Starting phenix.real_space_refine on Tue Mar 3 21:30:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vn7_21249/03_2026/6vn7_21249.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vn7_21249/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vn7_21249/03_2026/6vn7_21249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vn7_21249/03_2026/6vn7_21249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vn7_21249/03_2026/6vn7_21249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vn7_21249/03_2026/6vn7_21249.map" } 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-dev-5986/lib/python3.9/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: 2.03, 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: 0.70 Conformation dependent library (CDL) restraints added in 319.7 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: 0.19 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: 1.14 Time building geometry restraints manager: 0.95 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.060 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- 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 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 : 8.803 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 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 covalent geometry : bond 0.00406 ( 8815) covalent geometry : angle 0.90408 (11934) SS BOND : bond 0.00204 ( 3) SS BOND : angle 2.06536 ( 6) hydrogen bonds : bond 0.11880 ( 431) hydrogen bonds : angle 6.33938 ( 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 : 0.300 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: 0.1354 time to fit residues: 35.7457 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 : 0.361 ------------------------------------------------------------------------------- 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... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.216109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179592 restraints weight = 9550.021| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.28 r_work: 0.3956 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2211 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= 0.115 Angle : 0.539 12.452 11940 Z= 0.277 Chirality : 0.042 0.169 1328 Planarity : 0.004 0.057 1476 Dihedral : 6.437 58.507 1597 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.66 % Allowed : 7.55 % 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 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: -0.16 (0.25), residues: 1032 helix: 1.35 (0.24), residues: 407 sheet: -0.49 (0.34), residues: 216 loop : -1.37 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.027 0.001 TYR R 146 PHE 0.019 0.002 PHE A 315 TRP 0.025 0.002 TRP B 169 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8815) covalent geometry : angle 0.53697 (11934) SS BOND : bond 0.00260 ( 3) SS BOND : angle 2.12920 ( 6) hydrogen bonds : bond 0.03808 ( 431) hydrogen bonds : angle 4.62380 ( 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 168 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: R 227 MET cc_start: 0.7668 (ttm) cc_final: 0.7408 (mtt) REVERT: A 33 ASP cc_start: 0.7344 (t70) cc_final: 0.7053 (t70) REVERT: G 21 MET cc_start: 0.6382 (tmm) cc_final: 0.5475 (tpp) REVERT: N 80 TYR cc_start: 0.8219 (m-80) cc_final: 0.7292 (m-80) REVERT: N 82 GLN cc_start: 0.8011 (tp40) cc_final: 0.7661 (tp40) outliers start: 15 outliers final: 10 residues processed: 159 average time/residue: 0.1072 time to fit residues: 22.6671 Evaluate side-chains 137 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 323 LEU Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 263 THR 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 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 363 ASN L 1 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 = 0.4393 r_free = 0.4393 target = 0.210635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.175014 restraints weight = 9498.334| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.13 r_work: 0.3901 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8818 Z= 0.116 Angle : 0.508 11.453 11940 Z= 0.260 Chirality : 0.041 0.141 1328 Planarity : 0.004 0.053 1476 Dihedral : 6.137 59.161 1597 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.22 % Allowed : 9.10 % Favored : 88.68 % 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: 0.63 (0.26), residues: 1032 helix: 2.36 (0.25), residues: 404 sheet: -0.37 (0.33), residues: 225 loop : -1.15 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.023 0.001 TYR R 146 PHE 0.015 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 covalent geometry : bond 0.00261 ( 8815) covalent geometry : angle 0.50646 (11934) SS BOND : bond 0.00065 ( 3) SS BOND : angle 1.80917 ( 6) hydrogen bonds : bond 0.03542 ( 431) hydrogen bonds : angle 4.25022 ( 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: 20 poor density : 135 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: R 227 MET cc_start: 0.7730 (ttm) cc_final: 0.7514 (mtt) REVERT: A 33 ASP cc_start: 0.7532 (t70) cc_final: 0.7199 (t70) REVERT: B 163 ASP cc_start: 0.7807 (p0) cc_final: 0.7554 (p0) REVERT: B 219 ARG cc_start: 0.7124 (mmt90) cc_final: 0.6897 (mmt90) REVERT: G 21 MET cc_start: 0.6308 (tmm) cc_final: 0.5391 (tpp) REVERT: N 80 TYR cc_start: 0.8543 (m-80) cc_final: 0.7375 (m-80) REVERT: N 82 GLN cc_start: 0.8035 (tp40) cc_final: 0.7752 (tp40) outliers start: 20 outliers final: 14 residues processed: 145 average time/residue: 0.1180 time to fit residues: 22.4262 Evaluate side-chains 140 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 99 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 290 ASN R 363 ASN 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 = 0.4327 r_free = 0.4327 target = 0.203160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.167519 restraints weight = 9630.633| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.07 r_work: 0.3841 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8818 Z= 0.148 Angle : 0.536 9.824 11940 Z= 0.275 Chirality : 0.042 0.137 1328 Planarity : 0.004 0.056 1476 Dihedral : 6.309 59.652 1597 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.55 % Allowed : 9.32 % Favored : 88.12 % 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: 0.87 (0.27), residues: 1032 helix: 2.61 (0.25), residues: 405 sheet: -0.35 (0.33), residues: 216 loop : -1.01 (0.31), residues: 411 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 0.012 0.002 PHE N 108 TRP 0.025 0.002 TRP B 339 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8815) covalent geometry : angle 0.53509 (11934) SS BOND : bond 0.00048 ( 3) SS BOND : angle 1.77915 ( 6) hydrogen bonds : bond 0.03850 ( 431) hydrogen bonds : angle 4.26503 ( 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 166 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.318 Fit side-chains REVERT: R 227 MET cc_start: 0.7932 (ttm) cc_final: 0.7700 (mtt) REVERT: A 224 VAL cc_start: 0.8299 (t) cc_final: 0.7925 (m) REVERT: A 307 LYS cc_start: 0.4580 (tmtt) cc_final: 0.3224 (mttm) REVERT: B 219 ARG cc_start: 0.7537 (mmt90) cc_final: 0.7284 (mmt90) REVERT: G 21 MET cc_start: 0.6318 (tmm) cc_final: 0.5411 (tpp) REVERT: N 82 GLN cc_start: 0.8183 (tp40) cc_final: 0.7813 (tp40) outliers start: 23 outliers final: 19 residues processed: 153 average time/residue: 0.1015 time to fit residues: 20.9060 Evaluate side-chains 148 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 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 69 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN B 32 GLN B 220 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.202029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.166394 restraints weight = 9597.639| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.06 r_work: 0.3860 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8818 Z= 0.145 Angle : 0.533 11.599 11940 Z= 0.272 Chirality : 0.042 0.133 1328 Planarity : 0.004 0.055 1476 Dihedral : 6.350 56.017 1597 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.77 % Allowed : 11.21 % 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: 0.87 (0.27), residues: 1032 helix: 2.65 (0.25), residues: 405 sheet: -0.52 (0.33), residues: 229 loop : -0.94 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 12 TYR 0.022 0.001 TYR R 146 PHE 0.012 0.001 PHE N 108 TRP 0.018 0.002 TRP B 339 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8815) covalent geometry : angle 0.53215 (11934) SS BOND : bond 0.00074 ( 3) SS BOND : angle 1.69846 ( 6) hydrogen bonds : bond 0.03735 ( 431) hydrogen bonds : angle 4.16321 ( 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 159 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.360 Fit side-chains REVERT: A 224 VAL cc_start: 0.8381 (t) cc_final: 0.8031 (m) REVERT: A 378 ASP cc_start: 0.7886 (m-30) cc_final: 0.7614 (m-30) REVERT: G 21 MET cc_start: 0.6379 (tmm) cc_final: 0.5390 (tpp) REVERT: N 82 GLN cc_start: 0.8181 (tp40) cc_final: 0.7878 (tp40) REVERT: N 95 TYR cc_start: 0.9095 (m-80) cc_final: 0.8816 (m-80) outliers start: 25 outliers final: 20 residues processed: 147 average time/residue: 0.1040 time to fit residues: 20.6529 Evaluate side-chains 149 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 84 ASN Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 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 100 optimal weight: 0.0370 chunk 99 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.201674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.166310 restraints weight = 9508.399| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.07 r_work: 0.3834 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8818 Z= 0.135 Angle : 0.520 11.176 11940 Z= 0.265 Chirality : 0.041 0.133 1328 Planarity : 0.004 0.053 1476 Dihedral : 6.358 53.064 1597 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.66 % Allowed : 11.65 % 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: 0.89 (0.27), residues: 1032 helix: 2.68 (0.25), residues: 405 sheet: -0.53 (0.32), residues: 229 loop : -0.93 