Z= 0.219 Angle : 0.664 12.660 14653 Z= 0.340 Chirality : 0.042 0.193 1635 Planarity : 0.005 0.103 1857 Dihedral : 5.762 51.659 1536 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.67 % Allowed : 18.15 % Favored : 77.18 % 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: -2.03 (0.22), residues: 1333 helix: -0.25 (0.23), residues: 450 sheet: -0.68 (0.31), residues: 271 loop : -2.55 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 PHE 0.021 0.002 PHE H 32 TYR 0.017 0.001 TYR A 69 ARG 0.005 0.000 ARG R 400 *********************** 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 325 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 1.217 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 198 VAL cc_start: 0.8217 (m) cc_final: 0.7909 (p) REVERT: R 218 GLN cc_start: 0.8405 (mt0) cc_final: 0.7914 (mp10) REVERT: R 228 GLN cc_start: 0.9271 (mt0) cc_final: 0.9001 (tp40) REVERT: R 257 ARG cc_start: 0.8117 (mtp180) cc_final: 0.7728 (mmt90) REVERT: R 271 ASN cc_start: 0.8487 (p0) cc_final: 0.8214 (p0) REVERT: R 301 MET cc_start: 0.7489 (pmm) cc_final: 0.6584 (pmm) REVERT: R 351 GLN cc_start: 0.8284 (tt0) cc_final: 0.7661 (tp-100) REVERT: R 400 ARG cc_start: 0.8830 (ttp80) cc_final: 0.8565 (ttp80) REVERT: R 449 MET cc_start: 0.9285 (ttt) cc_final: 0.8787 (tpp) REVERT: R 485 ARG cc_start: 0.6341 (ttt180) cc_final: 0.4977 (tpp80) REVERT: A 74 TYR cc_start: 0.8338 (m-10) cc_final: 0.8100 (m-80) REVERT: A 79 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8730 (mt0) REVERT: A 147 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8921 (tm-30) REVERT: A 164 GLN cc_start: 0.8882 (pt0) cc_final: 0.8618 (tm-30) REVERT: A 198 MET cc_start: 0.8249 (tpt) cc_final: 0.7856 (tpt) REVERT: B 3 GLU cc_start: 0.8913 (tp30) cc_final: 0.8608 (pt0) REVERT: B 46 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7608 (mtt-85) REVERT: B 59 TYR cc_start: 0.8225 (m-80) cc_final: 0.7969 (m-80) REVERT: B 61 MET cc_start: 0.7894 (ppp) cc_final: 0.7338 (ppp) REVERT: B 95 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8017 (pp) REVERT: B 209 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7701 (mttp) REVERT: B 289 TYR cc_start: 0.8852 (m-80) cc_final: 0.8232 (m-80) REVERT: B 292 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: B 295 ASN cc_start: 0.8360 (p0) cc_final: 0.8028 (p0) REVERT: B 301 LYS cc_start: 0.7631 (mtmt) cc_final: 0.6877 (mmtt) REVERT: B 325 MET cc_start: 0.7295 (mtm) cc_final: 0.7018 (ttp) REVERT: B 333 ASP cc_start: 0.8550 (p0) cc_final: 0.8231 (p0) REVERT: G 14 LYS cc_start: 0.9335 (mtpp) cc_final: 0.9034 (mtmm) REVERT: G 17 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8951 (mt-10) REVERT: G 21 MET cc_start: 0.7873 (mmt) cc_final: 0.7593 (mmm) REVERT: L 59 VAL cc_start: 0.9375 (t) cc_final: 0.9121 (p) REVERT: L 97 ILE cc_start: 0.9358 (mm) cc_final: 0.8964 (mp) REVERT: H 50 TRP cc_start: 0.7936 (t60) cc_final: 0.7594 (t60) REVERT: H 120 TYR cc_start: 0.8089 (m-10) cc_final: 0.7778 (m-80) outliers start: 53 outliers final: 38 residues processed: 301 average time/residue: 0.2123 time to fit residues: 91.3778 Evaluate side-chains 296 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 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 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 95 LEU 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 292 PHE Chi-restraints excluded: chain B residue 338 ILE 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 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: 2.9990 chunk 103 optimal weight: 0.1980 chunk 78 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 21 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.105673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.087046 restraints weight = 35449.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.089552 restraints weight = 19872.