Starting phenix.real_space_refine on Sat Jul 26 19:59:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vn7_21249/07_2025/6vn7_21249.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vn7_21249/07_2025/6vn7_21249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vn7_21249/07_2025/6vn7_21249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vn7_21249/07_2025/6vn7_21249.map" model { file = "/net/cci-nas-00/data/ceres_data/6vn7_21249/07_2025/6vn7_21249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vn7_21249/07_2025/6vn7_21249.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 5561 2.51 5 N 1459 2.21 5 O 1549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8620 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2171 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 2 Chain: "L" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1981 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 2 Chain: "B" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 240 Unusual residues: {'CLR': 6, 'PLM': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 5.35, per 1000 atoms: 0.62 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: 1.94 Conformation dependent library (CDL) restraints added in 993.4 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: 0.94 Creating SS restraints... Processing helix chain 'R' and resid 129 through 167 removed outlier: 4.064A pdb=" N GLU R 133 " --> pdb=" O ALA R 129 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU R 154 " --> pdb=" O TYR R 150 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU R 157 " --> pdb=" O SER R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 201 removed outlier: 3.603A pdb=" N ALA R 198 " --> pdb=" O ILE R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 246 removed outlier: 4.001A pdb=" N ALA R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL R 226 " --> pdb=" O PHE R 222 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET R 227 " --> pdb=" O GLN R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 250 through 281 removed outlier: 3.929A pdb=" N TYR R 254 " --> pdb=" O SER R 250 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP R 256 " --> pdb=" O ARG R 252 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY R 257 " --> pdb=" O LYS R 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 260 " --> pdb=" O TRP R 256 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE R 261 " --> pdb=" O GLY R 257 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL R 265 " --> pdb=" O ILE R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix removed outlier: 3.665A pdb=" N GLU R 281 " --> pdb=" O ARG R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 295 Processing helix chain 'R' and resid 298 through 324 removed outlier: 4.198A pdb=" N LEU R 319 " --> pdb=" O ILE R 315 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU R 320 " --> pdb=" O ILE R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 345 Processing helix chain 'R' and resid 346 through 351 Processing helix chain 'R' and resid 352 through 357 Processing helix chain 'R' and resid 365 through 389 removed outlier: 4.359A pdb=" N LYS R 369 " --> pdb=" O LYS R 365 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET R 370 " --> pdb=" O PRO R 366 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE R 372 " --> pdb=" O VAL R 368 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE R 382 " --> pdb=" O SER R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 409 Processing helix chain 'L' and resid 2 through 27 Processing helix chain 'A' and resid 10 through 40 removed outlier: 4.062A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.525A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 301 through 304 removed outlier: 4.351A pdb=" N GLY A 304 " --> pdb=" O VAL A 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 304' Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.755A pdb=" N ASP A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.291A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 4.039A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.721A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.605A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.022A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.447A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.902A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.187A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.228A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.838A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.641A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.804A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.559A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.006A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.33 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: 0.620 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.310 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.22), residues: 1032 helix: -1.35 (0.21), residues: 400 sheet: -1.06 (0.32), residues: 217 