Starting phenix.real_space_refine on Wed Sep 25 02:59:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbi_0412/09_2024/6nbi_0412.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbi_0412/09_2024/6nbi_0412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbi_0412/09_2024/6nbi_0412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbi_0412/09_2024/6nbi_0412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbi_0412/09_2024/6nbi_0412.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nbi_0412/09_2024/6nbi_0412.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 57 5.16 5 C 5875 2.51 5 N 1599 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9195 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3020 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 10, 'TRANS': 358} Chain breaks: 4 Chain: "P" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 253 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "A" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1840 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.56, per 1000 atoms: 0.60 Number of scatterers: 9195 At special positions: 0 Unit cell: (127.764, 99.372, 148.044, 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 57 16.00 O 1664 8.00 N 1599 7.00 C 5875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.04 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.04 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 971.3 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 41.1% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'R' and resid 32 through 53 removed outlier: 4.162A pdb=" N GLU R 36 " --> pdb=" O MET R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 201 removed outlier: 3.878A pdb=" N GLU R 182 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL R 183 " --> pdb=" O ARG R 179 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG R 186 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU R 187 " --> pdb=" O VAL R 183 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU R 199 " --> pdb=" O TYR R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 218 through 250 removed outlier: 3.793A pdb=" N MET R 224 " --> pdb=" O ASN R 220 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS R 240 " --> pdb=" O SER R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 313 removed outlier: 4.227A pdb=" N ALA R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE R 311 " --> pdb=" O HIS R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 4.153A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.629A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 369 removed outlier: 3.546A pdb=" N GLN R 364 " --> pdb=" O LYS R 360 " (cutoff:3.500A) Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 371 through 395 removed outlier: 3.708A pdb=" N VAL R 384 " --> pdb=" O ASN R 380 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR R 392 " --> pdb=" O LYS R 388 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA R 394 " --> pdb=" O ARG R 390 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY R 395 " --> pdb=" O GLU R 391 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 412 Processing helix chain 'R' and resid 419 through 424 Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.747A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR R 459 " --> pdb=" O VAL R 455 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 Processing helix chain 'P' and resid 2 through 16 Processing helix chain 'P' and resid 17 through 25 removed outlier: 3.932A pdb=" N ARG P 21 " --> pdb=" O ASP P 17 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS P 25 " --> pdb=" O ARG P 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.667A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.725A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.502A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.797A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.099A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.636A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.515A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.025A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 126 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 213 removed outlier: 3.591A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS A 220 