Starting phenix.real_space_refine on Sat Dec 28 16:43:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vn7_21249/12_2024/6vn7_21249.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vn7_21249/12_2024/6vn7_21249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vn7_21249/12_2024/6vn7_21249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vn7_21249/12_2024/6vn7_21249.map" model { file = "/net/cci-nas-00/data/ceres_data/6vn7_21249/12_2024/6vn7_21249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vn7_21249/12_2024/6vn7_21249.cif" } resolution = 3.2 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= 0.004 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 51 5.16 5 C 5561 2.51 5 N 1459 2.21 5 O 1549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8620 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2171 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 2 Chain: "L" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1981 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 2 Chain: "B" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 240 Unusual residues: {'CLR': 6, 'PLM': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 4.72, per 1000 atoms: 0.55 Number of scatterers: 8620 At special positions: 0 Unit cell: (100.386, 97.344, 131.82, 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 51 16.00 O 1549 8.00 N 1459 7.00 C 5561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 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: 2.20 Conformation dependent library (CDL) restraints added in 1.0 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.3% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'R' and resid 129 through 167 removed outlier: 4.064A pdb=" N GLU R 133 " --> pdb=" O ALA R 129 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU R 154 " --> pdb=" O TYR R 150 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU R 157 " --> pdb=" O SER R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 201 removed outlier: 3.603A pdb=" N ALA R 198 " --> pdb=" O ILE R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 246 removed outlier: 4.001A pdb=" N ALA R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL R 226 " --> pdb=" O PHE R 222 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET R 227 " --> pdb=" O GLN R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 250 through 281 removed outlier: 3.929A pdb=" N TYR R 254 " --> pdb=" O SER R 250 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP R 256 " --> pdb=" O ARG R 252 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY R 257 " --> pdb=" O LYS R 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 260 " --> pdb=" O TRP R 256 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE R 261 " --> pdb=" O GLY R 257 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL R 265 " --> pdb=" O ILE R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix removed outlier: 3.665A pdb=" N GLU R 281 " --> pdb=" O ARG R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 295 Processing helix chain 'R' and resid 298 through 324 removed outlier: 4.198A pdb=" N LEU R 319 " --> pdb=" O ILE R 315 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU R 320 " --> pdb=" O ILE R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 345 Processing helix chain 'R' and resid 346 through 351 Processing helix chain 'R' and resid 352 through 357 Processing helix chain 'R' and resid 365 through 389 removed outlier: 4.359A pdb=" N LYS R 369 " --> pdb=" O LYS R 365 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET R 370 " --> pdb=" O PRO R 366 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE R 372 " --> pdb=" O VAL R 368 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE R 382 " --> pdb=" O SER R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 409 Processing helix chain 'L' and resid 2 through 27 Processing helix chain 'A' and resid 10 through 40 removed outlier: 4.062A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.525A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (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 293 through 300 Processing helix chain 'A' and resid 301 through 304 removed outlier: 4.351A pdb=" N GLY A 304 " --> pdb=" O VAL A 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 304' Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.755A pdb=" N ASP A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.291A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 