Starting phenix.real_space_refine on Wed Mar 4 04:21:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ot0_20190/03_2026/6ot0_20190.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ot0_20190/03_2026/6ot0_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ot0_20190/03_2026/6ot0_20190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ot0_20190/03_2026/6ot0_20190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ot0_20190/03_2026/6ot0_20190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ot0_20190/03_2026/6ot0_20190.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.52, per 1000 atoms: 0.24 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: 0.80 Conformation dependent library (CDL) restraints added in 452.5 milliseconds 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: 0.33 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: 1.57 Time building geometry restraints manager: 1.10 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: 1.690 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.610 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.312 10809 Z= 0.622 Angle : 1.131 14.010 14659 Z= 0.726 Chirality : 0.070 0.427 1635 Planarity : 0.006 0.132 1857 Dihedral : 14.443 77.489 3917 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.79 % Allowed : 7.67 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.009 0.001 ARG A 142 TYR 0.015 0.002 TYR A 302 PHE 0.016 0.002 PHE B 151 TRP 0.015 0.002 TRP R 206 HIS 0.007 0.002 HIS R 433 Details of bonding type rmsd covalent geometry : bond 0.00896 (10806) covalent geometry : angle 1.13045 (14653) SS BOND : bond 0.00441 ( 3) SS BOND : angle 1.36951 ( 6) hydrogen bonds : bond 0.15548 ( 442) hydrogen bonds : angle 6.93709 ( 1272) *********************** 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 : 0.435 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: 0.8524 (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: 0.1126 time to fit residues: 67.4794 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 : 0.379 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 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 = 0.3763 r_free = 0.3763 target = 0.106485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.086819 restraints weight = 35160.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.089422 restraints weight = 19826.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091205 restraints weight = 13336.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092423 restraints weight = 10031.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.093247 restraints weight = 8171.727| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10809 Z= 0.168 Angle : 0.684 11.070 14659 Z= 0.357 Chirality : 0.043 0.174 1635 Planarity : 0.005 0.102 1857 Dihedral : 6.030 50.074 1537 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.57 % Rotamer: Outliers : 3.79 % Allowed : 16.21 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.21), residues: 1333 helix: -0.69 (0.22), residues: 455 sheet: -0.91 (0.31), residues: 269 loop : -2.69 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 261 TYR 0.019 0.002 TYR H 120 PHE 0.023 0.002 PHE B 235 TRP 0.022 0.002 TRP R 339 HIS 0.007 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00371 (10806) covalent geometry : angle 0.68300 (14653) SS BOND : bond 0.00572 ( 3) SS BOND : angle 1.71667 ( 6) hydrogen bonds : bond 0.04385 ( 442) hydrogen bonds : angle 5.12809 ( 1272) *********************** 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 346 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 303 time to evaluate : 0.436 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: 0.8424 (mt0) cc_final: 0.7980 (mp10) REVERT: R 228 GLN cc_start: 0.9224 (mt0) cc_final: 0.8916 (tp40) REVERT: R 257 ARG cc_start: 0.7979 (mtp180) cc_final: 0.7665 (mmt90) REVERT: R 301 MET cc_start: 0.7420 (pmm) cc_final: 0.6740 (pmm) REVERT: R 340 HIS cc_start: 0.7191 (p-80) cc_final: 0.6682 (p-80) REVERT: R 351 GLN cc_start: 0.8424 (tt0) cc_final: 0.7709 (tp-100) REVERT: R 391 PHE cc_start: 0.5695 (OUTLIER) cc_final: 0.5485 (t80) REVERT: R 400 ARG cc_start: 0.8838 (ttp80) cc_final: 0.8459 (ttp80) REVERT: R 485 ARG cc_start: 0.6166 (ttt180) cc_final: 0.4792 (tpp80) REVERT: A 18 MET cc_start: 0.7682 (mmm) cc_final: 0.7236 (mmm) REVERT: A 79 GLN cc_start: 0.9094 (tp-100) cc_final: 0.8757 (mt0) REVERT: A 106 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8433 (tp40) REVERT: A 147 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8913 (tm-30) REVERT: A 175 LEU cc_start: 0.8646 (mm) cc_final: 0.8358 (pp) REVERT: A 243 MET cc_start: 0.8416 (ptt) cc_final: 0.7946 (ptt) REVERT: A 266 LEU cc_start: 0.9282 (tt) cc_final: 0.9062 (tt) REVERT: B 61 MET cc_start: 0.7853 (ppp) cc_final: 0.7482 (ppp) REVERT: B 82 TRP cc_start: 0.8900 (m100) cc_final: 0.8474 (m100) REVERT: B 127 LYS cc_start: 0.9105 (mmmm) cc_final: 0.8545 (mttt) REVERT: B 175 GLN cc_start: 0.8840 (tp40) cc_final: 0.8259 (tm-30) REVERT: B 289 TYR cc_start: 0.8862 (m-80) cc_final: 0.8240 (m-80) REVERT: B 