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091265 restraints weight = 13302.987| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10806 Z= 0.210 Angle : 0.646 13.666 14653 Z= 0.330 Chirality : 0.042 0.183 1635 Planarity : 0.005 0.102 1857 Dihedral : 5.603 58.043 1536 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.64 % Allowed : 19.47 % Favored : 74.89 % 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: -1.82 (0.22), residues: 1333 helix: -0.10 (0.23), residues: 452 sheet: -0.56 (0.32), residues: 271 loop : -2.42 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 PHE 0.022 0.001 PHE H 32 TYR 0.019 0.001 TYR A 69 ARG 0.005 0.000 ARG R 400 *********************** 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 334 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 1.527 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: 0.8331 (m) cc_final: 0.8029 (p) REVERT: R 218 GLN cc_start: 0.8421 (mt0) cc_final: 0.7868 (mp10) REVERT: R 228 GLN cc_start: 0.9280 (mt0) cc_final: 0.9034 (tp40) REVERT: R 257 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7718 (mmt90) REVERT: R 301 MET cc_start: 0.7522 (pmm) cc_final: 0.6573 (pmm) REVERT: R 351 GLN cc_start: 0.8097 (tt0) cc_final: 0.7562 (tp-100) REVERT: R 433 HIS cc_start: 0.6168 (OUTLIER) cc_final: 0.5738 (p-80) REVERT: R 485 ARG cc_start: 0.6373 (ttt180) cc_final: 0.5066 (tpp80) REVERT: R 523 PHE cc_start: 0.8735 (t80) cc_final: 0.8397 (t80) REVERT: A 18 MET cc_start: 0.7170 (mmm) cc_final: 0.6598 (tpp) REVERT: A 74 TYR cc_start: 0.8234 (m-10) cc_final: 0.7976 (m-80) REVERT: A 79 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8711 (mt0) REVERT: A 147 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8888 (tm-30) REVERT: A 283 LEU cc_start: 0.8510 (tt) cc_final: 0.8271 (tp) REVERT: B 46 ARG cc_start: 0.7818 (mtt-85) cc_final: 0.7554 (mtt-85) REVERT: B 61 MET cc_start: 0.7959 (ppp) cc_final: 0.7364 (ppp) REVERT: B 95 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8035 (pp) REVERT: B 127 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8767 (mtmt) REVERT: B 175 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8337 (tm-30) REVERT: B 289 TYR cc_start: 0.8831 (m-80) cc_final: 0.8189 (m-80) REVERT: B 292 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: B 295 ASN cc_start: 0.8328 (p0) cc_final: 0.7957 (p0) REVERT: B 325 MET cc_start: 0.7202 (mtm) cc_final: 0.6957 (ttp) REVERT: B 333 ASP cc_start: 0.8614 (p0) cc_final: 0.8277 (p0) REVERT: G 14 LYS cc_start: 0.9311 (mtpp) cc_final: 0.9008 (mtmm) REVERT: G 17 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8885 (mt-10) REVERT: G 21 MET cc_start: 0.7856 (mmt) cc_final: 0.7652 (mmm) REVERT: L 59 VAL cc_start: 0.9314 (t) cc_final: 0.9063 (p) REVERT: L 97 ILE cc_start: 0.9445 (mm) cc_final: 0.8969 (mm) REVERT: H 32 PHE cc_start: 0.8664 (t80) cc_final: 0.8408 (t80) REVERT: H 120 TYR cc_start: 0.8198 (m-10) cc_final: 0.7743 (m-10) outliers start: 64 outliers final: 49 residues processed: 309 average time/residue: 0.2109 time to fit residues: 94.3048 Evaluate side-chains 299 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 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 213 HIS 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 95 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN ** 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 = 0.3752 r_free = 0.3752 target = 0.105713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.087105 restraints weight = 35160.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089585 restraints weight = 19727.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091254 restraints weight = 13187.736| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10806 Z= 0.212 Angle : 0.664 11.552 14653 Z= 0.336 Chirality : 0.042 0.182 1635 Planarity : 0.005 0.100 1857 Dihedral : 5.628 66.793 1536 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.90 % Allowed : 21.23 % Favored : 72.86 % 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: -0.48 (0.31), residues: 276 loop : -2.41 (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 0.021 0.001 PHE H 71 TYR 0.019 0.001 TYR A 69 ARG 0.003 0.000 ARG L 25 *********************** 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 333 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8386 (m) cc_final: 0.8095 (p) REVERT: R 218 GLN cc_start: 0.8397 (mt0) cc_final: 0.7856 (mp10) REVERT: R 228 GLN cc_start: 0.9351 (mt0) cc_final: 0.9054 (tp40) REVERT: R 257 ARG cc_start: 0.8182 (mtp180) cc_final: 0.7748 (mmt90) REVERT: R 301 MET cc_start: 0.7547 (pmm) cc_final: 0.6642 (pmm) REVERT: R 351 GLN cc_start: 0.7943 (tt0) cc_final: 0.7405 (tp-100) REVERT: R 433 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.5657 (p-80) REVERT: R 447 GLU cc_start: 0.7996 (tp30) cc_final: 0.7415 (tm-30) REVERT: R 449 MET cc_start: 0.9201 (ttt) cc_final: 0.8624 (tpp) REVERT: R 485 ARG cc_start: 0.6302 (ttt180) cc_final: 0.5031 (tpp80) REVERT: A 74 TYR cc_start: 0.8209 (m-10) cc_final: 0.7970 (m-80) REVERT: A 79 GLN cc_start: 0.9025 (tp40) cc_final: 0.8676 (mt0) REVERT: A 132 LYS cc_start: 0.9354 (mttt) cc_final: 0.8859 (mttm) REVERT: A 198 MET cc_start: 0.8244 (tpt) cc_final: 0.7957 (tpt) REVERT: A 283 LEU cc_start: 0.8575 (tt) cc_final: 0.8341 (tp) REVERT: B 59 TYR cc_start: 0.8266 (m-80) cc_final: 0.7989 (m-80) REVERT: B 61 MET cc_start: 0.7950 (ppp) cc_final: 0.7288 (ppp) REVERT: B 82 TRP cc_start: 0.8945 (OUTLIER) cc_final: 0.8564 (m100) REVERT: B 127 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8727 (mttt) REVERT: B 209 LYS cc_start: 0.8029 (mmtp) cc_final: 0.7705 (mttt) REVERT: B 235 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.5956 (t80) REVERT: B 289 TYR cc_start: 0.8872 (m-80) cc_final: 0.8313 (m-80) REVERT: B 292 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: B 333 ASP cc_start: 0.8650 (p0) cc_final: 0.8312 (p0) REVERT: G 14 LYS cc_start: 0.9330 (mtpp) cc_final: 0.9056 (mtmm) REVERT: G 17 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8837 (mt-10) REVERT: G 29 LYS cc_start: 0.8484 (mmmm) cc_final: 0.8221 (mmmm) REVERT: G 32 LYS cc_start: 0.9417 (mmtm) cc_final: 0.9190 (mmtm) REVERT: G 36 ASP cc_start: 0.8789 (t0) cc_final: 0.8440 (m-30) REVERT: L 59 VAL cc_start: 0.9278 (t) cc_final: 0.9025 (p) REVERT: L 97 ILE cc_start: 0.9347 (mm) cc_final: 0.9120 (mp) REVERT: H 32 PHE cc_start: 0.8645 (t80) cc_final: 0.8357 (t80) REVERT: H 50 TRP cc_start: 0.7793 (t60) cc_final: 0.7407 (t60) REVERT: H 120 TYR cc_start: 0.8247 (m-10) cc_final: 0.7775 (m-10) outliers start: 67 outliers final: 52 residues processed: 305 average time/residue: 0.2035 time to fit residues: 90.3549 Evaluate side-chains 300 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 271 ASN 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 466 THR Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 545 TRP 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 266 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 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 TRP 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 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 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 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: 3.9990 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 361 HIS ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3728 r_free = 0.3728 target = 0.104150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.085542 restraints weight = 35564.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.087997 restraints weight = 20068.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089656 restraints weight = 13474.687| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10806 Z= 0.254 Angle : 0.681 10.908 14653 Z= 0.352 Chirality : 0.043 0.217 1635 Planarity : 0.005 0.102 1857 Dihedral : 5.806 77.402 1536 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 6.78 % Allowed : 21.41 % Favored : 71.81 % 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: -1.69 (0.22), residues: 1333 helix: 0.09 (0.23), residues: 454 sheet: -0.52 (0.32), residues: 271 loop : -2.40 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.016 0.002 PHE H 71 TYR 