4.039A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.721A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.605A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.022A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.447A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.902A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.187A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.228A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.838A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.641A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.804A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.559A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.006A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1236 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: 2.36 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2704 1.34 - 1.46: 1975 1.46 - 1.58: 4063 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8815 Sorted by residual: bond pdb=" C VAL R 265 " pdb=" N PRO R 266 " ideal model delta sigma weight residual 1.335 1.363 -0.027 1.36e-02 5.41e+03 4.02e+00 bond pdb=" C PRO R 325 " pdb=" N PRO R 326 " ideal model delta sigma weight residual 1.341 1.372 -0.031 1.60e-02 3.91e+03 3.86e+00 bond pdb=" C5 CLR R 602 " pdb=" C6 CLR R 602 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C ARG R 324 " pdb=" N PRO R 325 " ideal model delta sigma weight residual 1.329 1.348 -0.018 1.18e-02 7.18e+03 2.45e+00 bond pdb=" C5 CLR R 601 " pdb=" C6 CLR R 601 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 8810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 11480 2.13 - 4.26: 395 4.26 - 6.38: 41 6.38 - 8.51: 13 8.51 - 10.64: 5 Bond angle restraints: 11934 Sorted by residual: angle pdb=" CA TYR R 146 " pdb=" CB TYR R 146 " pdb=" CG TYR R 146 " ideal model delta sigma weight residual 113.90 121.11 -7.21 1.80e+00 3.09e-01 1.60e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 122.07 127.37 -5.30 1.43e+00 4.89e-01 1.37e+01 angle pdb=" N GLY R 299 " pdb=" CA GLY R 299 " pdb=" C GLY R 299 " ideal model delta sigma weight residual 112.34 119.31 -6.97 2.04e+00 2.40e-01 1.17e+01 angle pdb=" C MET R 137 " pdb=" N PHE R 138 " pdb=" CA PHE R 138 " ideal model delta sigma weight residual 120.79 125.30 -4.51 1.39e+00 5.18e-01 1.05e+01 angle pdb=" C GLY R 214 " pdb=" N CYS R 215 " pdb=" CA CYS R 215 " ideal model delta sigma weight residual 120.82 125.60 -4.78 1.50e+00 4.44e-01 1.02e+01 ... (remaining 11929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 5277 14.88 - 29.75: 191 29.75 - 44.63: 41 44.63 - 59.51: 8 59.51 - 74.38: 2 Dihedral angle restraints: 5519 sinusoidal: 2465 harmonic: 3054 Sorted by residual: dihedral pdb=" CA ILE R 315 " pdb=" C ILE R 315 " pdb=" N ILE R 316 " pdb=" CA ILE R 316 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.12e+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 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 5516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1172 0.088 - 0.176: 127 0.176 - 0.263: 17 0.263 - 0.351: 6 0.351 - 0.439: 6 Chirality restraints: 1328 Sorted by residual: chirality pdb=" C14 CLR R 606 " pdb=" C13 CLR R 606 " pdb=" C15 CLR R 606 " pdb=" C8 CLR R 606 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" C14 CLR R 603 " pdb=" C13 CLR R 603 " pdb=" C15 CLR R 603 " pdb=" C8 CLR R 603 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" C14 CLR R 604 " pdb=" C13 CLR R 604 " pdb=" C15 CLR R 604 " pdb=" C8 CLR R 604 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1325 not shown) Planarity restraints: 1476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 156 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C THR R 156 " 0.050 2.00e-02 2.50e+03 pdb=" O THR R 156 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU R 157 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO G 49 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 143 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C LYS R 143 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS R 143 " 0.018 2.00e-02 2.50e+03 pdb=" N THR R 144 " 0.016 2.00e-02 2.50e+03 ... (remaining 1473 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1570 2.78 - 3.31: 7564 3.31 - 3.84: 13488 3.84 - 4.37: 15647 4.37 - 4.90: 27482 Nonbonded interactions: 65751 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR A 360 " pdb=" OD2 ASP A 381 " model vdw 2.296 3.040 nonbonded pdb=" OG1 THR R 136 " pdb=" OH TYR L 13 " model vdw 2.297 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.313 3.040 ... (remaining 65746 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 individual isotropic 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: 0.580 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.340 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.004 0.053 8815 Z= 