295 ASN cc_start: 0.8348 (p0) cc_final: 0.8071 (p0) REVERT: B 301 LYS cc_start: 0.7555 (mtmt) cc_final: 0.6667 (mmtt) REVERT: B 325 MET cc_start: 0.7162 (mtm) cc_final: 0.6911 (ttp) REVERT: B 333 ASP cc_start: 0.8396 (p0) cc_final: 0.8101 (p0) REVERT: G 17 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8866 (mt-10) REVERT: G 21 MET cc_start: 0.7921 (mmt) cc_final: 0.7679 (mmt) REVERT: L 47 LEU cc_start: 0.9228 (pt) cc_final: 0.9024 (pp) REVERT: L 59 VAL cc_start: 0.9418 (t) cc_final: 0.9167 (p) REVERT: L 97 ILE cc_start: 0.9397 (mm) cc_final: 0.8962 (mm) REVERT: H 108 MET cc_start: 0.8802 (mtp) cc_final: 0.8337 (mtp) REVERT: H 118 MET cc_start: 0.8302 (mpp) cc_final: 0.7909 (mpp) REVERT: H 120 TYR cc_start: 0.8048 (m-10) cc_final: 0.7838 (m-80) REVERT: H 128 THR cc_start: 0.8700 (p) cc_final: 0.8484 (t) outliers start: 43 outliers final: 30 residues processed: 321 average time/residue: 0.0901 time to fit residues: 42.1272 Evaluate side-chains 299 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 391 PHE 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 R residue 528 THR 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 187 VAL 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 126 LEU 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 25 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 19 optimal weight: 0.0070 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 108 optimal weight: 0.0060 chunk 77 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.5414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 239 ASN ** B 259 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.108877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.090169 restraints weight = 35044.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.092780 restraints weight = 19536.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094573 restraints weight = 12986.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095796 restraints weight = 9687.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.096634 restraints weight = 7841.499| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10809 Z= 0.115 Angle : 0.651 12.753 14659 Z= 0.327 Chirality : 0.042 0.203 1635 Planarity : 0.004 0.099 1857 Dihedral : 5.541 51.259 1536 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.79 % Allowed : 19.21 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.22), residues: 1333 helix: -0.26 (0.23), residues: 450 sheet: -0.56 (0.32), residues: 266 loop : -2.51 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 290 TYR 0.019 0.001 TYR A 69 PHE 0.021 0.001 PHE A 108 TRP 0.029 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 Details of bonding type rmsd covalent geometry : bond 0.00253 (10806) covalent geometry : angle 0.64917 (14653) SS BOND : bond 0.00203 ( 3) SS BOND : angle 2.18040 ( 6) hydrogen bonds : bond 0.03816 ( 442) hydrogen bonds : angle 4.78380 ( 1272) *********************** 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 337 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 294 time to evaluate : 0.394 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: 0.8059 (m) cc_final: 0.7759 (p) REVERT: R 218 GLN cc_start: 0.8414 (mt0) cc_final: 0.7946 (mp10) REVERT: R 228 GLN cc_start: 0.9206 (mt0) cc_final: 0.8989 (tp40) REVERT: R 257 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7683 (mmt90) REVERT: R 271 ASN cc_start: 0.8408 (p0) cc_final: 0.8125 (p0) REVERT: R 301 MET cc_start: 0.7302 (pmm) cc_final: 0.6328 (pmm) REVERT: R 351 GLN cc_start: 0.8275 (tt0) cc_final: 0.7660 (tp-100) REVERT: R 447 GLU cc_start: 0.7514 (tp30) cc_final: 0.6929 (tm-30) REVERT: R 449 MET cc_start: 0.9240 (ttt) cc_final: 0.8740 (tpp) REVERT: R 485 ARG cc_start: 0.6307 (ttt180) cc_final: 0.4905 (tpp80) REVERT: A 18 MET cc_start: 0.7531 (mmm) cc_final: 0.6876 (tpp) REVERT: A 74 TYR cc_start: 0.8201 (m-10) cc_final: 0.7922 (m-80) REVERT: A 79 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8693 (mt0) REVERT: A 132 LYS cc_start: 0.9331 (mttt) cc_final: 0.8924 (mttt) REVERT: A 147 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8948 (tm-30) REVERT: A 175 LEU cc_start: 0.8663 (mm) cc_final: 0.8410 (pp) REVERT: A 198 MET cc_start: 0.8285 (tpt) cc_final: 0.7920 (tpt) REVERT: B 3 GLU cc_start: 0.8710 (tp30) cc_final: 0.8466 (pt0) REVERT: B 5 ASP cc_start: 0.8418 (m-30) cc_final: 0.8147 (m-30) REVERT: B 57 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8603 (mtpt) REVERT: B 59 TYR cc_start: 0.7996 (m-80) cc_final: 0.7699 (m-80) REVERT: B 61 MET cc_start: 0.7785 (ppp) cc_final: 0.7018 (ppp) REVERT: B 82 TRP cc_start: 0.8763 (m100) cc_final: 0.8517 (m100) REVERT: B 127 LYS cc_start: 0.9094 (mmmm) cc_final: 0.8663 (mttt) REVERT: B 175 GLN cc_start: 0.8800 (tp40) cc_final: 0.8402 (tm-30) REVERT: B 235 PHE cc_start: 0.6968 (t80) cc_final: 0.6716 (t80) REVERT: B 289 TYR cc_start: 0.8752 (m-80) cc_final: 0.8048 (m-80) REVERT: B 301 LYS cc_start: 0.7486 (mtmt) cc_final: 0.6724 (mmtt) REVERT: B 325 MET cc_start: 0.7014 (mtm) cc_final: 0.6779 (ttp) REVERT: B 333 ASP cc_start: 