Starting phenix.real_space_refine on Fri Sep 11 09:19:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vn7_21249/09_2026/6vn7_21249.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vn7_21249/09_2026/6vn7_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6vn7_21249/09_2026/6vn7_21249.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vn7_21249/09_2026/6vn7_21249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vn7_21249/09_2026/6vn7_21249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vn7_21249/09_2026/6vn7_21249.map" model { file = "/net/cci-nas-00/data/ceres_data/6vn7_21249/09_2026/6vn7_21249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vn7_21249/09_2026/6vn7_21249.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 2.05, per 1000 atoms: 0.24 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: 0.72 Conformation dependent library (CDL) restraints added in 479.0 milliseconds 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: 0.25 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: 1.36 Time building geometry restraints manager: 0.97 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: 4975 14.88 - 29.75: 172 29.75 - 44.63: 30 44.63 - 59.51: 4 59.51 - 74.38: 2 Dihedral angle restraints: 5183 sinusoidal: 2129 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 5180 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 8818 Z= 0.226 Angle : 0.905 10.641 11940 Z= 0.498 Chirality : 0.066 0.439 1328 Planarity : 0.007 0.070 1476 Dihedral : 8.540 74.384 3202 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (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 ARG 0.006 0.000 ARG N 118 TYR 0.022 0.002 TYR R 146 PHE 0.021 0.002 PHE A 246 TRP 0.018 0.002 TRP A 281 HIS 0.016 0.002 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.23 ( 8815) covalent geometry : angle 0.90408 / 0.50 (11934) SS BOND : bond 0.00204 / 0.07 ( 3) SS BOND : angle 2.06536 / 1.14 ( 6) hydrogen bonds : bond 0.11880 / 8.50 ( 431) hydrogen bonds : angle 6.33938 / 4.39 ( 1236) *********************** 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 : 0.281 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: 0.7594 (mt) REVERT: A 278 ASN cc_start: 0.7809 (m-40) cc_final: 0.7489 (m110) REVERT: A 344 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8446 (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: 0.8700 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1371 time to fit residues: 36.5350 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 : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.216053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.179480 restraints weight = 9552.751| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.29 r_work: 0.3958 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8818 Z= 0.116 Angle : 0.539 12.229 11940 Z= 0.277 Chirality : 0.041 0.165 1328 Planarity : 0.005 0.059 1476 Dihedral : 5.604 58.422 1261 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.89 % Allowed : 6.99 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.25), residues: 1032 helix: 1.33 (0.24), residues: 407 sheet: -0.52 (0.33), residues: 216 loop : -1.36 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.026 0.001 TYR R 146 PHE 0.020 0.002 PHE A 315 TRP 0.024 0.002 TRP B 169 HIS 0.002 0.001 HIS R 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8815) covalent geometry : angle 0.53693 / 0.28 (11934) SS BOND : bond 0.00167 / 0.06 ( 3) SS BOND : angle 2.10862 / 1.32 ( 6) hydrogen bonds : bond 0.03806 / 2.51 ( 431) hydrogen bonds : angle 4.60345 / 3.29 ( 1236) *********************** 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 169 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: R 227 MET cc_start: 0.7664 (ttm) cc_final: 0.7411 (mtt) REVERT: A 33 ASP cc_start: 0.7338 (t70) cc_final: 0.7040 (t70) REVERT: A 309 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: G 21 MET cc_start: 0.6390 (tmm) cc_final: 0.5473 (tpp) REVERT: N 80 TYR cc_start: 0.8210 (m-80) cc_final: 0.7213 (m-80) REVERT: N 82 GLN cc_start: 0.8022 (tp40) cc_final: 0.7675 (tp40) outliers start: 17 outliers final: 13 residues processed: 159 average time/residue: 0.1105 time to fit residues: 23.4272 Evaluate side-chains 144 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 407 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 309 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 6 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 363 ASN ** L 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 32 GLN B 220 GLN B 259 GLN N 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.213471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.177662 restraints weight = 9485.876| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.18 r_work: 0.3924 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8818 Z= 0.101 Angle : 0.488 11.200 11940 Z= 0.251 Chirality : 0.040 0.142 1328 Planarity : 0.004 0.052 1476 Dihedral : 5.273 57.710 1261 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.78 % Allowed : 9.32 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1032 helix: 2.47 (0.25), residues: 404 sheet: -0.39 (0.33), residues: 219 loop : -1.16 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 27 TYR 0.022 0.001 TYR R 146 PHE 0.014 0.001 PHE A 315 TRP 0.018 