0.265 Angle : 0.904 10.641 11934 Z= 0.498 Chirality : 0.066 0.439 1328 Planarity : 0.007 0.070 1476 Dihedral : 8.803 74.384 3538 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -2.38 (0.22), residues: 1032 helix: -1.35 (0.21), residues: 400 sheet: -1.06 (0.32), residues: 217 loop : -1.94 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 281 HIS 0.016 0.002 HIS A 220 PHE 0.021 0.002 PHE A 246 TYR 0.022 0.002 TYR R 146 ARG 0.006 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 346 LEU cc_start: 0.7925 (tp) cc_final: 0.7593 (mt) REVERT: A 278 ASN cc_start: 0.7809 (m-40) cc_final: 0.7490 (m110) REVERT: A 344 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8455 (mm-30) REVERT: A 378 ASP cc_start: 0.8226 (m-30) cc_final: 0.7950 (m-30) REVERT: B 256 ARG cc_start: 0.7535 (mmm160) cc_final: 0.7247 (mtm-85) REVERT: N 80 TYR cc_start: 0.8375 (m-80) cc_final: 0.7815 (m-80) REVERT: N 95 TYR cc_start: 0.8904 (m-10) cc_final: 0.8699 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3159 time to fit residues: 83.9179 Evaluate side-chains 132 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 GLN ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN R 279 HIS R 363 ASN ** L 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 220 HIS A 254 ASN B 91 HIS B 259 GLN B 266 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8815 Z= 0.192 Angle : 0.550 12.360 11934 Z= 0.282 Chirality : 0.042 0.160 1328 Planarity : 0.005 0.060 1476 Dihedral : 6.462 58.362 1597 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.22 % Allowed : 6.99 % Favored : 90.79 % 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 (0.25), residues: 1032 helix: 1.35 (0.24), residues: 407 sheet: -0.55 (0.33), residues: 207 loop : -1.40 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.018 0.002 PHE A 315 TYR 0.026 0.001 TYR R 146 ARG 0.004 0.000 ARG L 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 137 MET cc_start: 0.7896 (ttt) cc_final: 0.7604 (ttt) REVERT: R 223 GLN cc_start: 0.7831 (mm110) cc_final: 0.7618 (mm-40) REVERT: R 227 MET cc_start: 0.8036 (ttm) cc_final: 0.7793 (mtt) REVERT: A 33 ASP cc_start: 0.8091 (t70) cc_final: 0.7783 (t70) REVERT: B 32 GLN cc_start: 0.7386 (mt0) cc_final: 0.7162 (mt0) REVERT: G 21 MET cc_start: 0.6525 (tmm) cc_final: 0.5514 (tpp) REVERT: N 80 TYR cc_start: 0.8548 (m-80) cc_final: 0.7527 (m-80) outliers start: 20 outliers final: 15 residues processed: 162 average time/residue: 0.2433 time to fit residues: 52.4189 Evaluate side-chains 145 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 161 THR Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.0470 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8815 Z= 0.184 Angle : 0.517 10.837 11934 Z= 0.265 Chirality : 0.041 0.141 1328 Planarity : 0.004 0.053 1476 Dihedral : 6.243 59.858 1597 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.00 % Allowed : 8.99 % Favored : 89.01 % 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: 0.55 (0.26), residues: 1032 helix: 2.28 (0.25), residues: 406 sheet: -0.37 (0.33), residues: 212 loop : -1.21 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.003 0.001 HIS A 220 PHE 0.016 0.001 PHE A 315 TYR 0.023 0.001 TYR R 146 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: R 137 MET cc_start: 0.7832 (ttt) cc_final: 0.7552 (ttt) REVERT: B 32 GLN cc_start: 0.7358 (mt0) cc_final: 0.7110 (mt0) REVERT: B 325 MET cc_start: 0.8105 (tpp) cc_final: 0.7898 (mmt) REVERT: G 21 MET cc_start: 0.6560 (tmm) cc_final: 0.5582 (tpp) REVERT: N 80 TYR cc_start: 0.8779 (m-80) cc_final: 0.7672 (m-80) outliers start: 18 outliers final: 13 residues processed: 140 average time/residue: 0.2706 time to fit residues: 49.7941 Evaluate side-chains 134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN A 371 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8815 Z= 0.255 Angle : 0.550 9.790 11934 Z= 0.284 Chirality : 0.042 0.134 1328 Planarity : 0.004 0.057 1476 Dihedral : 6.504 57.920 1597 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.77 % Allowed : 9.88 % Favored : 87.35 % 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: 0.70 (0.27), residues: 1032 helix: 2.38 (0.25), residues: 411 sheet: -0.37 (0.34), residues: 216 loop : -1.09 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.005 0.001 HIS B 54 PHE 0.014 0.002 PHE N 108 TYR 0.023 0.002 TYR R 146 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.971 Fit side-chains REVERT: R 137 MET cc_start: 0.7927 (ttt) cc_final: 0.7694 (ttt) REVERT: A 317 ARG cc_start: 0.7977 (ttp-170) cc_final: 0.7685 (mpp-170) REVERT: B 32 GLN cc_start: 0.7528 (mt0) cc_final: 0.7309 (mt0) REVERT: G 21 MET cc_start: 0.6562 (tmm) cc_final: 