loop : -1.94 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 281 HIS 0.016 0.002 HIS A 220 PHE 0.021 0.002 PHE A 246 TYR 0.022 0.002 TYR R 146 ARG 0.006 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.11880 ( 431) hydrogen bonds : angle 6.33938 ( 1236) SS BOND : bond 0.00204 ( 3) SS BOND : angle 2.06536 ( 6) covalent geometry : bond 0.00406 ( 8815) covalent geometry : angle 0.90408 (11934) *********************** 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 : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 346 LEU cc_start: 0.7925 (tp) cc_final: 0.7593 (mt) REVERT: A 278 ASN cc_start: 0.7809 (m-40) cc_final: 0.7490 (m110) REVERT: A 344 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8455 (mm-30) REVERT: A 378 ASP cc_start: 0.8226 (m-30) cc_final: 0.7950 (m-30) REVERT: B 256 ARG cc_start: 0.7535 (mmm160) cc_final: 0.7247 (mtm-85) REVERT: N 80 TYR cc_start: 0.8375 (m-80) cc_final: 0.7815 (m-80) REVERT: N 95 TYR cc_start: 0.8904 (m-10) cc_final: 0.8699 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2945 time to fit residues: 77.9750 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 : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 GLN ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN R 279 HIS R 363 ASN ** L 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 220 HIS A 254 ASN B 91 HIS B 259 GLN B 266 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.213372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.176552 restraints weight = 9360.026| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.27 r_work: 0.3930 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8818 Z= 0.130 Angle : 0.551 12.360 11940 Z= 0.283 Chirality : 0.042 0.160 1328 Planarity : 0.005 0.060 1476 Dihedral : 6.462 58.362 1597 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.22 % Allowed : 6.99 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1032 helix: 1.35 (0.24), residues: 407 sheet: -0.55 (0.33), residues: 207 loop : -1.40 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.018 0.002 PHE A 315 TYR 0.026 0.001 TYR R 146 ARG 0.004 0.000 ARG L 12 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 431) hydrogen bonds : angle 4.59034 ( 1236) SS BOND : bond 0.01042 ( 3) SS BOND : angle 1.81562 ( 6) covalent geometry : bond 0.00292 ( 8815) covalent geometry : angle 0.54996 (11934) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 137 MET cc_start: 0.7371 (ttt) cc_final: 0.7095 (ttt) REVERT: R 227 MET cc_start: 0.7638 (ttm) cc_final: 0.7388 (mtt) REVERT: A 33 ASP cc_start: 0.7382 (t70) cc_final: 0.7069 (t70) REVERT: A 309 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: G 21 MET cc_start: 0.6304 (tmm) cc_final: 0.5399 (tpp) REVERT: N 80 TYR cc_start: 0.8314 (m-80) cc_final: 0.7249 (m-80) outliers start: 20 outliers final: 15 residues processed: 162 average time/residue: 0.2464 time to fit residues: 52.8405 Evaluate side-chains 146 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 161 THR Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.209032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.173204 restraints weight = 9560.957| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.12 r_work: 0.3893 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2934 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= 0.114 Angle : 0.508 10.872 11940 Z= 0.260 Chirality : 0.041 0.141 1328 Planarity : 0.004 0.053 1476 Dihedral : 6.188 59.449 1597 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.00 % Allowed : 9.21 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1032 helix: 2.33 (0.25), residues: 406 sheet: -0.37 (0.33), residues: 225 loop : -1.17 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 PHE 0.016 0.001 PHE A 315 TYR 0.023 0.001 TYR R 146 ARG 0.005 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 431) hydrogen bonds : angle 4.25371 ( 1236) SS BOND : bond 0.00069 ( 3) SS BOND : angle 1.75455 ( 6) covalent geometry : bond 0.00258 ( 8815) covalent geometry : angle 0.50643 (11934) *********************** 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 153 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: R 137 MET cc_start: 0.7512 (ttt) cc_final: 0.7244 (ttt) REVERT: R 321 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: A 33 ASP cc_start: 0.7571 (t70) cc_final: 0.7223 (t70) REVERT: A 309 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: G 21 MET cc_start: 0.6364 (tmm) cc_final: 0.5450 (tpp) REVERT: N 80 TYR cc_start: 0.8622 (m-80) cc_final: 0.7384 (m-80) outliers start: 18 outliers final: 13 residues processed: 143 average time/residue: 0.2577 time to fit residues: 48.3388 Evaluate side-chains 137 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 309 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 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 44 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 220 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.210735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.175626 restraints weight = 9505.564| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.09 r_work: 0.3942 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8818 Z= 0.100 Angle : 0.477 9.874 11940 Z= 0.244 Chirality : 0.040 0.137 1328 Planarity : 0.004 0.051 1476 Dihedral : 5.939 58.108 1597 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.66 % Allowed : 9.