0.8442 (p0) cc_final: 0.8084 (p0) REVERT: G 17 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8788 (mt-10) REVERT: G 32 LYS cc_start: 0.9366 (mmtm) cc_final: 0.9139 (mmtm) REVERT: G 36 ASP cc_start: 0.8698 (t0) cc_final: 0.8307 (m-30) REVERT: L 59 VAL cc_start: 0.9342 (t) cc_final: 0.9118 (p) REVERT: H 32 PHE cc_start: 0.8652 (t80) cc_final: 0.8383 (t80) REVERT: H 120 TYR cc_start: 0.8042 (m-10) cc_final: 0.7764 (m-80) outliers start: 43 outliers final: 29 residues processed: 318 average time/residue: 0.0870 time to fit residues: 40.6436 Evaluate side-chains 296 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 392 VAL Chi-restraints excluded: chain R residue 473 ASP 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 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 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 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 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 60 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 97 optimal weight: 0.0010 chunk 8 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** B 142 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.103954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.085261 restraints weight = 36290.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087735 restraints weight = 20466.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089425 restraints weight = 13722.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090567 restraints weight = 10309.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091362 restraints weight = 8409.394| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10809 Z= 0.196 Angle : 0.696 13.618 14659 Z= 0.359 Chirality : 0.044 0.190 1635 Planarity : 0.005 0.103 1857 Dihedral : 5.846 57.951 1536 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Rotamer: Outliers : 5.73 % Allowed : 20.70 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.22), residues: 1333 helix: -0.05 (0.23), residues: 451 sheet: -0.49 (0.32), residues: 266 loop : -2.47 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 100 TYR 0.018 0.002 TYR A 69 PHE 0.014 0.002 PHE H 32 TRP 0.035 0.002 TRP R 339 HIS 0.006 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00432 (10806) covalent geometry : angle 0.69481 (14653) SS BOND : bond 0.00480 ( 3) SS BOND : angle 2.03165 ( 6) hydrogen bonds : bond 0.03990 ( 442) hydrogen bonds : angle 4.99889 ( 1272) *********************** 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 325 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8254 (m) cc_final: 0.7936 (p) REVERT: R 218 GLN cc_start: 0.8406 (mt0) cc_final: 0.7882 (mp10) REVERT: R 228 GLN cc_start: 0.9340 (mt0) cc_final: 0.9039 (tp40) REVERT: R 257 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7738 (mmt90) REVERT: R 301 MET cc_start: 0.7536 (pmm) cc_final: 0.6641 (pmm) REVERT: R 351 GLN cc_start: 0.8032 (tt0) cc_final: 0.7523 (tp-100) REVERT: R 433 HIS cc_start: 0.6244 (OUTLIER) cc_final: 0.5760 (p-80) REVERT: R 485 ARG cc_start: 0.6419 (ttt180) cc_final: 0.5149 (tpp80) REVERT: R 523 PHE cc_start: 0.8728 (t80) cc_final: 0.8444 (t80) REVERT: A 33 GLU cc_start: 0.7873 (tp30) cc_final: 0.7611 (tp30) REVERT: A 79 GLN cc_start: 0.9032 (tp40) cc_final: 0.8697 (mt0) REVERT: A 147 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8867 (tm-30) REVERT: A 283 LEU cc_start: 0.8447 (tt) cc_final: 0.8167 (tp) REVERT: B 61 MET cc_start: 0.7946 (ppp) cc_final: 0.7414 (ppp) REVERT: B 136 SER cc_start: 0.8850 (m) cc_final: 0.8622 (t) REVERT: B 175 GLN cc_start: 0.8801 (tp40) cc_final: 0.8339 (tm-30) REVERT: B 289 TYR cc_start: 0.8914 (m-80) cc_final: 0.8460 (m-80) REVERT: B 295 ASN cc_start: 0.8422 (p0) cc_final: 0.8017 (p0) REVERT: B 325 MET cc_start: 0.7507 (mtm) cc_final: 0.7286 (ttp) REVERT: B 333 ASP cc_start: 0.8599 (p0) cc_final: 0.8248 (p0) REVERT: G 17 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8992 (mt-10) REVERT: G 32 LYS cc_start: 0.9523 (mmtm) cc_final: 0.9220 (mmtm) REVERT: G 36 ASP cc_start: 0.8778 (t0) cc_final: 0.8494 (m-30) REVERT: L 59 VAL cc_start: 0.9387 (t) cc_final: 0.9114 (p) outliers start: 65 outliers final: 51 residues processed: 298 average time/residue: 0.0855 time to fit residues: 38.0741 Evaluate side-chains 291 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 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 40 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 96 optimal weight: 0.0050 chunk 22 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.107299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.088412 restraints weight = 35103.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.090903 restraints weight = 19917.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092623 restraints weight = 13389.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093787 restraints weight = 10073.