Starting phenix.real_space_refine on Fri Sep 11 13:40:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nbf_0410/09_2026/6nbf_0410.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nbf_0410/09_2026/6nbf_0410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nbf_0410/09_2026/6nbf_0410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nbf_0410/09_2026/6nbf_0410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nbf_0410/09_2026/6nbf_0410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nbf_0410/09_2026/6nbf_0410.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nbf_0410/09_2026/6nbf_0410.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nbf_0410/09_2026/6nbf_0410.cif" } resolution = 3.0 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= 0.005 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 58 5.16 5 C 6067 2.51 5 N 1617 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9424 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3025 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 11, 'TRANS': 356} Chain breaks: 3 Chain: "P" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "A" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1890 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 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: 2.27, per 1000 atoms: 0.24 Number of scatterers: 9424 At special positions: 0 Unit cell: (123.708, 99.372, 151.086, 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 58 16.00 O 1682 8.00 N 1617 7.00 C 6067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 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: 0.85 Conformation dependent library (CDL) restraints added in 323.5 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 41.0% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 35 through 55 removed outlier: 3.632A pdb=" N PHE R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 201 removed outlier: 3.774A pdb=" N PHE R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU R 199 " --> pdb=" O TYR R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 218 through 246 removed outlier: 3.826A pdb=" N MET R 224 " --> pdb=" O ASN R 220 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS R 240 " --> pdb=" O SER R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 312 removed outlier: 4.262A pdb=" N ARG R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE R 311 " --> pdb=" O HIS R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 346 removed outlier: 4.087A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.622A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 369 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 371 through 391 Processing helix chain 'R' and resid 400 through 412 Processing helix chain 'R' and resid 419 through 424 Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.757A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR R 459 " --> pdb=" O VAL R 455 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 Processing helix chain 'P' and resid 2 through 32 removed outlier: 3.757A pdb=" N ARG P 20 " --> pdb=" O GLN P 16 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG P 21 " --> pdb=" O ASP P 17 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS P 26 " --> pdb=" O ALA P 22 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU P 27 " --> pdb=" O PHE P 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.681A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.903A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.806A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.517A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.584A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.392A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.601A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.621A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.956A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 111 through 112 Processing sheet with id=AA2, first strand: chain 'R' and resid 126 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.485A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.927A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.169A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.055A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.501A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.557A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.536A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.630A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.845A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1287 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: 1.32 Time building geometry restraints manager: 1.01 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: 2951 1.34 - 1.46: 1913 1.46 - 1.58: 4694 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9640 Sorted by residual: bond pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 1.518 1.539 -0.021 1.13e-02 7.83e+03 3.43e+00 bond pdb=" C GLU A 327 " pdb=" N PRO A 328 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.30e-02 5.92e+03 2.35e+00 bond pdb=" CA ASN A 239 " pdb=" C ASN A 239 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.80e-02 3.09e+03 2.03e+00 bond pdb=" N HIS R 114 " pdb=" CA HIS R 114 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 1.99e+00 bond pdb=" C LEU R 331 " pdb=" N PRO R 332 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.95e+00 ... (remaining 9635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 12106 1.60 - 3.20: 813 3.20 - 4.80: 111 4.80 - 6.40: 27 6.40 - 8.00: 3 Bond angle restraints: 13060 Sorted by residual: angle pdb=" C THR N 61 " pdb=" N GLY N 62 " pdb=" CA GLY N 62 " ideal model delta sigma weight residual 120.03 125.08 -5.05 1.12e+00 7.97e-01 2.03e+01 angle pdb=" N VAL R 412 " pdb=" CA VAL R 412 " pdb=" C VAL R 412 " ideal model delta sigma weight residual 112.29 108.22 4.07 9.40e-01 1.13e+00 1.88e+01 angle pdb=" CA TYR R 191 " pdb=" CB TYR R 191 " pdb=" CG TYR R 191 " ideal model delta sigma weight residual 113.90 121.11 -7.21 1.80e+00 3.09e-01 1.60e+01 angle pdb=" C GLU A 370 " pdb=" N ASN A 371 " pdb=" CA ASN A 371 " ideal model delta sigma weight residual 120.54 125.61 -5.07 1.35e+00 5.49e-01 1.41e+01 angle pdb=" N PRO B 236 " pdb=" CA PRO B 236 " pdb=" C PRO B 236 " ideal model delta sigma weight residual 112.47 119.83 -7.36 2.06e+00 2.36e-01 1.28e+01 ... (remaining 13055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.18: 5367 14.18 - 28.37: 244 28.37 - 42.55: 51 42.55 - 56.74: 11 56.74 - 70.92: 3 Dihedral angle restraints: 5676 sinusoidal: 2337 harmonic: 3339 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 