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 8815) covalent geometry : angle 0.48705 / 0.25 (11934) SS BOND : bond 0.00107 / 0.05 ( 3) SS BOND : angle 1.70436 / 1.08 ( 6) hydrogen bonds : bond 0.03356 / 2.19 ( 431) hydrogen bonds : angle 4.16959 / 2.99 ( 1236) *********************** 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 155 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 227 MET cc_start: 0.7636 (ttm) cc_final: 0.7430 (mtt) REVERT: R 321 GLN cc_start: 0.8147 (tt0) cc_final: 0.7942 (tt0) REVERT: A 33 ASP cc_start: 0.7401 (t70) cc_final: 0.7148 (t70) REVERT: B 163 ASP cc_start: 0.7567 (p0) cc_final: 0.7366 (p0) REVERT: G 21 MET cc_start: 0.6300 (tmm) cc_final: 0.5409 (tpp) REVERT: N 80 TYR cc_start: 0.8434 (m-80) cc_final: 0.7303 (m-80) outliers start: 16 outliers final: 12 residues processed: 146 average time/residue: 0.1288 time to fit residues: 24.7337 Evaluate side-chains 139 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER 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 407 HIS 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 110 VAL Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 363 ASN L 1 HIS A 14 ASN A 371 ASN B 32 GLN B 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.204275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.168880 restraints weight = 9649.594| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.05 r_work: 0.3850 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8818 Z= 0.153 Angle : 0.540 9.998 11940 Z= 0.278 Chirality : 0.042 0.133 1328 Planarity : 0.004 0.057 1476 Dihedral : 5.808 58.508 1261 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.55 % Allowed : 9.43 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.27), residues: 1032 helix: 2.55 (0.25), residues: 411 sheet: -0.43 (0.33), residues: 218 loop : -1.03 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.023 0.001 TYR R 146 PHE 0.013 0.002 PHE N 108 TRP 0.029 0.002 TRP B 169 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 8815) covalent geometry : angle 0.53881 / 0.28 (11934) SS BOND : bond 0.00052 / 0.02 ( 3) SS BOND : angle 1.73458 / 1.09 ( 6) hydrogen bonds : bond 0.03857 / 2.50 ( 431) hydrogen bonds : angle 4.30032 / 3.09 ( 1236) *********************** 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 158 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.314 Fit side-chains REVERT: R 227 MET cc_start: 0.7917 (ttm) cc_final: 0.7681 (mtt) REVERT: A 224 VAL cc_start: 0.8273 (t) cc_final: 0.7918 (p) REVERT: G 21 MET cc_start: 0.6287 (tmm) cc_final: 0.5382 (tpp) REVERT: N 80 TYR cc_start: 0.8780 (m-80) cc_final: 0.7576 (m-80) outliers start: 23 outliers final: 19 residues processed: 146 average time/residue: 0.1055 time to fit residues: 20.7675 Evaluate side-chains 145 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER 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 407 HIS Chi-restraints excluded: chain A residue 263 THR 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 84 ASN Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.0030 chunk 22 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 290 ASN A 14 ASN B 32 GLN B 220 GLN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.203034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.167213 restraints weight = 9615.275| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.07 r_work: 0.3869 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8818 Z= 0.146 Angle : 0.533 11.319 11940 Z= 0.272 Chirality : 0.041 0.134 1328 Planarity : 0.004 0.054 1476 Dihedral : 5.957 56.129 1261 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.66 % Allowed : 10.65 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 1032 helix: 2.67 (0.25), residues: 405 sheet: -0.50 (0.32), residues: 229 loop : -0.94 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.022 0.001 TYR R 146 PHE 0.012 0.001 PHE N 108 TRP 0.023 0.002 TRP B 169 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 8815) covalent geometry : angle 0.53220 / 0.27 (11934) SS BOND : bond 0.00078 / 0.04 ( 3) SS BOND : angle 1.70270 / 1.07 ( 6) hydrogen bonds : bond 0.03721 / 2.41 ( 431) hydrogen bonds : angle 4.16121 / 2.99 ( 1236) *********************** 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 160 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 224 VAL cc_start: 0.8363 (t) cc_final: 0.8021 (p) REVERT: A 307 LYS cc_start: 0.4544 (tmtt) cc_final: 0.3049 (mttm) REVERT: A 378 ASP cc_start: 0.7881 (m-30) cc_final: 0.7613 (m-30) REVERT: G 21 MET cc_start: 0.6292 (tmm) cc_final: 0.5344 (tpp) REVERT: N 95 TYR cc_start: 0.9094 (m-80) cc_final: 0.8790 (m-80) REVERT: N 111 THR cc_start: 0.8045 (m) cc_final: 0.7836 (p) outliers start: 24 outliers final: 19 residues processed: 147 average time/residue: 0.1117 time to fit residues: 21.9270 Evaluate side-chains 141 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 407 HIS Chi-restraints excluded: chain A residue 263 THR 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 B residue 312 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.205193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.170492 restraints weight = 9428.064| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.01 r_work: 0.3894 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8818 