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.133A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.133A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.866A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.534A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.001A 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: 3.660A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.595A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.626A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.819A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1206 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: 2.50 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2960 1.35 - 1.47: 2312 1.47 - 1.59: 4051 1.59 - 1.71: 0 1.71 - 1.83: 80 Bond restraints: 9403 Sorted by residual: bond pdb=" C THR A 320 " pdb=" N PRO A 321 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.19e-02 7.06e+03 6.81e+00 bond pdb=" C MET R 414 " pdb=" N PRO R 415 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.23e-02 6.61e+03 4.91e+00 bond pdb=" C PHE A 312 " pdb=" O PHE A 312 " ideal model delta sigma weight residual 1.249 1.232 0.017 8.50e-03 1.38e+04 4.05e+00 bond pdb=" C ALA R 122 " pdb=" N PRO R 123 " ideal model delta sigma weight residual 1.331 1.354 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 1.518 1.539 -0.021 1.13e-02 7.83e+03 3.36e+00 ... (remaining 9398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 11283 1.33 - 2.66: 1286 2.66 - 3.99: 150 3.99 - 5.32: 25 5.32 - 6.65: 2 Bond angle restraints: 12746 Sorted by residual: angle pdb=" C ASP A 354 " pdb=" N GLY A 355 " pdb=" CA GLY A 355 " ideal model delta sigma weight residual 119.98 124.68 -4.70 1.11e+00 8.12e-01 1.79e+01 angle pdb=" N VAL R 171 " pdb=" CA VAL R 171 " pdb=" C VAL R 171 " ideal model delta sigma weight residual 106.21 109.86 -3.65 1.07e+00 8.73e-01 1.17e+01 angle pdb=" C THR N 61 " pdb=" N GLY N 62 " pdb=" CA GLY N 62 " ideal model delta sigma weight residual 120.03 123.78 -3.75 1.12e+00 7.97e-01 1.12e+01 angle pdb=" C GLU A 370 " pdb=" N ASN A 371 " pdb=" CA ASN A 371 " ideal model delta sigma weight residual 120.38 124.88 -4.50 1.37e+00 5.33e-01 1.08e+01 angle pdb=" C GLN R 451 " pdb=" N GLY R 452 " pdb=" CA GLY R 452 " ideal model delta sigma weight residual 119.99 123.65 -3.66 1.13e+00 7.83e-01 1.05e+01 ... (remaining 12741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.33: 5337 13.33 - 26.67: 297 26.67 - 40.00: 53 40.00 - 53.33: 15 53.33 - 66.66: 6 Dihedral angle restraints: 5708 sinusoidal: 2391 harmonic: 3317 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 134.92 -41.92 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 162.20 17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU R 289 " pdb=" C LEU R 289 " pdb=" N TYR R 290 " pdb=" CA TYR R 290 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 5705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 871 0.046 - 0.091: 428 0.091 - 0.137: 97 0.137 - 0.183: 19 0.183 - 0.228: 1 Chirality restraints: 1416 Sorted by residual: chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C10 CLR R 603 " pdb=" C1 CLR R 603 " pdb=" C5 CLR R 603 " pdb=" C9 CLR R 603 " both_signs ideal model delta sigma weight residual False -2.85 -2.67 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" C10 CLR R 602 " pdb=" C1 CLR R 602 " pdb=" C5 CLR R 602 " pdb=" C9 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.85 -2.67 -0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 1413 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS R 34 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C LYS R 34 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS R 34 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU R 35 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.032 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO G 49 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 32 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.91e+00 pdb=" C LYS A 32 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS A 32 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 33 " -0.010 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2845 2.85 - 3.36: 7823 3.36 - 3.87: 14237 3.87 - 4.39: 16041 4.39 - 4.90: 28235 Nonbonded interactions: 69181 Sorted by model distance: nonbonded pdb=" OH TYR R 421 " pdb=" OE1 GLN R 451 " model vdw 2.337 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.373 3.040 nonbonded pdb=" O MET R 425 " pdb=" N ALA P 1 " model vdw 2.373 3.120 nonbonded pdb=" O SER R 341 " pdb=" OG1 THR R 345 " model vdw 2.390 3.040 ... (remaining 69176 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.250 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.005 0.031 9403 Z= 0.341 Angle : 0.876 6.654 12746 Z= 0.593 Chirality : 0.053 0.228 1416 Planarity : 0.004 0.068 1604 Dihedral : 8.927 66.664 3544 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.31 % Allowed : 0.72 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.22), residues: 1115 helix: -0.65 (0.22), residues: 447 sheet: -0.86 (0.33), residues: 217 loop : -1.61 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 154 HIS 0.006 0.001 HIS A 387 PHE 0.014 0.002 PHE R 447 TYR 0.025 0.002 TYR R 191 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 528 time to evaluate : 1.023 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 307 HIS cc_start: 0.8222 (t-90) cc_final: 0.7726 (t-90) REVERT: R 445 MET cc_start: 0.8003 (mmp) cc_final: 0.7612 (mmp) REVERT: A 13 ARG cc_start: 0.8455 (mtt180) cc_final: 0.7537 (mpt180) REVERT: A 16 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8821 (pt0) REVERT: A 278 ASN cc_start: 0.8348 (m110) cc_final: 0.7768 (m-40) REVERT: A 286 SER cc_start: 0.9489 (t) cc_final: 0.9265 (p) REVERT: B 10 GLU cc_start: 0.9371 (tt0) cc_final: 0.9099 (tm-30) REVERT: B 20 ASP cc_start: 0.9095 (m-30) cc_final: 0.8651 (m-30) REVERT: B 51 LEU cc_start: 0.7980 (mt) cc_final: 0.7775 (mp) REVERT: B 184 THR cc_start: 0.8195 (p) cc_final: 0.7920 (t) REVERT: B 301 LYS cc_start: 0.8297 (mmmm) cc_final: 0.7861 (mmtp) REVERT: B 316 SER cc_start: 0.8935 (p) cc_final: 0.8730 (t) REVERT: G 38 MET cc_start: 0.9299 (mtm) cc_final: 0.9086 (mtt) REVERT: N 77 ASN cc_start: 0.9057 (m-40) cc_final: 0.8783 (t0) REVERT: N 122 THR cc_start: 0.7406 (t) cc_final: 0.6816 (p) outliers start: 3 outliers final: 2 residues processed: 530 average time/residue: 0.2577 time to fit residues: 175.7729 Evaluate side-chains 302 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 300 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 44 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.0370 chunk 64 optimal weight: 0.0470 chunk 100 optimal weight: 20.0000 overall best weight: 1.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 438 GLN ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS B 156 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9403 Z= 0.210 Angle : 0.680 10.185 12746 Z= 0.354 Chirality : 0.044 0.353 1416 Planarity : 0.005 0.045 1604 Dihedral : 5.497 43.356 1449 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.01 % Allowed : 16.98 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1115 helix: 1.05 (0.25), residues: 437 sheet: -0.28 (0.32), residues: 224 loop : -1.20 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 14 HIS 0.005 0.001 HIS B 54 PHE 0.012 0.001 PHE R 315 TYR 0.013 0.002 TYR N 32 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 323 time to evaluate : 1.056 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.8901 (p0) cc_final: 0.8661 (p0) REVERT: B 12 GLU cc_start: 0.8965 (tp30) cc_final: 0.8713 (tp30) REVERT: B 16 ASN cc_start: 0.8900 (m-40) cc_final: 0.8301 (m-40) REVERT: B 20 ASP cc_start: 0.9200 (m-30) cc_final: 0.8863 (m-30) REVERT: B 51 LEU cc_start: 0.8218 (mt) cc_final: 0.8000 (mp) REVERT: B 184 THR cc_start: 0.8142 (p) cc_final: 0.7903 (t) REVERT: G 11 GLN cc_start: 0.8957 (pt0) cc_final: 0.8450 (pp30) REVERT: N 20 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6323 (mt) REVERT: N 81 LEU cc_start: 0.6728 (tp) cc_final: 0.6288 (tt) outliers start: 39 outliers final: 22 residues processed: 346 average time/residue: 0.2273 time to fit residues: 105.8631 Evaluate side-chains 287 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 264 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 288 PHE Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 388 LYS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 50.0000 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN R 307 HIS ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN A 19 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN B 220 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9403 