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.094618 restraints weight = 8220.358| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10809 Z= 0.117 Angle : 0.667 11.611 14659 Z= 0.335 Chirality : 0.042 0.185 1635 Planarity : 0.004 0.098 1857 Dihedral : 5.579 62.823 1536 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.76 % Allowed : 23.08 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.22), residues: 1333 helix: 0.10 (0.23), residues: 453 sheet: -0.35 (0.33), residues: 261 loop : -2.33 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 25 TYR 0.019 0.001 TYR A 69 PHE 0.025 0.001 PHE H 32 TRP 0.039 0.002 TRP H 50 HIS 0.008 0.001 HIS R 227 Details of bonding type rmsd covalent geometry : bond 0.00263 (10806) covalent geometry : angle 0.66680 (14653) SS BOND : bond 0.00219 ( 3) SS BOND : angle 1.46297 ( 6) hydrogen bonds : bond 0.03620 ( 442) hydrogen bonds : angle 4.76306 ( 1272) *********************** 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 329 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 275 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8369 (m) cc_final: 0.8118 (p) REVERT: R 218 GLN cc_start: 0.8369 (mt0) cc_final: 0.7857 (mp10) REVERT: R 228 GLN cc_start: 0.9324 (mt0) cc_final: 0.9029 (tp40) REVERT: R 252 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8030 (t80) REVERT: R 257 ARG cc_start: 0.8200 (mtp180) cc_final: 0.7806 (mmt90) REVERT: R 301 MET cc_start: 0.7402 (pmm) cc_final: 0.6469 (pmm) REVERT: R 339 TRP cc_start: 0.9140 (OUTLIER) cc_final: 0.8915 (m-90) REVERT: R 351 GLN cc_start: 0.7976 (tt0) cc_final: 0.7427 (tp-100) REVERT: R 433 HIS cc_start: 0.6144 (OUTLIER) cc_final: 0.5632 (p-80) REVERT: R 447 GLU cc_start: 0.7918 (tp30) cc_final: 0.7352 (tm-30) REVERT: R 449 MET cc_start: 0.9178 (ttt) cc_final: 0.8348 (tpp) REVERT: R 485 ARG cc_start: 0.6365 (ttt180) cc_final: 0.5083 (tpp80) REVERT: R 523 PHE cc_start: 0.8693 (t80) cc_final: 0.8409 (t80) REVERT: A 18 MET cc_start: 0.7301 (mmm) cc_final: 0.6703 (tpp) REVERT: A 74 TYR cc_start: 0.8180 (m-10) cc_final: 0.7897 (m-80) REVERT: A 79 GLN cc_start: 0.9097 (tp40) cc_final: 0.8701 (mt0) REVERT: A 132 LYS cc_start: 0.9349 (mttt) cc_final: 0.8865 (mttm) REVERT: A 283 LEU cc_start: 0.8437 (tt) cc_final: 0.8213 (tp) REVERT: B 3 GLU cc_start: 0.8778 (tp30) cc_final: 0.8427 (pt0) REVERT: B 57 LYS cc_start: 0.9125 (mtpt) cc_final: 0.8687 (mtpt) REVERT: B 59 TYR cc_start: 0.8181 (m-80) cc_final: 0.7898 (m-80) REVERT: B 61 MET cc_start: 0.7890 (ppp) cc_final: 0.7540 (ppp) REVERT: B 289 TYR cc_start: 0.8761 (m-80) cc_final: 0.8198 (m-80) REVERT: B 333 ASP cc_start: 0.8532 (p0) cc_final: 0.8128 (p0) REVERT: G 14 LYS cc_start: 0.9300 (mtpp) cc_final: 0.9039 (mtmm) REVERT: G 17 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8806 (mt-10) REVERT: G 32 LYS cc_start: 0.9461 (mmtm) cc_final: 0.9246 (mptt) REVERT: G 36 ASP cc_start: 0.8737 (t0) cc_final: 0.8477 (m-30) REVERT: L 59 VAL cc_start: 0.9310 (t) cc_final: 0.9058 (p) REVERT: H 32 PHE cc_start: 0.8638 (t80) cc_final: 0.8340 (t80) REVERT: H 120 TYR cc_start: 0.8112 (m-10) cc_final: 0.7799 (m-80) outliers start: 54 outliers final: 42 residues processed: 305 average time/residue: 0.0846 time to fit residues: 37.8723 Evaluate side-chains 296 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 252 PHE Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 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 392 VAL Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 191 SER 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 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 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP 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 111 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 ASN R 361 HIS ** R 433 HIS ** 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 142 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.101723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.083214 restraints weight = 36237.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.085544 restraints weight = 20659.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.087130 restraints weight = 13996.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.088219 restraints weight = 10601.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088970 restraints weight = 8704.811| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 10809 Z= 0.256 Angle : 0.737 10.581 14659 Z= 0.389 Chirality : 0.046 0.227 1635 Planarity : 0.005 0.106 1857 Dihedral : 6.254 78.911 1536 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.35 % Favored : 92.57 % Rotamer: Outliers : 6.61 % Allowed : 23.35 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.22), residues: 1333 helix: -0.06 (0.23), residues: 459 sheet: -0.67 (0.32), residues: 260 loop : -2.54 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 100 TYR 0.022 0.002 TYR R 337 PHE 0.019 0.002 PHE A 95 TRP 0.068 0.003 TRP H 50 HIS 0.006 0.002 HIS R 433 Details of bonding type rmsd covalent geometry : bond 0.00563 (10806) covalent geometry : angle 0.73636 (14653) SS BOND : bond 0.00672 ( 3) SS BOND : angle 1.39881 ( 6) hydrogen bonds : bond 0.04215 ( 442) hydrogen bonds : angle 5.14674 ( 1272) *********************** 