Z= 0.108 Angle : 0.498 9.777 11940 Z= 0.254 Chirality : 0.040 0.136 1328 Planarity : 0.003 0.050 1476 Dihedral : 5.747 48.258 1261 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.00 % Allowed : 11.21 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 1032 helix: 2.85 (0.25), residues: 405 sheet: -0.46 (0.32), residues: 229 loop : -0.87 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 12 TYR 0.020 0.001 TYR R 146 PHE 0.013 0.001 PHE R 138 TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 8815) covalent geometry : angle 0.49743 / 0.25 (11934) SS BOND : bond 0.00066 / 0.03 ( 3) SS BOND : angle 1.52268 / 0.96 ( 6) hydrogen bonds : bond 0.03405 / 2.21 ( 431) hydrogen bonds : angle 3.99449 / 2.87 ( 1236) *********************** 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 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 VAL cc_start: 0.8304 (t) cc_final: 0.7967 (m) REVERT: B 219 ARG cc_start: 0.7307 (mmt90) cc_final: 0.7076 (mmt90) REVERT: G 21 MET cc_start: 0.6396 (tmm) cc_final: 0.5420 (tpp) REVERT: N 95 TYR cc_start: 0.9059 (m-80) cc_final: 0.8824 (m-80) outliers start: 18 outliers final: 17 residues processed: 141 average time/residue: 0.1140 time to fit residues: 21.5135 Evaluate side-chains 145 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 15 GLU 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 B residue 312 ASP Chi-restraints excluded: chain N residue 30 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 223 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.207235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.172843 restraints weight = 9532.324| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.01 r_work: 0.3909 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8818 Z= 0.103 Angle : 0.485 9.323 11940 Z= 0.249 Chirality : 0.040 0.137 1328 Planarity : 0.003 0.050 1476 Dihedral : 5.553 54.226 1261 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.00 % Allowed : 11.43 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.27), residues: 1032 helix: 3.01 (0.25), residues: 404 sheet: -0.36 (0.33), residues: 228 loop : -0.89 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 12 TYR 0.019 0.001 TYR R 146 PHE 0.014 0.001 PHE R 138 TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 8815) covalent geometry : angle 0.48440 / 0.25 (11934) SS BOND : bond 0.00080 / 0.04 ( 3) SS BOND : angle 1.50814 / 0.95 ( 6) hydrogen bonds : bond 0.03233 / 2.09 ( 431) hydrogen bonds : angle 3.83869 / 2.76 ( 1236) *********************** 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 156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 VAL cc_start: 0.8281 (t) cc_final: 0.7969 (m) REVERT: A 370 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7218 (mt-10) REVERT: B 134 ARG cc_start: 0.6646 (ptt-90) cc_final: 0.6038 (mmp80) REVERT: G 21 MET cc_start: 0.6317 (tmm) cc_final: 0.5368 (tpp) outliers start: 18 outliers final: 15 residues processed: 148 average time/residue: 0.1049 time to fit residues: 20.9474 Evaluate side-chains 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 263 THR 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 312 ASP Chi-restraints excluded: chain N residue 30 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.206594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.171662 restraints weight = 9459.326| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.05 r_work: 0.3906 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8818 Z= 0.107 Angle : 0.491 9.604 11940 Z= 0.253 Chirality : 0.040 0.137 1328 Planarity : 0.003 0.050 1476 Dihedral : 5.559 58.460 1261 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.22 % Allowed : 11.65 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.27), residues: 1032 helix: 3.04 (0.25), residues: 404 sheet: -0.38 (0.33), residues: 229 loop : -0.87 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 12 TYR 0.019 0.001 TYR R 146 PHE 0.014 0.001 PHE R 138 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 8815) covalent geometry : angle 0.49038 / 0.25 (11934) SS BOND : bond 0.00078 / 0.04 ( 3) SS BOND : angle 1.49245 / 0.94 ( 6) hydrogen bonds : bond 0.03246 / 2.10 ( 431) hydrogen bonds : angle 3.84114 / 2.76 ( 1236) *********************** 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 147 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7415 (tt0) cc_final: 0.7202 (pt0) REVERT: A 224 VAL cc_start: 0.8230 (t) cc_final: 0.7917 (m) REVERT: B 44 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7851 (mp10) REVERT: B 134 ARG cc_start: 0.6665 (ptt-90) cc_final: 0.6060 (mmp80) REVERT: B 219 ARG cc_start: 0.7378 (mmt90) cc_final: 0.7077 (mmt90) REVERT: B 234 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: G 21 MET cc_start: 0.6347 (tmm) cc_final: 0.5394 (tpp) outliers start: 20 outliers final: 18 residues processed: 138 average time/residue: 0.1065 time to fit residues: 19.7966 Evaluate side-chains 144 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 15 GLU Chi-restraints excluded: chain A residue 263 THR 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 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 312 ASP 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 83 MET 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 9 optimal weight: 0.2980 chunk 4 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 41 optimal weight: 0.0050 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.209287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.175119 restraints weight = 9387.356| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.02 r_work: 0.3931 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8818 Z= 0.090 Angle : 0.466 9.285 11940 Z= 0.240 Chirality : 0.039 0.137 1328 Planarity : 0.003 0.047 1476 Dihedral : 5.264 54.758 1261 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.00 % Allowed : 11.