0.018 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 *********************** 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: 77 poor density : 260 time to evaluate : 1.152 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: 0.8322 (m) cc_final: 0.8039 (p) REVERT: R 218 GLN cc_start: 0.8474 (mt0) cc_final: 0.7932 (mp10) REVERT: R 228 GLN cc_start: 0.9373 (mt0) cc_final: 0.9053 (tp40) REVERT: R 257 ARG cc_start: 0.8101 (mtp180) cc_final: 0.7698 (mmt180) REVERT: R 301 MET cc_start: 0.7582 (pmm) cc_final: 0.6780 (pmm) REVERT: R 339 TRP cc_start: 0.9221 (OUTLIER) cc_final: 0.9015 (m-90) REVERT: R 351 GLN cc_start: 0.8005 (tt0) cc_final: 0.7488 (tp-100) REVERT: R 433 HIS cc_start: 0.6243 (OUTLIER) cc_final: 0.5762 (p-80) REVERT: R 447 GLU cc_start: 0.8014 (tp30) cc_final: 0.7426 (tm-30) REVERT: R 485 ARG cc_start: 0.6401 (ttt180) cc_final: 0.5189 (tpp80) REVERT: R 523 PHE cc_start: 0.8744 (t80) cc_final: 0.8382 (t80) REVERT: A 74 TYR cc_start: 0.8173 (m-10) cc_final: 0.7880 (m-80) REVERT: A 79 GLN cc_start: 0.9067 (tp40) cc_final: 0.8718 (mt0) REVERT: A 232 LEU cc_start: 0.8766 (mp) cc_final: 0.7968 (tp) REVERT: A 283 LEU cc_start: 0.8549 (tt) cc_final: 0.8304 (tp) REVERT: B 3 GLU cc_start: 0.8832 (tp30) cc_final: 0.8565 (tp30) REVERT: B 46 ARG cc_start: 0.7702 (mtt-85) cc_final: 0.7497 (mtt-85) REVERT: B 61 MET cc_start: 0.7930 (ppp) cc_final: 0.7535 (ppp) REVERT: B 82 TRP cc_start: 0.9017 (OUTLIER) cc_final: 0.8791 (m100) REVERT: B 175 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8520 (tm-30) REVERT: B 235 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5867 (t80) REVERT: B 289 TYR cc_start: 0.8901 (m-80) cc_final: 0.8384 (m-80) REVERT: B 292 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 295 ASN cc_start: 0.8384 (p0) cc_final: 0.8021 (p0) REVERT: B 325 MET cc_start: 0.7455 (ttp) cc_final: 0.7214 (ttm) REVERT: B 333 ASP cc_start: 0.8670 (p0) cc_final: 0.8324 (p0) REVERT: G 17 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8869 (mt-10) REVERT: G 29 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8276 (mmmm) REVERT: L 59 VAL cc_start: 0.9258 (t) cc_final: 0.9002 (p) REVERT: L 97 ILE cc_start: 0.9415 (mm) cc_final: 0.9038 (mm) REVERT: H 32 PHE cc_start: 0.8613 (t80) cc_final: 0.8344 (t80) REVERT: H 68 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8418 (ptpp) outliers start: 77 outliers final: 59 residues processed: 309 average time/residue: 0.2083 time to fit residues: 92.8646 Evaluate side-chains 310 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 245 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 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 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 266 LEU Chi-restraints excluded: chain A residue 268 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 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU 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 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 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 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 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 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: 8.9990 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.101071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.082770 restraints weight = 36372.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.085142 restraints weight = 20575.