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 1032 helix: 2.71 (0.25), residues: 410 sheet: -0.33 (0.33), residues: 217 loop : -1.00 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE A 315 TYR 0.021 0.001 TYR R 146 ARG 0.005 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 431) hydrogen bonds : angle 4.02925 ( 1236) SS BOND : bond 0.00055 ( 3) SS BOND : angle 1.54027 ( 6) covalent geometry : bond 0.00221 ( 8815) covalent geometry : angle 0.47615 (11934) *********************** 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 157 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 137 MET cc_start: 0.7456 (ttt) cc_final: 0.7172 (ttt) REVERT: A 317 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7361 (mpp-170) REVERT: B 169 TRP cc_start: 0.8755 (m100) cc_final: 0.8549 (m100) REVERT: G 21 MET cc_start: 0.6260 (tmm) cc_final: 0.5354 (tpp) REVERT: N 80 TYR cc_start: 0.8645 (m-80) cc_final: 0.7408 (m-80) outliers start: 24 outliers final: 18 residues processed: 143 average time/residue: 0.2574 time to fit residues: 48.9864 Evaluate side-chains 149 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 A residue 263 THR Chi-restraints excluded: chain A residue 314 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 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 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 290 ASN A 14 ASN A 371 ASN B 32 GLN B 156 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 = 0.4297 r_free = 0.4297 target = 0.199603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.163755 restraints weight = 9464.465| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.09 r_work: 0.3830 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8818 Z= 0.203 Angle : 0.595 10.519 11940 Z= 0.306 Chirality : 0.043 0.138 1328 Planarity : 0.004 0.061 1476 Dihedral : 6.703 56.397 1597 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.33 % Allowed : 9.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1032 helix: 2.48 (0.25), residues: 405 sheet: -0.44 (0.33), residues: 216 loop : -1.10 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 339 HIS 0.007 0.002 HIS B 54 PHE 0.016 0.002 PHE N 108 TYR 0.024 0.002 TYR R 146 ARG 0.005 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 431) hydrogen bonds : angle 4.38357 ( 1236) SS BOND : bond 0.00055 ( 3) SS BOND : angle 1.86315 ( 6) covalent geometry : bond 0.00482 ( 8815) covalent geometry : angle 0.59391 (11934) *********************** 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 156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 137 MET cc_start: 0.7573 (ttt) cc_final: 0.7335 (ttt) REVERT: A 209 GLU cc_start: 0.7373 (tt0) cc_final: 0.7165 (pt0) REVERT: G 21 MET cc_start: 0.6393 (tmm) cc_final: 0.5401 (tpp) REVERT: N 95 TYR cc_start: 0.9121 (m-80) cc_final: 0.8683 (m-80) outliers start: 30 outliers final: 26 residues processed: 140 average time/residue: 0.2450 time to fit residues: 45.3201 Evaluate side-chains 152 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 296 ILE Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 321 GLN Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 363 ASN Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain 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 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 0.4980 chunk 72 optimal weight: 0.0270 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4345 r_free = 0.4345 target = 0.205732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170687 restraints weight = 9445.229| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.05 r_work: 0.3897 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8818 Z= 0.101 Angle : 0.485 9.251 11940 Z= 0.247 Chirality : 0.040 0.138 1328 Planarity : 0.003 0.048 1476 Dihedral : 6.232 53.915 1597 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.33 % Allowed : 11.88 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 1032 helix: 2.88 (0.25), residues: 404 sheet: -0.35 (0.33), residues: 224 loop : -0.92 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 232 HIS 0.003 0.001 HIS R 178 PHE 0.012 0.001 PHE A 222 TYR 0.020 0.001 TYR R 146 ARG 0.007 0.000 ARG L 12 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 431) hydrogen bonds : angle 3.98237 ( 1236) SS BOND : bond 0.00090 ( 3) SS BOND : angle 1.63364 ( 6) covalent geometry : bond 0.00227 ( 8815) covalent geometry : angle 0.48353 (11934) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: R 137 MET cc_start: 0.7537 (ttt) cc_final: 0.7284 (ttt) REVERT: R 344 LEU cc_start: 0.7818 (mt) cc_final: 0.7473 (mt) REVERT: A 224 VAL cc_start: 0.8293 (t) cc_final: 0.7940 (m) REVERT: B 219 ARG cc_start: 0.7428 (mmt90) cc_final: 0.7211 (mmt90) REVERT: G 21 MET cc_start: 0.6388 (tmm) cc_final: 