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.27), residues: 1032 helix: 3.07 (0.25), residues: 412 sheet: -0.28 (0.33), residues: 228 loop : -0.98 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.018 0.001 TYR R 146 PHE 0.015 0.001 PHE R 138 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 ( 8815) covalent geometry : angle 0.46535 / 0.24 (11934) SS BOND : bond 0.00067 / 0.03 ( 3) SS BOND : angle 1.47564 / 0.93 ( 6) hydrogen bonds : bond 0.02989 / 1.93 ( 431) hydrogen bonds : angle 3.70972 / 2.67 ( 1236) *********************** 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 143 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7406 (tt0) cc_final: 0.7160 (pt0) REVERT: A 224 VAL cc_start: 0.8098 (t) cc_final: 0.7801 (m) REVERT: A 307 LYS cc_start: 0.4342 (tmtt) cc_final: 0.3024 (mttm) REVERT: A 370 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7157 (mt-10) REVERT: B 134 ARG cc_start: 0.6611 (ptt-90) cc_final: 0.5996 (mmp80) REVERT: B 234 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: G 21 MET cc_start: 0.6339 (tmm) cc_final: 0.5362 (tpp) outliers start: 18 outliers final: 16 residues processed: 137 average time/residue: 0.1047 time to fit residues: 19.3961 Evaluate side-chains 140 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 15 GLU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE 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 N residue 30 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 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 41 optimal weight: 0.4980 chunk 86 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 223 GLN B 32 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.203432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.168249 restraints weight = 9542.284| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.07 r_work: 0.3881 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8818 Z= 0.144 Angle : 0.539 9.805 11940 Z= 0.278 Chirality : 0.041 0.131 1328 Planarity : 0.004 0.055 1476 Dihedral : 5.697 50.225 1261 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.00 % Allowed : 12.43 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.27), residues: 1032 helix: 2.89 (0.25), residues: 410 sheet: -0.42 (0.33), residues: 229 loop : -0.88 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 12 TYR 0.021 0.001 TYR R 146 PHE 0.015 0.001 PHE R 138 TRP 0.033 0.002 TRP B 169 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 8815) covalent geometry : angle 0.53765 / 0.28 (11934) SS BOND : bond 0.00072 / 0.04 ( 3) SS BOND : angle 1.52942 / 0.96 ( 6) hydrogen bonds : bond 0.03617 / 2.34 ( 431) hydrogen bonds : angle 3.95308 / 2.84 ( 1236) ********************** 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 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: R 368 VAL cc_start: 0.7209 (p) cc_final: 0.6999 (p) REVERT: A 224 VAL cc_start: 0.8135 (t) cc_final: 0.7825 (m) REVERT: A 317 ARG cc_start: 0.7599 (ttp-170) cc_final: 0.7150 (mpp-170) REVERT: B 219 ARG cc_start: 0.7460 (mmt90) cc_final: 0.7202 (mmt90) REVERT: B 234 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8560 (m-80) REVERT: G 21 MET cc_start: 0.6422 (tmm) cc_final: 0.5409 (tpp) outliers start: 18 outliers final: 15 residues processed: 128 average time/residue: 0.1075 time to fit residues: 18.4959 Evaluate side-chains 134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE 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 N residue 30 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 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 101 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 254 ASN B 32 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.206800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.164988 restraints weight = 9283.187| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.65 r_work: 0.3845 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8818 Z= 0.111 Angle : 0.509 9.526 11940 Z= 0.264 Chirality : 0.040 0.167 1328 Planarity : 0.004 0.050 1476 Dihedral : 5.535 46.117 1261 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.27), residues: 1032 helix: 2.96 (0.25), residues: 408 sheet: -0.37 (0.33), residues: 228 loop : -0.88 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.019 0.001 TYR R 146 PHE 0.014 0.001 PHE R 138 TRP 0.034 0.002 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 8815) covalent geometry : angle 0.50790 / 0.26 (11934) SS BOND : bond 0.00074 / 0.04 ( 3) SS BOND : angle 1.50508 / 0.95 ( 6) hydrogen bonds : bond 0.03307 / 2.14 ( 431) hydrogen bonds : angle 3.85411 / 2.77 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.41 seconds wall clock time: 40 minutes 19.73 seconds (2419.73 seconds total)