0.5533 (tpp) REVERT: N 90 ASP cc_start: 0.8351 (m-30) cc_final: 0.8067 (m-30) outliers start: 25 outliers final: 23 residues processed: 150 average time/residue: 0.2562 time to fit residues: 50.6105 Evaluate side-chains 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 161 THR Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 321 GLN Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 363 ASN Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 0.0050 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 220 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8815 Z= 0.232 Angle : 0.533 9.577 11934 Z= 0.273 Chirality : 0.042 0.136 1328 Planarity : 0.004 0.054 1476 Dihedral : 6.540 56.524 1597 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.33 % Allowed : 10.65 % Favored : 86.02 % 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: 0.78 (0.27), residues: 1032 helix: 2.50 (0.25), residues: 407 sheet: -0.45 (0.33), residues: 218 loop : -1.00 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 232 HIS 0.004 0.001 HIS B 54 PHE 0.012 0.001 PHE N 108 TYR 0.022 0.001 TYR R 146 ARG 0.007 0.000 ARG L 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.976 Fit side-chains REVERT: R 137 MET cc_start: 0.7925 (ttt) cc_final: 0.7673 (ttt) REVERT: R 219 MET cc_start: 0.7222 (mmm) cc_final: 0.6948 (mmm) REVERT: A 224 VAL cc_start: 0.8091 (t) cc_final: 0.7816 (m) REVERT: B 76 ASP cc_start: 0.8398 (p0) cc_final: 0.8053 (p0) REVERT: B 101 MET cc_start: 0.9230 (mtp) cc_final: 0.9021 (mtp) REVERT: G 21 MET cc_start: 0.6629 (tmm) cc_final: 0.5534 (tpp) REVERT: N 90 ASP cc_start: 0.8311 (m-30) cc_final: 0.8004 (m-30) REVERT: N 95 TYR cc_start: 0.8990 (m-80) cc_final: 0.8667 (m-80) outliers start: 30 outliers final: 25 residues processed: 149 average time/residue: 0.2385 time to fit residues: 47.4454 Evaluate side-chains 147 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 161 THR Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 321 GLN Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 363 ASN Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 0.0370 chunk 11 optimal weight: 0.4980 chunk 56 optimal weight: 0.4980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 GLN L 1 HIS A 14 ASN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8815 Z= 0.131 Angle : 0.477 9.954 11934 Z= 0.243 Chirality : 0.040 0.140 1328 Planarity : 0.003 0.047 1476 Dihedral : 6.168 51.960 1597 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.00 % Allowed : 12.32 % Favored : 85.68 % 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: 1.12 (0.27), residues: 1032 helix: 2.87 (0.26), residues: 406 sheet: -0.37 (0.33), residues: 228 loop : -0.84 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 339 HIS 0.003 0.001 HIS B 311 PHE 0.009 0.001 PHE A 222 TYR 0.018 0.001 TYR R 146 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 137 MET cc_start: 0.7862 (ttt) cc_final: 0.7607 (ttt) REVERT: A 224 VAL cc_start: 0.8026 (t) cc_final: 0.7778 (m) REVERT: B 32 GLN cc_start: 0.7646 (mt0) cc_final: 0.7412 (mt0) REVERT: B 76 ASP cc_start: 0.8368 (p0) cc_final: 0.8074 (p0) REVERT: B 101 MET cc_start: 0.9232 (mtp) cc_final: 0.9023 (mtp) REVERT: G 21 MET cc_start: 0.6569 (tmm) cc_final: 0.5477 (tpp) outliers start: 18 outliers final: 15 residues processed: 146 average time/residue: 0.2643 time to fit residues: 50.8913 Evaluate side-chains 143 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8815 Z= 0.194 Angle : 0.511 9.655 11934 Z= 0.261 Chirality : 0.041 0.134 1328 Planarity : 0.004 0.053 1476 Dihedral : 6.325 55.084 1597 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.66 % Allowed : 12.21 % Favored : 85.13 % 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: 1.10 (0.27), residues: 1032 helix: 2.89 (0.25), residues: 405 sheet: -0.45 (0.33), residues: 229 loop : -0.85 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.004 0.001 HIS B 54 PHE 0.011 0.001 PHE N 108 TYR 0.020 0.001 TYR R 146 ARG 0.008 0.000 ARG L 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 137 MET cc_start: 0.7897 (ttt) cc_final: 0.7639 (ttt) REVERT: A 224 VAL cc_start: 0.7988 (t) cc_final: 0.7696 (m) REVERT: B 44 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: B 101 MET cc_start: 0.9269 (mtp) cc_final: 0.9036 (mtp) REVERT: B 105 TYR cc_start: 0.8216 (t80) cc_final: 0.7228 (t80) REVERT: G 21 MET cc_start: 0.6576 (tmm) cc_final: 0.5516 (tpp) outliers start: 24 outliers final: 22 residues processed: 135 average time/residue: 0.2583 time to fit residues: 45.6440 Evaluate side-chains 149 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 321 GLN Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 363 