0.5381 (tpp) REVERT: N 95 TYR cc_start: 0.9073 (m-80) cc_final: 0.8757 (m-80) REVERT: N 111 THR cc_start: 0.7900 (m) cc_final: 0.7663 (p) outliers start: 21 outliers final: 18 residues processed: 145 average time/residue: 0.2441 time to fit residues: 46.9796 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 : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 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 83 MET Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.206428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.171365 restraints weight = 9493.180| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.05 r_work: 0.3897 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8818 Z= 0.100 Angle : 0.485 9.327 11940 Z= 0.249 Chirality : 0.040 0.136 1328 Planarity : 0.003 0.049 1476 Dihedral : 6.047 49.677 1597 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.44 % Allowed : 12.32 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.27), residues: 1032 helix: 3.04 (0.25), residues: 404 sheet: -0.32 (0.33), residues: 226 loop : -0.82 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 232 HIS 0.003 0.001 HIS R 178 PHE 0.012 0.001 PHE A 222 TYR 0.019 0.001 TYR R 146 ARG 0.005 0.000 ARG L 12 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 431) hydrogen bonds : angle 3.86288 ( 1236) SS BOND : bond 0.00084 ( 3) SS BOND : angle 1.52579 ( 6) covalent geometry : bond 0.00224 ( 8815) covalent geometry : angle 0.48408 (11934) *********************** 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 157 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: R 137 MET cc_start: 0.7533 (ttt) cc_final: 0.7282 (ttt) REVERT: R 344 LEU cc_start: 0.7784 (mt) cc_final: 0.7420 (mt) REVERT: A 209 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6898 (pt0) REVERT: A 224 VAL cc_start: 0.8149 (t) cc_final: 0.7791 (m) REVERT: B 134 ARG cc_start: 0.6626 (ptt-90) cc_final: 0.5985 (mmp80) REVERT: B 219 ARG cc_start: 0.7605 (mmt90) cc_final: 0.7362 (mmt90) REVERT: B 234 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8650 (m-80) REVERT: G 21 MET cc_start: 0.6375 (tmm) cc_final: 0.5363 (tpp) REVERT: N 95 TYR cc_start: 0.9076 (m-80) cc_final: 0.8819 (m-80) REVERT: N 111 THR cc_start: 0.7835 (m) cc_final: 0.7613 (p) outliers start: 22 outliers final: 18 residues processed: 144 average time/residue: 0.2410 time to fit residues: 46.1149 Evaluate side-chains 145 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 363 ASN Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 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 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 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.0570 chunk 32 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 GLN A 14 ASN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.204914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.162630 restraints weight = 9500.095| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.66 r_work: 0.3803 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8818 Z= 0.178 Angle : 0.566 9.841 11940 Z= 0.294 Chirality : 0.043 0.134 1328 Planarity : 0.004 0.058 1476 Dihedral : 6.655 58.546 1597 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.77 % Allowed : 11.99 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 1032 helix: 2.71 (0.25), residues: 404 sheet: -0.53 (0.33), residues: 227 loop : -0.89 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.006 0.001 HIS B 54 PHE 0.015 0.002 PHE N 108 TYR 0.023 0.002 TYR R 146 ARG 0.008 0.000 ARG L 12 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 431) hydrogen bonds : angle 4.16688 ( 1236) SS BOND : bond 0.00082 ( 3) SS BOND : angle 1.68692 ( 6) covalent geometry : bond 0.00424 ( 8815) covalent geometry : angle 0.56483 (11934) *********************** 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 148 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ARG cc_start: 0.7572 (ttp-170) cc_final: 0.7046 (mpp-170) REVERT: A 378 ASP cc_start: 0.7765 (m-30) cc_final: 0.7549 (m-30) REVERT: B 219 ARG cc_start: 0.7586 (mmt90) cc_final: 0.7316 (mmt90) REVERT: B 234 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8536 (m-80) REVERT: G 21 MET cc_start: 0.6212 (tmm) cc_final: 0.5238 (tpp) REVERT: G 52 THR cc_start: 0.7416 (m) cc_final: 0.7194 (p) outliers start: 25 outliers final: 22 residues processed: 136 average time/residue: 0.2500 time to fit residues: 44.6529 Evaluate side-chains 138 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 321 GLN Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 363 ASN Chi-restraints excluded: chain R residue 407 HIS Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 314 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 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 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 25 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.206630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164518 restraints weight = 9452.492| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.66 r_work: 0.3778 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.4363 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= 0.144 Angle : 0.532 9.504 11940 Z= 0.275 Chirality : 0.042 0.135 1328 Planarity : 0.004 0.052 1476 Dihedral : 6.509 56.979 1597 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.55 % Allowed : 11.