Z= 0.191 Angle : 0.634 10.469 12746 Z= 0.327 Chirality : 0.043 0.332 1416 Planarity : 0.004 0.060 1604 Dihedral : 5.175 46.741 1449 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.04 % Allowed : 18.52 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1115 helix: 1.22 (0.25), residues: 431 sheet: -0.08 (0.31), residues: 244 loop : -0.99 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.015 0.001 HIS P 9 PHE 0.015 0.001 PHE R 378 TYR 0.024 0.001 TYR R 191 ARG 0.010 0.001 ARG P 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 290 time to evaluate : 1.095 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 445 MET cc_start: 0.8250 (mmp) cc_final: 0.7835 (mmp) REVERT: A 240 ASP cc_start: 0.8963 (p0) cc_final: 0.8682 (p0) REVERT: B 6 GLN cc_start: 0.9382 (pp30) cc_final: 0.9107 (pm20) REVERT: B 12 GLU cc_start: 0.8968 (tp30) cc_final: 0.7774 (tp30) REVERT: B 16 ASN cc_start: 0.8870 (m-40) cc_final: 0.8119 (m-40) REVERT: B 184 THR cc_start: 0.8189 (p) cc_final: 0.7842 (t) REVERT: G 11 GLN cc_start: 0.8970 (pt0) cc_final: 0.8527 (pp30) REVERT: N 4 LEU cc_start: 0.8084 (mm) cc_final: 0.7702 (mm) REVERT: N 81 LEU cc_start: 0.7087 (tp) cc_final: 0.6566 (tt) REVERT: N 122 THR cc_start: 0.7763 (t) cc_final: 0.7506 (t) outliers start: 49 outliers final: 36 residues processed: 313 average time/residue: 0.2068 time to fit residues: 88.5390 Evaluate side-chains 282 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 246 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 288 PHE Chi-restraints excluded: chain R residue 374 ASN Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 67 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS R 295 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN A 31 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 236 GLN A 271 ASN B 142 HIS ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9403 Z= 0.345 Angle : 0.723 8.752 12746 Z= 0.383 Chirality : 0.044 0.243 1416 Planarity : 0.005 0.048 1604 Dihedral : 5.371 49.724 1449 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 6.38 % Allowed : 20.58 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1115 helix: 0.77 (0.24), residues: 445 sheet: -0.07 (0.31), residues: 238 loop : -0.99 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 352 HIS 0.020 0.002 HIS P 9 PHE 0.036 0.002 PHE R 184 TYR 0.018 0.002 TYR A 358 ARG 0.012 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 263 time to evaluate : 1.034 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: P 6 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.9098 (tp40) REVERT: A 33 ASP cc_start: 0.9422 (p0) cc_final: 0.8954 (t0) REVERT: A 221 MET cc_start: 0.9011 (tmm) cc_final: 0.8559 (tmm) REVERT: A 240 ASP cc_start: 0.9158 (p0) cc_final: 0.8792 (p0) REVERT: A 365 CYS cc_start: 0.7923 (t) cc_final: 0.7502 (m) REVERT: B 6 GLN cc_start: 0.9390 (pp30) cc_final: 0.9093 (pm20) REVERT: B 12 GLU cc_start: 0.8918 (tp30) cc_final: 0.8075 (tp30) REVERT: B 215 GLU cc_start: 0.9484 (mp0) cc_final: 0.8985 (mp0) REVERT: G 11 GLN cc_start: 0.9074 (pt0) cc_final: 0.8581 (pp30) REVERT: G 61 PHE cc_start: 0.8840 (m-80) cc_final: 0.8538 (m-80) REVERT: N 4 LEU cc_start: 0.8383 (mm) cc_final: 0.8045 (mm) REVERT: N 19 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7600 (ttp80) REVERT: N 81 LEU cc_start: 0.7264 (tp) cc_final: 0.6968 (tt) REVERT: N 91 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7460 (t) outliers start: 62 outliers final: 45 residues processed: 301 average time/residue: 0.2100 time to fit residues: 86.6639 Evaluate side-chains 278 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 231 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 288 PHE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9403 Z= 0.192 Angle : 0.674 11.383 12746 Z= 0.345 Chirality : 0.044 0.338 1416 Planarity : 0.004 0.050 1604 Dihedral : 4.926 50.474 1449 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.42 % Allowed : 23.87 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1115 helix: 1.15 (0.25), residues: 436 sheet: 0.25 (0.32), residues: 234 loop : -0.96 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 339 HIS 0.017 0.001 HIS P 9 PHE 0.021 0.001 PHE R 184 TYR 0.022 0.001 TYR R 421 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 263 time to evaluate : 1.021 