ASN Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 290 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8815 Z= 0.173 Angle : 0.498 9.431 11934 Z= 0.256 Chirality : 0.041 0.136 1328 Planarity : 0.004 0.051 1476 Dihedral : 6.244 58.090 1597 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.55 % Allowed : 12.43 % Favored : 85.02 % 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: 1.15 (0.27), residues: 1032 helix: 2.97 (0.25), residues: 404 sheet: -0.44 (0.33), residues: 228 loop : -0.84 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.003 0.001 HIS R 178 PHE 0.009 0.001 PHE B 234 TYR 0.020 0.001 TYR R 146 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: R 137 MET cc_start: 0.7871 (ttt) cc_final: 0.7619 (ttt) REVERT: A 224 VAL cc_start: 0.8029 (t) cc_final: 0.7768 (m) REVERT: G 21 MET cc_start: 0.6574 (tmm) cc_final: 0.5508 (tpp) REVERT: N 77 ASN cc_start: 0.8101 (m-40) cc_final: 0.7585 (m110) outliers start: 23 outliers final: 21 residues processed: 136 average time/residue: 0.2899 time to fit residues: 51.5153 Evaluate side-chains 141 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 363 ASN Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8815 Z= 0.276 Angle : 0.570 9.860 11934 Z= 0.294 Chirality : 0.043 0.138 1328 Planarity : 0.004 0.058 1476 Dihedral : 6.612 55.459 1597 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.77 % Allowed : 12.32 % Favored : 84.91 % 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: 0.87 (0.27), residues: 1032 helix: 2.60 (0.25), residues: 410 sheet: -0.56 (0.33), residues: 229 loop : -0.90 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 339 HIS 0.006 0.001 HIS B 54 PHE 0.015 0.002 PHE N 108 TYR 0.022 0.002 TYR R 146 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: R 137 MET cc_start: 0.7832 (ttt) cc_final: 0.7585 (ttt) REVERT: A 317 ARG cc_start: 0.7825 (ttp-170) cc_final: 0.7459 (mpp-170) REVERT: G 21 MET cc_start: 0.6538 (tmm) cc_final: 0.5528 (tpp) REVERT: N 77 ASN cc_start: 0.8081 (m-40) cc_final: 0.7579 (m110) outliers start: 25 outliers final: 23 residues processed: 126 average time/residue: 0.2564 time to fit residues: 42.8330 Evaluate side-chains 137 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 321 GLN Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 363 ASN Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.0040 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8815 Z= 0.161 Angle : 0.496 9.313 11934 Z= 0.255 Chirality : 0.040 0.137 1328 Planarity : 0.004 0.048 1476 Dihedral : 6.200 56.305 1597 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.44 % Allowed : 13.32 % Favored : 84.24 % 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: 1.08 (0.27), residues: 1032 helix: 2.85 (0.25), residues: 410 sheet: -0.47 (0.33), residues: 228 loop : -0.88 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 232 HIS 0.003 0.001 HIS R 178 PHE 0.010 0.001 PHE B 234 TYR 0.019 0.001 TYR R 146 ARG 0.006 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: R 137 MET cc_start: 0.7804 (ttt) cc_final: 0.7559 (ttt) REVERT: A 224 VAL cc_start: 0.8021 (t) cc_final: 0.7743 (m) REVERT: A 317 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7430 (mpp-170) REVERT: B 32 GLN cc_start: 0.7540 (mt0) cc_final: 0.7266 (tt0) REVERT: G 21 MET cc_start: 0.6577 (tmm) cc_final: 0.5505 (tpp) REVERT: N 77 ASN cc_start: 0.8065 (m-40) cc_final: 0.7564 (m110) REVERT: N 94 TYR cc_start: 0.8816 (m-80) cc_final: 0.8503 (m-80) outliers start: 22 outliers final: 19 residues processed: 135 average time/residue: 0.2692 time to fit residues: 48.6913 Evaluate side-chains 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.0270 chunk 81 optimal weight: 0.0870 chunk 33 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.213866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.172249 restraints weight = 9326.878| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.64 r_work: 0.3903 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 8815 Z= 0.133 Angle : 0.475 9.217 11934 Z= 0.245 Chirality : 0.040 0.147 1328 Planarity : 0.003 0.046 1476 Dihedral : 5.809 52.291 1597 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.11 % Allowed : 13.54 % Favored : 84.35 % 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: 1.23 (0.27), residues: 1032 helix: 2.99 (0.25), residues: 411 sheet: -0.37 (0.33), residues: 228 loop : -0.83 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 232 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE B 241 TYR 0.017 0.001 TYR R 146 ARG 0.005 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2088.60 seconds wall clock time: 38 minutes 39.93 seconds (2319.93 seconds total)