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 324 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 249 time to evaluate : 0.422 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: R 218 GLN cc_start: 0.8473 (mt0) cc_final: 0.7881 (mp10) REVERT: R 228 GLN cc_start: 0.9419 (mt0) cc_final: 0.9083 (tp40) REVERT: R 257 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7765 (mmt180) REVERT: R 301 MET cc_start: 0.7657 (pmm) cc_final: 0.6907 (pmm) REVERT: R 339 TRP cc_start: 0.9207 (OUTLIER) cc_final: 0.8898 (m-90) REVERT: R 433 HIS cc_start: 0.6436 (OUTLIER) cc_final: 0.5838 (p-80) REVERT: R 485 ARG cc_start: 0.6392 (ttt180) cc_final: 0.5132 (tpp80) REVERT: A 79 GLN cc_start: 0.9048 (tp40) cc_final: 0.8791 (mt0) REVERT: A 164 GLN cc_start: 0.8602 (tp40) cc_final: 0.8027 (tm-30) REVERT: B 3 GLU cc_start: 0.8669 (tp30) cc_final: 0.8418 (tp30) REVERT: B 46 ARG cc_start: 0.7701 (tpt-90) cc_final: 0.6849 (tpp80) REVERT: B 136 SER cc_start: 0.8954 (m) cc_final: 0.8726 (t) REVERT: B 289 TYR cc_start: 0.8874 (m-80) cc_final: 0.8365 (m-80) REVERT: B 325 MET cc_start: 0.7510 (mtm) cc_final: 0.7305 (ttp) REVERT: B 333 ASP cc_start: 0.8661 (p0) cc_final: 0.8321 (p0) REVERT: G 17 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8971 (mt-10) REVERT: L 59 VAL cc_start: 0.9397 (t) cc_final: 0.9098 (p) REVERT: L 90 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8399 (tm-30) REVERT: H 118 MET cc_start: 0.8460 (mpp) cc_final: 0.8222 (mpp) REVERT: H 120 TYR cc_start: 0.8295 (m-10) cc_final: 0.7871 (m-10) outliers start: 75 outliers final: 57 residues processed: 295 average time/residue: 0.0872 time to fit residues: 38.1772 Evaluate side-chains 294 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 307 THR Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain R residue 544 ILE Chi-restraints excluded: chain R residue 545 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 SER 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 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 47 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 142 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 = 0.3731 r_free = 0.3731 target = 0.104191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085579 restraints weight = 35385.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.087997 restraints weight = 19956.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.089625 restraints weight = 13413.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090773 restraints weight = 10120.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091504 restraints weight = 8268.442| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10809 Z= 0.163 Angle : 0.705 13.957 14659 Z= 0.359 Chirality : 0.044 0.250 1635 Planarity : 0.005 0.103 1857 Dihedral : 6.020 82.952 1536 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.29 % Allowed : 24.32 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.22), residues: 1333 helix: 0.18 (0.23), residues: 452 sheet: -0.65 (0.33), residues: 257 loop : -2.44 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.019 0.001 TYR A 69 PHE 0.021 0.002 PHE A 95 TRP 0.047 0.002 TRP H 50 HIS 0.007 0.001 HIS R 227 Details of bonding type rmsd covalent geometry : bond 0.00374 (10806) covalent geometry : angle 0.70475 (14653) SS BOND : bond 0.00227 ( 3) SS BOND : angle 1.27561 ( 6) hydrogen bonds : bond 0.03846 ( 442) hydrogen bonds : angle 4.97487 ( 1272) *********************** 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 311 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 251 time to evaluate : 0.411 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: 0.8192 (m) cc_final: 0.7902 (p) REVERT: R 218 GLN cc_start: 0.8462 (mt0) cc_final: 0.7848 (mp10) REVERT: R 228 GLN cc_start: 0.9389 (mt0) cc_final: 0.9074 (tp40) REVERT: R 257 ARG cc_start: 0.8282 (mtp180) cc_final: 0.7759 (mmt180) REVERT: R 301 MET cc_start: 0.7550 (pmm) cc_final: 0.6745 (pmm) REVERT: R 339 TRP cc_start: 0.9187 (OUTLIER) cc_final: 0.8905 (m-90) REVERT: R 433 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.5864 (p-80) REVERT: R 447 GLU cc_start: 0.8069 (tp30) cc_final: 0.7491 (tm-30) REVERT: R 485 ARG cc_start: 0.6487 (ttt180) cc_final: 0.5291 (tpp80) REVERT: R 491 GLN cc_start: 0.8016 (tp40) cc_final: 0.7704 (tp40) REVERT: A 33 GLU cc_start: 0.7768 (tp30) cc_final: 0.7549 (tp30) REVERT: A 74 TYR cc_start: 0.8157 (m-10) cc_final: 0.7871 (m-80) REVERT: A 79 GLN cc_start: 0.9080 (tp40) cc_final: 0.8707 (mt0) REVERT: A 232 LEU cc_start: 0.8708 (mp) cc_final: 0.8026 (tt) REVERT: B 3 GLU cc_start: 0.8693 (tp30) cc_final: 0.8469 (tp30) REVERT: B 46 ARG cc_start: 0.7702 (tpt-90) cc_final: 0.6842 (tpp80) REVERT: B 289 TYR cc_start: 0.8778 (m-80) cc_final: 0.8271 (m-80) REVERT: B 301 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7187 (mmtt) REVERT: B 325 MET cc_start: 0.7310 (mtm) cc_final: 0.7076 (ttm) REVERT: B 333 ASP cc_start: 0.8640 (p0) cc_final: 0.8267 (p0) REVERT: G 17 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8823 (mt-10) REVERT: G 21 MET cc_start: 0.7912 (mmt) cc_final: 0.7693 (mmt) REVERT: L 59 VAL cc_start: 0.9350 (t) cc_final: 0.9044 (p) REVERT: L 90 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8335 (tm-30) REVERT: H 68 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8432 (ptpp) outliers start: 60 outliers final: 50 residues processed: 286 average time/residue: 0.0898 time to fit residues: 37.9579 Evaluate side-chains 293 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 336 THR Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 348 THR 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 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 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 30 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ILE 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 191 SER 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 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 48 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 142 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 = 0.3707 r_free = 0.3707 target = 0.102626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.084059 restraints weight = 35947.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.086394 restraints weight = 20611.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.087969 restraints weight = 14006.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.089082 restraints weight = 10646.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.089831 restraints weight = 8759.749| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10809 Z= 0.211 Angle : 0.724 13.414 14659 Z= 0.375 Chirality : 0.044 0.200 1635 Planarity : 0.005 0.104 1857 Dihedral : 6.201 85.142 1536 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.73 % Favored : 92.20 % Rotamer: Outliers : 6.17 % Allowed : 24.41 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.22), residues: 1333 helix: 0.09 (0.23), residues: 452 sheet: -0.76 (0.32), residues: 265 loop : -2.59 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.018 0.002 TYR A 69 PHE 0.024 0.002 PHE A 95 TRP 0.065 0.002 TRP H 50 HIS 0.005 0.002 HIS R 433 Details of bonding type rmsd covalent geometry : bond 0.00475 (10806) covalent geometry : angle 0.72348 (14653) SS BOND : bond 0.00331 ( 3) SS BOND : angle 1.38402 ( 6) hydrogen bonds : bond 0.04029 ( 442) hydrogen bonds : angle 5.08280 ( 1272) *********************** 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 316 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 246 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8453 (mt0) cc_final: 0.7825 (mp10) REVERT: R 228 GLN cc_start: 0.9406 (mt0) cc_final: 0.9084 (tp40) REVERT: R 257 ARG cc_start: 0.8149 (mtp180) cc_final: 0.7814 (mmt180) REVERT: R 301 MET cc_start: 0.7597 (pmm) cc_final: 0.6798 (pmm) REVERT: R 339 TRP cc_start: 0.9119 (OUTLIER) cc_final: 0.8868 (m-90) REVERT: R 433 HIS cc_start: 0.6563 (OUTLIER) cc_final: 0.5756 (p-80) REVERT: R 447 GLU cc_start: 0.8112 (tp30) cc_final: 0.7592 (tm-30) REVERT: R 485 ARG cc_start: 0.6437 (ttt180) cc_final: 0.5219 (tpp80) REVERT: R 491 GLN cc_start: 0.8047 (tp40) cc_final: 0.7755 (tp40) REVERT: A 33 GLU cc_start: 0.7863 (tp30) cc_final: 0.7644 (tp30) REVERT: A 74 TYR cc_start: 0.8137 (m-10) cc_final: 0.7827 (m-80) REVERT: B 46 ARG cc_start: 0.7642 (tpt-90) cc_final: 0.6793 (tpp80) REVERT: B 57 LYS cc_start: 0.9243 (mtpt) cc_final: 0.8937 (mtmt) REVERT: B 136 SER cc_start: 0.8767 (m) cc_final: 0.8473 (t) REVERT: B 289 TYR cc_start: 0.8769 (m-80) cc_final: 0.8377 (m-80) REVERT: B 301 LYS cc_start: 0.7785 (mtmt) cc_final: 0.7154 (mmtp) REVERT: B 333 ASP cc_start: 0.8657 (p0) cc_final: 0.8328 (p0) REVERT: G 17 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8895 (mt-10) REVERT: L 12 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6807 (pp) REVERT: L 59 VAL cc_start: 0.9341 (t) cc_final: 0.9050 (p) REVERT: L 76 ILE cc_start: 0.9033 (mt) cc_final: 0.8713 (tt) REVERT: L 90 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8321 (tm-30) REVERT: H 68 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8402 (ptpp) REVERT: H 120 TYR cc_start: 0.8175 (m-10) cc_final: 0.7822 (m-10) outliers start: 70 outliers final: 56 residues processed: 291 average time/residue: 0.0872 time to fit residues: 37.5306 Evaluate side-chains 297 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 336 THR Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 348 THR 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 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 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 80 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 SER 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 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 95 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 142 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 = 0.3750 r_free = 0.3750 target = 0.105464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086682 restraints weight = 35101.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089141 restraints weight = 19861.