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.27), residues: 1032 helix: 2.73 (0.25), residues: 404 sheet: -0.56 (0.32), residues: 227 loop : -0.92 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 339 HIS 0.004 0.001 HIS B 54 PHE 0.020 0.001 PHE A 222 TYR 0.021 0.001 TYR R 146 ARG 0.005 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 431) hydrogen bonds : angle 4.06712 ( 1236) SS BOND : bond 0.00096 ( 3) SS BOND : angle 1.63004 ( 6) covalent geometry : bond 0.00341 ( 8815) covalent geometry : angle 0.53039 (11934) *********************** 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 134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 ARG cc_start: 0.6400 (ptt-90) cc_final: 0.5617 (mmp80) REVERT: B 219 ARG cc_start: 0.7549 (mmt90) cc_final: 0.7312 (mmt90) REVERT: B 234 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: G 21 MET cc_start: 0.6161 (tmm) cc_final: 0.5178 (tpp) outliers start: 23 outliers final: 20 residues processed: 125 average time/residue: 0.2471 time to fit residues: 40.9316 Evaluate side-chains 134 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 314 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 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 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 13 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 32 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.208126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.165909 restraints weight = 9377.791| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.66 r_work: 0.3807 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.4423 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= 0.116 Angle : 0.503 9.413 11940 Z= 0.259 Chirality : 0.041 0.135 1328 Planarity : 0.004 0.049 1476 Dihedral : 6.271 55.118 1597 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.55 % Allowed : 12.43 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.27), residues: 1032 helix: 2.85 (0.25), residues: 402 sheet: -0.49 (0.33), residues: 227 loop : -0.92 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 232 HIS 0.003 0.001 HIS R 178 PHE 0.009 0.001 PHE N 108 TYR 0.019 0.001 TYR R 146 ARG 0.005 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 431) hydrogen bonds : angle 3.92787 ( 1236) SS BOND : bond 0.00080 ( 3) SS BOND : angle 1.57769 ( 6) covalent geometry : bond 0.00269 ( 8815) covalent geometry : angle 0.50144 (11934) ********************** 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 138 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: R 344 LEU cc_start: 0.7262 (mt) cc_final: 0.6917 (mt) REVERT: A 33 ASP cc_start: 0.7212 (t70) cc_final: 0.6982 (t70) REVERT: A 317 ARG cc_start: 0.7477 (ttp-170) cc_final: 0.6944 (mpp-170) REVERT: B 44 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: B 134 ARG cc_start: 0.6421 (ptt-90) cc_final: 0.5648 (mmp80) REVERT: B 219 ARG cc_start: 0.7525 (mmt90) cc_final: 0.7279 (mmt90) REVERT: B 234 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: G 21 MET cc_start: 0.6151 (tmm) cc_final: 0.5142 (tpp) REVERT: N 94 TYR cc_start: 0.8470 (m-80) cc_final: 0.8268 (m-80) outliers start: 23 outliers final: 19 residues processed: 131 average time/residue: 0.3212 time to fit residues: 57.6374 Evaluate side-chains 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 314 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 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 101 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 0.0020 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5546 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.206688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165101 restraints weight = 9430.459| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.65 r_work: 0.3834 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4445 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= 0.097 Angle : 0.482 9.272 11940 Z= 0.250 Chirality : 0.040 0.156 1328 Planarity : 0.003 0.047 1476 Dihedral : 6.030 55.094 1597 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.22 % Allowed : 12.87 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1032 helix: 3.02 (0.25), residues: 402 sheet: -0.38 (0.33), residues: 225 loop : -0.87 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 339 HIS 0.003 0.001 HIS R 178 PHE 0.009 0.001 PHE A 315 TYR 0.018 0.001 TYR R 146 ARG 0.005 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 431) hydrogen bonds : angle 3.82455 ( 1236) SS BOND : bond 0.00062 ( 3) SS BOND : angle 1.56059 ( 6) covalent geometry : bond 0.00216 ( 8815) covalent geometry : angle 0.48060 (11934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4950.91 seconds wall clock time: 87 minutes 37.45 seconds (5257.45 seconds total)