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086706 restraints weight = 13838.718| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10806 Z= 0.361 Angle : 0.743 10.539 14653 Z= 0.390 Chirality : 0.045 0.197 1635 Planarity : 0.005 0.104 1857 Dihedral : 6.366 88.002 1536 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.18 % Favored : 91.75 % Rotamer: Outliers : 7.22 % Allowed : 21.85 % 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: -1.99 (0.22), residues: 1333 helix: -0.08 (0.23), residues: 463 sheet: -0.69 (0.32), residues: 265 loop : -2.66 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP H 50 HIS 0.007 0.002 HIS R 227 PHE 0.014 0.002 PHE R 471 TYR 0.024 0.002 TYR R 337 ARG 0.004 0.001 ARG R 551 *********************** 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 329 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8504 (mt0) cc_final: 0.7908 (mp10) REVERT: R 228 GLN cc_start: 0.9417 (mt0) cc_final: 0.9086 (tp40) REVERT: R 257 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7762 (mmt180) REVERT: R 301 MET cc_start: 0.7496 (pmm) cc_final: 0.6642 (pmm) REVERT: R 339 TRP cc_start: 0.9211 (OUTLIER) cc_final: 0.8987 (m-90) REVERT: R 418 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8601 (t80) REVERT: R 433 HIS cc_start: 0.6573 (OUTLIER) cc_final: 0.5952 (p-80) REVERT: R 447 GLU cc_start: 0.8133 (tp30) cc_final: 0.7531 (tm-30) REVERT: R 485 ARG cc_start: 0.6418 (ttt180) cc_final: 0.5171 (tpp80) REVERT: R 491 GLN cc_start: 0.7741 (tp40) cc_final: 0.7311 (tp40) REVERT: B 3 GLU cc_start: 0.8770 (tp30) cc_final: 0.8539 (tp30) REVERT: B 46 ARG cc_start: 0.7738 (mtt-85) cc_final: 0.7382 (mtt-85) REVERT: B 61 MET cc_start: 0.7962 (ppp) cc_final: 0.7527 (ppp) REVERT: B 110 ASN cc_start: 0.8690 (p0) cc_final: 0.8156 (p0) REVERT: B 136 SER cc_start: 0.8806 (m) cc_final: 0.8575 (t) REVERT: B 235 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.6077 (t80) REVERT: B 289 TYR cc_start: 0.8997 (m-80) cc_final: 0.8508 (m-80) REVERT: B 292 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: B 295 ASN cc_start: 0.8469 (p0) cc_final: 0.8171 (p0) REVERT: B 325 MET cc_start: 0.7622 (ttp) cc_final: 0.7390 (ttm) REVERT: B 333 ASP cc_start: 0.8765 (p0) cc_final: 0.8524 (p0) REVERT: G 17 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8997 (mt-10) REVERT: G 29 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8487 (mmmm) REVERT: L 59 VAL cc_start: 0.9337 (t) cc_final: 0.9030 (p) REVERT: L 76 ILE cc_start: 0.9011 (mt) cc_final: 0.8697 (tt) REVERT: L 90 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8354 (tm-30) REVERT: L 97 ILE cc_start: 0.9419 (mm) cc_final: 0.9170 (mm) REVERT: H 68 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8374 (ptpp) REVERT: H 120 TYR cc_start: 0.8297 (m-10) cc_final: 0.7936 (m-10) outliers start: 82 outliers final: 58 residues processed: 294 average time/residue: 0.2013 time to fit residues: 86.0528 Evaluate side-chains 300 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 236 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 333 VAL 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 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 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 R residue 544 ILE 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 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 47 THR Chi-restraints excluded: chain B residue 67 SER 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 119 ASN 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 171 ILE 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 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 89 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 20 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 108 optimal weight: 0.2980 chunk 24 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 491 GLN ** 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** B 340 ASN ** L 90 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 = 0.3757 r_free = 0.3757 target = 0.106130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.087349 restraints weight = 34950.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.089850 restraints weight = 19729.