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090839 restraints weight = 13355.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091979 restraints weight = 10057.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092779 restraints weight = 8214.341| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10809 Z= 0.137 Angle : 0.705 13.512 14659 Z= 0.358 Chirality : 0.043 0.204 1635 Planarity : 0.005 0.101 1857 Dihedral : 5.953 86.828 1536 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.02 % Allowed : 26.70 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.22), residues: 1333 helix: 0.21 (0.24), residues: 450 sheet: -0.61 (0.33), residues: 252 loop : -2.41 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.031 0.001 TYR H 34 PHE 0.024 0.001 PHE A 95 TRP 0.050 0.002 TRP H 50 HIS 0.007 0.001 HIS R 227 Details of bonding type rmsd covalent geometry : bond 0.00317 (10806) covalent geometry : angle 0.70428 (14653) SS BOND : bond 0.00195 ( 3) SS BOND : angle 1.14914 ( 6) hydrogen bonds : bond 0.03748 ( 442) hydrogen bonds : angle 4.91132 ( 1272) *********************** 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 318 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 0.418 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: 0.8187 (m) cc_final: 0.7917 (p) REVERT: R 218 GLN cc_start: 0.8480 (mt0) cc_final: 0.7877 (mp10) REVERT: R 228 GLN cc_start: 0.9369 (mt0) cc_final: 0.9073 (tp40) REVERT: R 257 ARG cc_start: 0.8188 (mtp180) cc_final: 0.7753 (mmt180) REVERT: R 301 MET cc_start: 0.7449 (pmm) cc_final: 0.6624 (pmm) REVERT: R 339 TRP cc_start: 0.9109 (OUTLIER) cc_final: 0.8879 (m-90) REVERT: R 418 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8347 (t80) REVERT: R 433 HIS cc_start: 0.6418 (OUTLIER) cc_final: 0.5775 (p-80) REVERT: R 447 GLU cc_start: 0.8249 (tp30) cc_final: 0.7754 (tm-30) REVERT: R 449 MET cc_start: 0.8940 (ttt) cc_final: 0.8520 (tpp) REVERT: R 485 ARG cc_start: 0.6542 (ttt180) cc_final: 0.5373 (tpp80) REVERT: A 18 MET cc_start: 0.7365 (mmm) cc_final: 0.6763 (tpp) REVERT: A 74 TYR cc_start: 0.8241 (m-10) cc_final: 0.7943 (m-80) REVERT: A 232 LEU cc_start: 0.8732 (mp) cc_final: 0.8199 (tt) REVERT: A 283 LEU cc_start: 0.8268 (tt) cc_final: 0.8007 (tp) REVERT: A 322 HIS cc_start: 0.7992 (t-90) cc_final: 0.7668 (t-90) REVERT: B 46 ARG cc_start: 0.7722 (tpt-90) cc_final: 0.6887 (tpp80) REVERT: B 136 SER cc_start: 0.8676 (m) cc_final: 0.8465 (t) REVERT: B 289 TYR cc_start: 0.8665 (m-80) cc_final: 0.8212 (m-80) REVERT: B 301 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7271 (mttt) REVERT: B 325 MET cc_start: 0.7311 (ttm) cc_final: 0.7017 (ttm) REVERT: B 333 ASP cc_start: 0.8635 (p0) cc_final: 0.8242 (p0) REVERT: G 14 LYS cc_start: 0.9336 (mtpp) cc_final: 0.9062 (mtmm) REVERT: G 17 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8827 (mt-10) REVERT: G 21 MET cc_start: 0.7976 (mmt) cc_final: 0.7686 (mmm) REVERT: G 32 LYS cc_start: 0.9367 (mmtm) cc_final: 0.9120 (mmtm) REVERT: G 36 ASP cc_start: 0.8771 (t0) cc_final: 0.8469 (m-30) REVERT: L 59 VAL cc_start: 0.9295 (t) cc_final: 0.8999 (p) REVERT: L 90 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8297 (tm-30) REVERT: H 68 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8422 (ptpp) REVERT: H 120 TYR cc_start: 0.8167 (m-10) cc_final: 0.7827 (m-10) outliers start: 57 outliers final: 48 residues processed: 295 average time/residue: 0.0868 time to fit residues: 38.0666 Evaluate side-chains 302 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 250 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 336 THR Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 348 THR 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 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 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 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 SER 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 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS 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 14 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 48 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 73 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 241 ASN ** 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 142 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 = 0.3746 r_free = 0.3746 target = 0.105178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.086403 restraints weight = 35189.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.088862 restraints weight = 20011.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.090538 restraints weight = 13497.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.091676 restraints weight = 10187.