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 440 GLN cc_start: 0.9174 (pp30) cc_final: 0.8962 (pp30) REVERT: P 6 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.9016 (tp40) REVERT: A 14 ASN cc_start: 0.8928 (m110) cc_final: 0.8485 (p0) REVERT: A 33 ASP cc_start: 0.9375 (p0) cc_final: 0.8990 (t0) REVERT: A 365 CYS cc_start: 0.7934 (t) cc_final: 0.7452 (m) REVERT: B 6 GLN cc_start: 0.9404 (pp30) cc_final: 0.9056 (pm20) REVERT: B 12 GLU cc_start: 0.8827 (tp30) cc_final: 0.8323 (tp30) REVERT: B 15 LYS cc_start: 0.6952 (pttp) cc_final: 0.6546 (pttp) REVERT: B 16 ASN cc_start: 0.8871 (m-40) cc_final: 0.8453 (m-40) REVERT: B 215 GLU cc_start: 0.9448 (mp0) cc_final: 0.8931 (mp0) REVERT: B 337 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7655 (mmtm) REVERT: B 339 TRP cc_start: 0.8076 (m100) cc_final: 0.7790 (m100) REVERT: G 11 GLN cc_start: 0.9050 (pt0) cc_final: 0.8570 (pp30) REVERT: G 17 GLU cc_start: 0.8623 (pp20) cc_final: 0.8269 (pp20) REVERT: G 22 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8521 (mt-10) REVERT: N 4 LEU cc_start: 0.8216 (mm) cc_final: 0.7805 (mm) REVERT: N 19 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7715 (ttp80) REVERT: N 81 LEU cc_start: 0.7394 (tp) cc_final: 0.7093 (tt) REVERT: N 87 LYS cc_start: 0.8533 (ttpt) cc_final: 0.7865 (pptt) REVERT: N 90 ASP cc_start: 0.8687 (m-30) cc_final: 0.8130 (m-30) outliers start: 43 outliers final: 32 residues processed: 289 average time/residue: 0.2135 time to fit residues: 84.7978 Evaluate side-chains 266 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 233 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.7391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9403 Z= 0.181 Angle : 0.678 9.819 12746 Z= 0.350 Chirality : 0.043 0.240 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.760 51.627 1449 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.14 % Allowed : 24.49 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1115 helix: 1.18 (0.25), residues: 438 sheet: 0.21 (0.33), residues: 230 loop : -0.87 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 322 HIS 0.018 0.001 HIS P 9 PHE 0.048 0.002 PHE R 324 TYR 0.029 0.001 TYR R 191 ARG 0.007 0.000 ARG P 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 269 time to evaluate : 1.028 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 177 GLU cc_start: 0.9431 (mm-30) cc_final: 0.9195 (mm-30) REVERT: R 440 GLN cc_start: 0.9164 (pp30) cc_final: 0.8959 (pp30) REVERT: P 6 GLN cc_start: 0.9354 (mt0) cc_final: 0.9037 (tp40) REVERT: A 14 ASN cc_start: 0.8903 (m110) cc_final: 0.8454 (p0) REVERT: A 240 ASP cc_start: 0.9025 (p0) cc_final: 0.8655 (p0) REVERT: A 365 CYS cc_start: 0.8039 (t) cc_final: 0.7674 (m) REVERT: B 12 GLU cc_start: 0.8830 (tp30) cc_final: 0.7334 (tp30) REVERT: B 15 LYS cc_start: 0.7059 (pttp) cc_final: 0.6627 (pttm) REVERT: B 16 ASN cc_start: 0.8877 (m-40) cc_final: 0.8337 (m-40) REVERT: B 215 GLU cc_start: 0.9477 (mp0) cc_final: 0.8908 (mp0) REVERT: B 339 TRP cc_start: 0.8053 (m100) cc_final: 0.7686 (m100) REVERT: G 11 GLN cc_start: 0.9035 (pt0) cc_final: 0.8564 (pp30) REVERT: G 17 GLU cc_start: 0.8607 (pp20) cc_final: 0.8305 (pp20) REVERT: N 4 LEU cc_start: 0.8100 (mm) cc_final: 0.7645 (mm) REVERT: N 5 GLN cc_start: 0.7785 (tp40) cc_final: 0.7521 (tp40) REVERT: N 81 LEU cc_start: 0.7426 (tp) cc_final: 0.7083 (tt) REVERT: N 87 LYS cc_start: 0.8556 (ttpt) cc_final: 0.7918 (pptt) REVERT: N 90 ASP cc_start: 0.8648 (m-30) cc_final: 0.8039 (m-30) outliers start: 50 outliers final: 38 residues processed: 298 average time/residue: 0.1950 time to fit residues: 80.6538 Evaluate side-chains 277 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 239 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.7640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9403 Z= 0.198 Angle : 0.693 8.762 12746 Z= 0.362 Chirality : 0.042 0.215 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.721 52.708 1449 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.04 % Allowed : 23.87 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1115 helix: 1.08 (0.25), residues: 443 sheet: 0.20 (0.34), residues: 219 loop : -0.88 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 322 HIS 0.009 0.001 HIS P 9 PHE 0.020 0.002 PHE R 184 TYR 0.022 0.001 TYR R 421 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 