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.091558 restraints weight = 13227.262| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10806 Z= 0.185 Angle : 0.701 13.883 14653 Z= 0.355 Chirality : 0.043 0.206 1635 Planarity : 0.005 0.099 1857 Dihedral : 5.883 87.141 1536 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.85 % Allowed : 25.02 % Favored : 70.13 % 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: -1.67 (0.22), residues: 1333 helix: 0.12 (0.23), residues: 453 sheet: -0.45 (0.33), residues: 266 loop : -2.41 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP H 50 HIS 0.007 0.001 HIS R 227 PHE 0.014 0.001 PHE H 71 TYR 0.019 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 *********************** 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 332 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 277 time to evaluate : 1.246 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 198 VAL cc_start: 0.8215 (m) cc_final: 0.7941 (p) REVERT: R 218 GLN cc_start: 0.8489 (mt0) cc_final: 0.7938 (mp10) REVERT: R 228 GLN cc_start: 0.9366 (mt0) cc_final: 0.9049 (tp40) REVERT: R 257 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7734 (mmt180) REVERT: R 301 MET cc_start: 0.7426 (pmm) cc_final: 0.6792 (pmm) REVERT: R 433 HIS cc_start: 0.6381 (OUTLIER) cc_final: 0.5823 (p-80) REVERT: R 447 GLU cc_start: 0.8055 (tp30) cc_final: 0.7501 (tm-30) REVERT: R 485 ARG cc_start: 0.6495 (ttt180) cc_final: 0.5273 (tpp80) REVERT: R 491 GLN cc_start: 0.7744 (tp40) cc_final: 0.7405 (tp40) REVERT: A 9 ASP cc_start: 0.8401 (m-30) cc_final: 0.8117 (m-30) REVERT: A 18 MET cc_start: 0.7253 (mmm) cc_final: 0.6685 (tpp) REVERT: A 33 GLU cc_start: 0.7587 (tp30) cc_final: 0.7291 (tp30) REVERT: A 74 TYR cc_start: 0.8204 (m-10) cc_final: 0.7887 (m-80) REVERT: A 178 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6999 (mtt180) REVERT: A 232 LEU cc_start: 0.8800 (mp) cc_final: 0.8140 (tt) REVERT: A 283 LEU cc_start: 0.8335 (tt) cc_final: 0.8060 (tp) REVERT: B 45 MET cc_start: 0.8911 (tpp) cc_final: 0.8320 (mmt) REVERT: B 61 MET cc_start: 0.8095 (ppp) cc_final: 0.7811 (ppp) REVERT: B 79 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8783 (mm) REVERT: B 110 ASN cc_start: 0.8462 (p0) cc_final: 0.8054 (p0) REVERT: B 289 TYR cc_start: 0.8907 (m-80) cc_final: 0.8296 (m-80) REVERT: B 292 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: B 301 LYS cc_start: 0.7485 (mtmt) cc_final: 0.6814 (mmtt) REVERT: B 325 MET cc_start: 0.7208 (ttp) cc_final: 0.6965 (ttm) REVERT: B 333 ASP cc_start: 0.8589 (p0) cc_final: 0.8261 (p0) REVERT: G 14 LYS cc_start: 0.9331 (mtpp) cc_final: 0.9055 (mtmm) REVERT: G 17 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8870 (mt-10) REVERT: G 21 MET cc_start: 0.7820 (mmt) cc_final: 0.7584 (mmt) REVERT: L 12 LEU cc_start: 0.7344 (pp) cc_final: 0.6977 (pp) REVERT: L 59 VAL cc_start: 0.9274 (t) cc_final: 0.8994 (p) REVERT: H 120 TYR cc_start: 0.8234 (m-10) cc_final: 0.7861 (m-10) outliers start: 55 outliers final: 43 residues processed: 312 average time/residue: 0.2011 time to fit residues: 90.8213 Evaluate side-chains 295 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 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 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 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 268 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 30 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 121 CYS 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 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 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 23 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 491 GLN ** 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 = 0.3760 r_free = 0.3760 target = 0.106307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.087525 restraints weight = 35631.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.090054 restraints weight = 20026.