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 12 TYR 0.021 0.001 TYR R 146 PHE 0.013 0.001 PHE R 138 TRP 0.016 0.002 TRP B 339 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8815) covalent geometry : angle 0.51898 (11934) SS BOND : bond 0.00063 ( 3) SS BOND : angle 1.66464 ( 6) hydrogen bonds : bond 0.03661 ( 431) hydrogen bonds : angle 4.08259 ( 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 154 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 VAL cc_start: 0.8290 (t) cc_final: 0.7959 (m) REVERT: G 21 MET cc_start: 0.6363 (tmm) cc_final: 0.5444 (tpp) REVERT: N 82 GLN cc_start: 0.8142 (tp40) cc_final: 0.7876 (tp40) REVERT: N 95 TYR cc_start: 0.9083 (m-80) cc_final: 0.8869 (m-80) outliers start: 24 outliers final: 23 residues processed: 141 average time/residue: 0.0990 time to fit residues: 18.7572 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 : 0.295 ------------------------------------------------------------------------------- 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 323 LEU Chi-restraints excluded: chain R residue 363 ASN 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 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 84 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.0010 chunk 32 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.206070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.171494 restraints weight = 9580.656| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.05 r_work: 0.3895 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8818 Z= 0.100 Angle : 0.486 10.073 11940 Z= 0.248 Chirality : 0.040 0.138 1328 Planarity : 0.003 0.049 1476 Dihedral : 6.116 52.840 1597 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.89 % Allowed : 11.99 % 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: 1.15 (0.27), residues: 1032 helix: 2.95 (0.25), residues: 404 sheet: -0.30 (0.33), residues: 226 loop : -0.91 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.019 0.001 TYR R 146 PHE 0.013 0.001 PHE R 138 TRP 0.023 0.001 TRP B 339 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8815) covalent geometry : angle 0.48485 (11934) SS BOND : bond 0.00075 ( 3) SS BOND : angle 1.56076 ( 6) hydrogen bonds : bond 0.03251 ( 431) hydrogen bonds : angle 3.86402 ( 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 151 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7437 (tt0) cc_final: 0.7185 (pt0) REVERT: A 224 VAL cc_start: 0.8209 (t) cc_final: 0.7892 (m) REVERT: B 134 ARG cc_start: 0.6641 (ptt-90) cc_final: 0.6048 (mmp80) REVERT: B 234 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8568 (m-80) REVERT: G 21 MET cc_start: 0.6366 (tmm) cc_final: 0.5438 (tpp) REVERT: N 82 GLN cc_start: 0.7997 (tp40) cc_final: 0.7714 (tp40) outliers start: 17 outliers final: 15 residues processed: 144 average time/residue: 0.1066 time to fit residues: 20.4191 Evaluate side-chains 145 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 234 PHE 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: 1.9990 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4315 r_free = 0.4315 target = 0.202436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.167968 restraints weight = 9528.763| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.00 r_work: 0.3828 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8818 Z= 0.134 Angle : 0.524 9.821 11940 Z= 0.268 Chirality : 0.041 0.133 1328 Planarity : 0.004 0.054 1476 Dihedral : 6.306 55.571 1597 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.22 % Allowed : 11.76 % 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: 1.08 (0.27), residues: 1032 helix: 2.89 (0.25), residues: 404 sheet: -0.40 (0.33), residues: 227 loop : -0.91 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 12 TYR 0.020 0.001 TYR R 146 PHE 0.017 0.001 PHE A 222 TRP 0.022 0.002 TRP B 339 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8815) covalent geometry : angle 0.52272 (11934) SS BOND : bond 0.00082 ( 3) SS BOND : angle 1.58022 ( 6) hydrogen bonds : bond 0.03561 ( 431) hydrogen bonds : angle 3.99465 ( 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 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 224 VAL cc_start: 0.8219 (t) cc_final: 0.7883 (m) REVERT: B 44 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7856 (mp10) REVERT: B 219 ARG cc_start: 0.7516 (mmt90) cc_final: 0.7315 (mmt90) REVERT: B 234 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: G 21 MET cc_start: 0.6360 (tmm) cc_final: 0.5375 (tpp) REVERT: N 82 GLN cc_start: 0.8037 (tp40) cc_final: 0.7737 (tp40) outliers start: 20 outliers final: 17 residues processed: 140 average time/residue: 0.1134 time to fit residues: 20.9602 Evaluate side-chains 140 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 234 PHE 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 111 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: 0.9990 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.208144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.166497 restraints weight = 