249 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 6 GLN cc_start: 0.9361 (mt0) cc_final: 0.9068 (tp40) REVERT: A 14 ASN cc_start: 0.8918 (m110) cc_final: 0.8413 (p0) REVERT: A 383 ILE cc_start: 0.8633 (mm) cc_final: 0.8431 (mm) REVERT: B 12 GLU cc_start: 0.8847 (tp30) cc_final: 0.7564 (tp30) REVERT: B 15 LYS cc_start: 0.6975 (pttp) cc_final: 0.6526 (pttm) REVERT: B 16 ASN cc_start: 0.8842 (m-40) cc_final: 0.8395 (m-40) REVERT: B 215 GLU cc_start: 0.9447 (mp0) cc_final: 0.8903 (mp0) REVERT: B 339 TRP cc_start: 0.8186 (m100) cc_final: 0.7735 (m100) REVERT: G 11 GLN cc_start: 0.9033 (pt0) cc_final: 0.8550 (pp30) REVERT: G 17 GLU cc_start: 0.8524 (pp20) cc_final: 0.8149 (pp20) REVERT: N 4 LEU cc_start: 0.8106 (mm) cc_final: 0.7611 (mm) REVERT: N 5 GLN cc_start: 0.7761 (tp40) cc_final: 0.7534 (tp40) REVERT: N 81 LEU cc_start: 0.7437 (tp) cc_final: 0.7162 (tt) REVERT: N 87 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8199 (ttpt) REVERT: N 90 ASP cc_start: 0.8703 (m-30) cc_final: 0.8205 (m-30) outliers start: 49 outliers final: 41 residues processed: 276 average time/residue: 0.2077 time to fit residues: 78.7827 Evaluate side-chains 272 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 231 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 422 ILE Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.7848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9403 Z= 0.204 Angle : 0.708 10.877 12746 Z= 0.367 Chirality : 0.042 0.195 1416 Planarity : 0.004 0.062 1604 Dihedral : 4.615 53.042 1449 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.73 % Allowed : 24.69 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1115 helix: 1.14 (0.25), residues: 443 sheet: 0.07 (0.33), residues: 226 loop : -0.92 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 322 HIS 0.012 0.001 HIS P 9 PHE 0.020 0.002 PHE R 184 TYR 0.029 0.002 TYR R 191 ARG 0.011 0.001 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 254 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 ILE cc_start: 0.8353 (mp) cc_final: 0.8146 (pt) REVERT: R 177 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9168 (mm-30) REVERT: P 6 GLN cc_start: 0.9344 (mt0) cc_final: 0.8984 (tp40) REVERT: A 360 TYR cc_start: 0.7387 (m-80) cc_final: 0.7088 (m-80) REVERT: A 365 CYS cc_start: 0.8200 (t) cc_final: 0.7688 (m) REVERT: B 8 ARG cc_start: 0.7564 (mpp80) cc_final: 0.7250 (mpp80) REVERT: B 12 GLU cc_start: 0.8845 (tp30) cc_final: 0.8026 (tp30) REVERT: B 16 ASN cc_start: 0.8836 (m-40) cc_final: 0.8313 (m-40) REVERT: B 215 GLU cc_start: 0.9473 (mp0) cc_final: 0.8915 (mp0) REVERT: B 339 TRP cc_start: 0.8222 (m100) cc_final: 0.7656 (m100) REVERT: G 11 GLN cc_start: 0.8985 (pt0) cc_final: 0.8557 (pp30) REVERT: G 17 GLU cc_start: 0.8592 (pp20) cc_final: 0.8211 (pp20) REVERT: G 18 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8185 (pp30) REVERT: N 4 LEU cc_start: 0.8041 (mm) cc_final: 0.7513 (mm) REVERT: N 81 LEU cc_start: 0.7652 (tp) cc_final: 0.7321 (tt) REVERT: N 87 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8164 (ttpt) REVERT: N 90 ASP cc_start: 0.8716 (m-30) cc_final: 0.8291 (m-30) outliers start: 46 outliers final: 44 residues processed: 281 average time/residue: 0.2067 time to fit residues: 79.7491 Evaluate side-chains 275 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 231 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.0370 chunk 78 optimal weight: 0.0370 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.0270 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 451 GLN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.7956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9403 Z= 0.192 Angle : 0.746 10.714 12746 Z= 0.382 Chirality : 0.044 0.311 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.514 53.175 1449 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.81 % Allowed : 26.23 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1115 helix: 1.02 (0.25), residues: 439 sheet: 0.11 (0.33), residues: 234 loop : -0.89 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 322 HIS 0.011 0.001 HIS P 9 PHE 0.025 0.001 PHE R 227 TYR 0.021 0.001 TYR R 421 ARG 0.010 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 260 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.1095 (mmt) cc_final: 0.0452 (mmt) REVERT: R 115 ILE cc_start: 0.8227 (mp) cc_final: 0.8018 (pt) REVERT: R 177 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9165 (mm-30) REVERT: R 240 LYS cc_start: 0.9091 (tppt) cc_final: 0.8856 (tppt) REVERT: P 6 GLN cc_start: 0.9287 (mt0) cc_final: 0.8899 (tp40) REVERT: A 240 ASP cc_start: 0.8920 (p0) cc_final: 0.8558 (p0) REVERT: B 16 ASN cc_start: 0.8701 (m-40) cc_final: 0.8344 (m110) REVERT: B 215 GLU cc_start: 0.9475 (mp0) cc_final: 0.8907 (mp0) REVERT: B 339 TRP cc_start: 0.8065 (m100) cc_final: 0.7457 (m100) REVERT: G 11 GLN cc_start: 0.8977 (pt0) cc_final: 0.8599 (pp30) REVERT: G 17 GLU cc_start: 0.8610 (pp20) cc_final: 0.8168 (pp20) REVERT: G 18 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8070 (pp30) REVERT: G 21 MET cc_start: 0.8420 (tpt) cc_final: 0.8084 (ttt) REVERT: N 4 LEU cc_start: 0.7798 (mm) cc_final: 0.7234 (mm) REVERT: N 81 LEU cc_start: 0.7451 (tp) cc_final: 0.7136 (tt) REVERT: N 85 SER cc_start: 0.8196 (t) cc_final: 0.7953 (p) REVERT: N 90 ASP cc_start: 0.8668 (m-30) cc_final: 0.8258 (m-30) outliers start: 37 outliers final: 32 residues processed: 280 average time/residue: 0.2109 time to fit residues: 80.9512 Evaluate side-chains 267 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 235 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.0870 chunk 110 optimal weight: 0.0050 chunk 101 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.8163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9403 Z= 0.204 Angle : 0.797 12.826 12746 Z= 0.407 Chirality : 0.044 0.250 1416 Planarity : 0.004 0.051 1604 Dihedral : 4.496 53.792 1447 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.29 % Allowed : 27.88 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1115 helix: 1.01 (0.25), residues: 431 sheet: 0.11 (0.32), residues: 239 loop : -0.88 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 322 HIS 0.010 0.001 HIS P 9 PHE 0.028 0.002 PHE R 227 TYR 0.029 0.001 TYR R 191 ARG 0.010 0.001 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.1278 (mmt) cc_final: 0.0587 (mmt) REVERT: R 115 ILE cc_start: 0.8284 (mp) cc_final: 0.8075 (pt) REVERT: P 6 GLN cc_start: 0.9235 (mt0) cc_final: 0.8826 (tp40) REVERT: A 240 ASP cc_start: 0.8917 (p0) cc_final: 0.8578 (p0) REVERT: B 10 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8861 (pp20) REVERT: B 16 ASN cc_start: 0.8742 (m-40) cc_final: 0.8480 (m110) REVERT: B 215 GLU cc_start: 0.9480 (mp0) cc_final: 0.8931 (mp0) REVERT: B 339 TRP cc_start: 0.8146 (m100) cc_final: 0.7363 (m100) REVERT: G 11 GLN cc_start: 0.9006 (pt0) cc_final: 0.8626 (pp30) REVERT: G 18 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8102 (pp30) REVERT: G 25 ILE cc_start: 0.7480 (mt) cc_final: 0.7172 (mt) REVERT: N 4 LEU cc_start: 0.7720 (mm) cc_final: 0.7167 (mm) REVERT: N 85 SER cc_start: 0.8273 (t) cc_final: 0.7974 (p) REVERT: N 90 ASP cc_start: 0.8742 (m-30) cc_final: 0.8326 (m-30) outliers start: 32 outliers final: 30 residues processed: 260 average time/residue: 0.1961 time to fit residues: 71.0634 Evaluate side-chains 265 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 235 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 466 VAL Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 88 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 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 = 0.3897 r_free = 0.3897 target = 0.110292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.088102 restraints weight = 30684.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.090391 restraints weight = 19740.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091913 restraints weight = 14414.101| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.8298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9403 Z= 0.215 Angle : 0.804 12.648 12746 Z= 0.412 Chirality : 0.044 0.282 1416 Planarity : 0.004 0.064 1604 Dihedral : 4.559 54.847 1447 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.50 % Allowed : 28.50 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1115 helix: 0.93 (0.25), residues: 440 sheet: 0.08 (0.32), residues: 239 loop : -0.85 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 322 HIS 0.009 0.001 HIS P 9 PHE 0.027 0.002 PHE R 227 TYR 0.017 0.001 TYR R 421 ARG 0.015 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.65 seconds wall clock time: 42 minutes 59.88 seconds (2579.88 seconds total)