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091782 restraints weight = 13402.138| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10806 Z= 0.195 Angle : 0.719 13.487 14653 Z= 0.363 Chirality : 0.044 0.195 1635 Planarity : 0.005 0.096 1857 Dihedral : 5.850 86.587 1536 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.93 % Allowed : 26.26 % Favored : 68.81 % 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: -1.62 (0.23), residues: 1333 helix: 0.16 (0.24), residues: 451 sheet: -0.37 (0.33), residues: 266 loop : -2.41 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 PHE 0.028 0.001 PHE A 95 TYR 0.018 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 *********************** 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 319 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8210 (m) cc_final: 0.7947 (p) REVERT: R 218 GLN cc_start: 0.8494 (mt0) cc_final: 0.7939 (mp10) REVERT: R 228 GLN cc_start: 0.9382 (mt0) cc_final: 0.9054 (tp40) REVERT: R 257 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7657 (mmt180) REVERT: R 301 MET cc_start: 0.7451 (pmm) cc_final: 0.6615 (pmm) REVERT: R 339 TRP cc_start: 0.9201 (m-90) cc_final: 0.8731 (m-90) REVERT: R 418 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8566 (t80) REVERT: R 433 HIS cc_start: 0.6325 (OUTLIER) cc_final: 0.5760 (p-80) REVERT: R 447 GLU cc_start: 0.8112 (tp30) cc_final: 0.7573 (tm-30) REVERT: R 485 ARG cc_start: 0.6620 (ttt180) cc_final: 0.5470 (tpp80) REVERT: R 491 GLN cc_start: 0.7733 (tp40) cc_final: 0.7444 (tp40) REVERT: A 9 ASP cc_start: 0.8463 (m-30) cc_final: 0.8183 (m-30) REVERT: A 33 GLU cc_start: 0.7572 (tp30) cc_final: 0.7243 (tp30) REVERT: A 232 LEU cc_start: 0.8879 (mp) cc_final: 0.8282 (tp) REVERT: A 283 LEU cc_start: 0.8406 (tt) cc_final: 0.8165 (tp) REVERT: A 296 TYR cc_start: 0.7763 (p90) cc_final: 0.7550 (p90) REVERT: B 10 GLU cc_start: 0.7802 (tt0) cc_final: 0.7332 (mm-30) REVERT: B 61 MET cc_start: 0.8108 (ppp) cc_final: 0.7849 (ppp) REVERT: B 79 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8788 (mm) REVERT: B 110 ASN cc_start: 0.8553 (p0) cc_final: 0.8177 (p0) REVERT: B 136 SER cc_start: 0.8674 (m) cc_final: 0.8466 (t) REVERT: B 289 TYR cc_start: 0.8895 (m-80) cc_final: 0.8274 (m-80) REVERT: B 292 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: B 325 MET cc_start: 0.7186 (ttp) cc_final: 0.6910 (ttm) REVERT: B 333 ASP cc_start: 0.8650 (p0) cc_final: 0.8304 (p0) REVERT: G 14 LYS cc_start: 0.9331 (mtpp) cc_final: 0.9066 (mtmm) REVERT: G 17 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8839 (mt-10) REVERT: G 21 MET cc_start: 0.7857 (mmt) cc_final: 0.7629 (mmt) REVERT: G 36 ASP cc_start: 0.8834 (t0) cc_final: 0.8485 (m-30) REVERT: L 12 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7062 (pp) REVERT: L 59 VAL cc_start: 0.9259 (t) cc_final: 0.8979 (p) REVERT: H 120 TYR cc_start: 0.8246 (m-10) cc_final: 0.7882 (m-10) outliers start: 56 outliers final: 46 residues processed: 296 average time/residue: 0.2091 time to fit residues: 91.1236 Evaluate side-chains 306 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 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 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 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 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 30 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 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 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 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 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 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: 10.0000 chunk 92 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 491 GLN ** 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 = 0.3764 r_free = 0.3764 target = 0.106451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087734 restraints weight = 35504.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.090271 restraints weight = 19972.