9367.024| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.66 r_work: 0.3812 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.4354 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= 0.130 Angle : 0.521 9.723 11940 Z= 0.268 Chirality : 0.041 0.164 1328 Planarity : 0.004 0.052 1476 Dihedral : 6.252 58.110 1597 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.44 % Allowed : 11.32 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.04 (0.27), residues: 1032 helix: 2.87 (0.25), residues: 404 sheet: -0.47 (0.33), residues: 229 loop : -0.90 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 52 TYR 0.020 0.001 TYR R 146 PHE 0.014 0.001 PHE R 138 TRP 0.018 0.002 TRP B 339 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8815) covalent geometry : angle 0.51965 (11934) SS BOND : bond 0.00059 ( 3) SS BOND : angle 1.56134 ( 6) hydrogen bonds : bond 0.03514 ( 431) hydrogen bonds : angle 3.99132 ( 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 145 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7561 (tt0) cc_final: 0.7068 (pt0) REVERT: A 224 VAL cc_start: 0.8318 (t) cc_final: 0.7938 (m) REVERT: A 317 ARG cc_start: 0.7441 (ttp-170) cc_final: 0.6890 (mpp-170) REVERT: B 44 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: B 134 ARG cc_start: 0.6434 (ptt-90) cc_final: 0.5640 (mmp80) REVERT: B 234 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8395 (m-80) REVERT: G 21 MET cc_start: 0.6169 (tmm) cc_final: 0.5185 (tpp) REVERT: N 82 GLN cc_start: 0.7846 (tp40) cc_final: 0.7446 (tp40) outliers start: 22 outliers final: 18 residues processed: 135 average time/residue: 0.0996 time to fit residues: 17.8728 Evaluate side-chains 137 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 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 297 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 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 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 41 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.202669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.160261 restraints weight = 9388.160| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.68 r_work: 0.3750 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8818 Z= 0.184 Angle : 0.579 9.848 11940 Z= 0.300 Chirality : 0.043 0.155 1328 Planarity : 0.004 0.059 1476 Dihedral : 6.638 56.008 1597 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.55 % Allowed : 11.76 % 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: 0.83 (0.27), residues: 1032 helix: 2.69 (0.26), residues: 398 sheet: -0.59 (0.33), residues: 230 loop : -0.96 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 12 TYR 0.023 0.002 TYR R 146 PHE 0.015 0.002 PHE N 108 TRP 0.024 0.002 TRP B 339 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8815) covalent geometry : angle 0.57840 (11934) SS BOND : bond 0.00070 ( 3) SS BOND : angle 1.69296 ( 6) hydrogen bonds : bond 0.04062 ( 431) hydrogen bonds : angle 4.21464 ( 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 134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7705 (tt0) cc_final: 0.7281 (pt0) REVERT: B 44 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: B 219 ARG cc_start: 0.7272 (mmt90) cc_final: 0.6966 (mmt90) REVERT: B 234 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: G 21 MET cc_start: 0.6194 (tmm) cc_final: 0.5204 (tpp) REVERT: N 82 GLN cc_start: 0.7963 (tp40) cc_final: 0.7677 (tp40) outliers start: 23 outliers final: 20 residues processed: 125 average time/residue: 0.1108 time to fit residues: 18.2754 Evaluate side-chains 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 297 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 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 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: 5.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 88 optimal weight: 0.0040 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.209139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166538 restraints weight = 9389.679| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.71 r_work: 0.3809 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8818 Z= 0.108 Angle : 0.503 9.286 11940 Z= 0.259 Chirality : 0.041 0.135 1328 Planarity : 0.004 0.048 1476 Dihedral : 6.190 54.232 1597 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.44 % Allowed : 12.54 % 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 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: 1.04 (0.27), residues: 1032 helix: 2.87 (0.25), residues: 404 sheet: -0.46 (0.33), residues: 228 loop : -0.92 (0.31), residues: 400 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 0.015 0.001 TRP R 232 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8815) covalent geometry : angle 0.50209 (11934) SS BOND : bond 0.00054 ( 3) SS BOND : angle 1.60289 ( 6) hydrogen bonds : bond 0.03355 ( 431) hydrogen bonds : angle 3.94254 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.99 seconds wall clock time: 39 minutes 35.02 seconds (2375.02 seconds total)