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.092422 restraints weight = 8331.523| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10809 Z= 0.149 Angle : 0.714 13.782 14659 Z= 0.363 Chirality : 0.044 0.196 1635 Planarity : 0.005 0.099 1857 Dihedral : 5.929 86.468 1536 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.93 % Allowed : 26.70 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.22), residues: 1333 helix: 0.14 (0.24), residues: 453 sheet: -0.70 (0.33), residues: 258 loop : -2.36 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.038 0.002 TYR H 34 PHE 0.020 0.001 PHE A 95 TRP 0.048 0.002 TRP H 50 HIS 0.005 0.001 HIS R 433 Details of bonding type rmsd covalent geometry : bond 0.00345 (10806) covalent geometry : angle 0.71387 (14653) SS BOND : bond 0.00245 ( 3) SS BOND : angle 1.52797 ( 6) hydrogen bonds : bond 0.03781 ( 442) hydrogen bonds : angle 4.95351 ( 1272) ********************** 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 317 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 0.415 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: 0.8194 (m) cc_final: 0.7925 (p) REVERT: R 218 GLN cc_start: 0.8484 (mt0) cc_final: 0.7873 (mp10) REVERT: R 228 GLN cc_start: 0.9380 (mt0) cc_final: 0.9081 (tp40) REVERT: R 257 ARG cc_start: 0.8286 (mtp180) cc_final: 0.7848 (mmt180) REVERT: R 301 MET cc_start: 0.7450 (pmm) cc_final: 0.6635 (pmm) REVERT: R 339 TRP cc_start: 0.9104 (OUTLIER) cc_final: 0.8856 (m-90) REVERT: R 418 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8372 (t80) REVERT: R 433 HIS cc_start: 0.6483 (OUTLIER) cc_final: 0.5772 (p-80) REVERT: R 447 GLU cc_start: 0.8285 (tp30) cc_final: 0.7800 (tm-30) REVERT: R 449 MET cc_start: 0.8908 (ttt) cc_final: 0.8478 (tpp) REVERT: R 485 ARG cc_start: 0.6513 (ttt180) cc_final: 0.5374 (tpp80) REVERT: R 491 GLN cc_start: 0.7753 (tp40) cc_final: 0.7282 (tp40) REVERT: A 33 GLU cc_start: 0.7404 (tp30) cc_final: 0.7138 (tp30) REVERT: A 232 LEU cc_start: 0.8774 (mp) cc_final: 0.8248 (tp) REVERT: A 283 LEU cc_start: 0.8307 (tt) cc_final: 0.8099 (tp) REVERT: A 322 HIS cc_start: 0.8083 (t-90) cc_final: 0.7761 (t-90) REVERT: B 10 GLU cc_start: 0.7760 (tt0) cc_final: 0.7285 (mm-30) REVERT: B 46 ARG cc_start: 0.7684 (tpt-90) cc_final: 0.6850 (tpp80) REVERT: B 61 MET cc_start: 0.7977 (ppp) cc_final: 0.7725 (ppp) REVERT: B 136 SER cc_start: 0.8691 (m) cc_final: 0.8473 (t) REVERT: B 176 GLN cc_start: 0.9137 (pt0) cc_final: 0.8364 (pp30) REVERT: B 289 TYR cc_start: 0.8780 (m-80) cc_final: 0.8340 (m-80) REVERT: B 301 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7097 (mmtp) REVERT: B 325 MET cc_start: 0.7426 (ttm) cc_final: 0.7077 (ttm) REVERT: B 333 ASP cc_start: 0.8643 (p0) cc_final: 0.8276 (p0) REVERT: G 17 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8894 (mt-10) REVERT: G 32 LYS cc_start: 0.9374 (mmtm) cc_final: 0.9098 (mmtm) REVERT: G 36 ASP cc_start: 0.8833 (t0) cc_final: 0.8608 (m-30) REVERT: L 12 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6950 (pp) REVERT: L 59 VAL cc_start: 0.9284 (t) cc_final: 0.8987 (p) REVERT: L 90 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8293 (tm-30) REVERT: H 120 TYR cc_start: 0.8105 (m-10) cc_final: 0.7762 (m-10) outliers start: 56 outliers final: 48 residues processed: 295 average time/residue: 0.0937 time to fit residues: 40.8086 Evaluate side-chains 306 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 336 THR Chi-restraints excluded: chain R residue 339 TRP 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 466 THR Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 SER 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 296 VAL Chi-restraints excluded: chain G residue 41 CYS 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 L residue 89 CYS Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 114 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 112 optimal weight: 0.3980 chunk 40 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 142 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 = 0.106403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087608 restraints weight = 35335.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.090089 restraints weight = 20092.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.091816 restraints weight = 13490.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092971 restraints weight = 10160.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093727 restraints weight = 8285.213| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10809 Z= 0.134 Angle : 0.709 13.618 14659 Z= 0.358 Chirality : 0.043 0.197 1635 Planarity : 0.004 0.096 1857 Dihedral : 5.816 86.482 1535 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.58 % Allowed : 27.40 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.22), residues: 1333 helix: 0.25 (0.24), residues: 451 sheet: -0.47 (0.33), residues: 252 loop : -2.37 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.043 0.001 TYR H 34 PHE 0.019 0.001 PHE A 95 TRP 0.040 0.002 TRP H 50 HIS 0.005 0.001 HIS R 433 Details of bonding type rmsd covalent geometry : bond 0.00310 (10806) covalent geometry : angle 0.70871 (14653) SS BOND : bond 0.00137 ( 3) SS BOND : angle 1.19434 ( 6) hydrogen bonds : bond 0.03671 ( 442) hydrogen bonds : angle 4.89642 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2163.71 seconds wall clock time: 38 minutes 9.29 seconds (2289.29 seconds total)