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092005 restraints weight = 13377.659| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10806 Z= 0.199 Angle : 0.709 13.569 14653 Z= 0.359 Chirality : 0.043 0.189 1635 Planarity : 0.005 0.094 1857 Dihedral : 5.783 86.004 1535 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.32 % Allowed : 27.14 % Favored : 68.55 % 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: -1.58 (0.23), residues: 1333 helix: 0.13 (0.24), residues: 451 sheet: -0.44 (0.32), residues: 271 loop : -2.29 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 PHE 0.028 0.001 PHE R 484 TYR 0.035 0.001 TYR H 34 ARG 0.004 0.000 ARG L 25 ********************** 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 312 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8197 (m) cc_final: 0.7939 (p) REVERT: R 218 GLN cc_start: 0.8492 (mt0) cc_final: 0.7934 (mp10) REVERT: R 228 GLN cc_start: 0.9391 (mt0) cc_final: 0.9069 (tp40) REVERT: R 257 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7723 (mmt180) REVERT: R 301 MET cc_start: 0.7452 (pmm) cc_final: 0.6626 (pmm) REVERT: R 339 TRP cc_start: 0.9191 (m-90) cc_final: 0.8746 (m-90) REVERT: R 433 HIS cc_start: 0.6389 (OUTLIER) cc_final: 0.5916 (p-80) REVERT: R 447 GLU cc_start: 0.8304 (tp30) cc_final: 0.7808 (tm-30) REVERT: R 449 MET cc_start: 0.8936 (ttt) cc_final: 0.8577 (mmt) REVERT: R 485 ARG cc_start: 0.6717 (ttt180) cc_final: 0.5749 (tpp80) REVERT: R 491 GLN cc_start: 0.7803 (tp40) cc_final: 0.7478 (tp40) REVERT: A 9 ASP cc_start: 0.8515 (m-30) cc_final: 0.8270 (m-30) REVERT: A 18 MET cc_start: 0.7298 (mmm) cc_final: 0.6759 (tpp) REVERT: A 33 GLU cc_start: 0.7471 (tp30) cc_final: 0.7156 (tp30) REVERT: A 74 TYR cc_start: 0.8190 (m-10) cc_final: 0.7928 (m-80) REVERT: A 232 LEU cc_start: 0.8698 (mp) cc_final: 0.8263 (tp) REVERT: A 283 LEU cc_start: 0.8411 (tt) cc_final: 0.8190 (tp) REVERT: B 10 GLU cc_start: 0.7818 (tt0) cc_final: 0.7364 (mm-30) REVERT: B 61 MET cc_start: 0.8122 (ppp) cc_final: 0.7859 (ppp) REVERT: B 79 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8811 (mm) REVERT: B 127 LYS cc_start: 0.9093 (mmmm) cc_final: 0.8569 (mttt) REVERT: B 136 SER cc_start: 0.8683 (m) cc_final: 0.8461 (t) REVERT: B 289 TYR cc_start: 0.8907 (m-80) cc_final: 0.8293 (m-80) REVERT: B 292 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: B 325 MET cc_start: 0.7211 (ttp) cc_final: 0.6950 (ttm) REVERT: B 333 ASP cc_start: 0.8637 (p0) cc_final: 0.8274 (p0) REVERT: G 14 LYS cc_start: 0.9331 (mtpp) cc_final: 0.9062 (mtmm) REVERT: G 17 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8837 (mt-10) REVERT: G 21 MET cc_start: 0.7913 (mmt) cc_final: 0.7685 (mmt) REVERT: G 36 ASP cc_start: 0.8862 (t0) cc_final: 0.8530 (m-30) REVERT: L 59 VAL cc_start: 0.9252 (t) cc_final: 0.8974 (p) REVERT: H 120 TYR cc_start: 0.8254 (m-10) cc_final: 0.7917 (m-10) outliers start: 49 outliers final: 43 residues processed: 289 average time/residue: 0.1998 time to fit residues: 84.2130 Evaluate side-chains 300 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 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 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 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 30 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 133 VAL 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 76 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 491 GLN ** 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 = 0.3777 r_free = 0.3777 target = 0.107359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088734 restraints weight = 34686.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.091275 restraints weight = 19620.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092973 restraints weight = 13130.847| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10806 Z= 0.190 Angle : 0.717 13.441 14653 Z= 0.362 Chirality : 0.044 0.211 1635 Planarity : 0.005 0.100 1857 Dihedral : 5.686 85.341 1535 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.23 % Allowed : 27.22 % Favored : 68.55 % 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: -1.56 (0.23), residues: 1333 helix: 0.12 (0.24), residues: 451 sheet: -0.25 (0.33), residues: 265 loop : -2.32 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.022 0.001 PHE A 95 TYR 0.029 0.001 TYR H 34 ARG 0.004 0.000 ARG L 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3808.81 seconds wall clock time: 69 minutes 8.92 seconds (4148.92 seconds total)