129.14 -36.14 1 1.00e+01 1.00e-02 1.85e+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 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LEU R 289 " pdb=" C LEU R 289 " pdb=" N TYR R 290 " pdb=" CA TYR R 290 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1146 0.065 - 0.130: 260 0.130 - 0.195: 27 0.195 - 0.260: 11 0.260 - 0.324: 6 Chirality restraints: 1450 Sorted by residual: chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.59e+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 -2.61 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1447 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.045 5.00e-02 4.00e+02 6.93e-02 7.69e+00 pdb=" N PRO G 49 " 0.120 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=" C THR A 325 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO A 326 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 40 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C VAL B 40 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL B 40 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY B 41 " -0.012 2.00e-02 2.50e+03 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2563 2.83 - 3.34: 8029 3.34 - 3.86: 14716 3.86 - 4.38: 16817 4.38 - 4.90: 29684 Nonbonded interactions: 71809 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.307 3.040 nonbonded pdb=" OH TYR R 195 " pdb=" OE2 GLU P 4 " model vdw 2.319 3.040 nonbonded pdb=" O TRP N 47 " pdb=" OG1 THR N 61 " model vdw 2.329 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.338 3.040 nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.358 3.120 ... (remaining 71804 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 9.670 Find NCS groups from input model: 0.030 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:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9646 Z= 0.282 Angle : 0.903 7.995 13072 Z= 0.544 Chirality : 0.059 0.324 1450 Planarity : 0.005 0.069 1621 Dihedral : 8.850 70.921 3498 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.10 % Allowed : 0.51 % Favored : 99.39 % 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: -1.40 (0.23), residues: 1124 helix: -0.38 (0.23), residues: 436 sheet: -0.75 (0.32), residues: 227 loop : -1.43 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 11 TYR 0.030 0.002 TYR R 297 PHE 0.018 0.002 PHE B 199 TRP 0.026 0.003 TRP B 99 HIS 0.013 0.002 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.28 ( 9640) covalent geometry : angle 0.90192 / 0.54 (13060) SS BOND : bond 0.00251 / 0.13 ( 6) SS BOND : angle 1.72845 / 1.04 ( 12) hydrogen bonds : bond 0.13358 / 9.23 ( 452) hydrogen bonds : angle 6.81163 / 4.73 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.6003 (mmmt) cc_final: 0.5058 (mtmt) REVERT: N 46 GLU cc_start: 0.9068 (pt0) cc_final: 0.8853 (pt0) outliers start: 1 outliers final: 2 residues processed: 204 average time/residue: 0.5020 time to fit residues: 110.0853 Evaluate side-chains 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 325 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0050 chunk 106 optimal weight: 1.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 42 HIS R 139 ASN R 140 HIS R 223 HIS R 225 HIS R 295 ASN P 32 HIS B 91 HIS B 266 HIS B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.187452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.133405 restraints weight = 10547.163| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.74 r_work: 0.3623 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9646 Z= 0.169 Angle : 0.571 6.975 13072 Z= 0.304 Chirality : 0.043 0.155 1450 Planarity : 0.004 0.054 1621 Dihedral : 5.730 51.475 1374 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.95 % Allowed : 9.36 % Favored : 87.69 % 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: 0.10 (0.25), residues: 1124 helix: 1.42 (0.25), residues: 441 sheet: -0.37 (0.31), residues: 233 loop : -1.01 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.027 0.002 TYR R 191 PHE 0.019 0.002 PHE B 222 TRP 0.019 0.002 TRP R 298 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 9640) covalent geometry : angle 0.57109 / 0.30 (13060) SS BOND : bond 0.00193 / 0.11 ( 6) SS BOND : angle 0.69176 / 0.42 ( 12) hydrogen bonds : bond 0.04510 / 3.00 ( 452) hydrogen bonds : angle 4.82601 / 3.43 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: R 423 VAL cc_start: 0.8532 (t) cc_final: 0.8309 (m) REVERT: A 24 LYS cc_start: 0.7160 (mttt) cc_final: 0.6751 (mmmt) REVERT: A 31 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7739 (tp-100) REVERT: A 314 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7913 (pt0) REVERT: B 42 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.5582 (mmt180) REVERT: B 181 THR cc_start: 0.8935 (p) cc_final: 0.8643 (p) REVERT: B 219 ARG cc_start: 0.7433 (mtt180) cc_final: 0.7227 (mtp85) REVERT: B 220 GLN cc_start: 0.8139 (mt0) cc_final: 0.7716 (mt0) REVERT: B 254 ASP cc_start: 0.8397 (t70) cc_final: 0.8075 (t0) REVERT: N 46 GLU cc_start: 0.8240 (pt0) cc_final: 0.7946 (pt0) REVERT: N 53 GLN cc_start: 0.8093 (mp10) cc_final: 0.7604 (mp10) REVERT: N 59 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7655 (p) outliers start: 29 outliers final: 10 residues processed: 161 average time/residue: 0.5317 time to fit residues: 91.7799 Evaluate side-chains 137 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 88 optimal weight: 0.0980 chunk 78 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 84 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 32 HIS A 239 ASN A 390 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.188295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133932 restraints weight = 10428.072| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.82 r_work: 0.3674 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9646 Z= 0.098 Angle : 0.469 5.639 13072 Z= 0.249 Chirality : 0.040 0.151 1450 Planarity : 0.004 0.048 1621 Dihedral : 5.089 58.450 1369 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.75 % Allowed : 12.82 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.73 (0.25), residues: 1124 helix: 2.15 (0.25), residues: 433 sheet: -0.11 (0.32), residues: 232 loop : -0.82 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.026 0.001 TYR R 191 PHE 0.012 0.001 PHE B 222 TRP 0.013 0.001 TRP R 298 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 9640) covalent geometry : angle 0.46884 / 0.25 (13060) SS BOND : bond 0.00158 / 0.09 ( 6) SS BOND : angle 0.53409 / 0.32 ( 12) hydrogen bonds : bond 0.03515 / 2.34 ( 452) hydrogen bonds : angle 4.29470 / 3.07 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 8 MET cc_start: 0.7876 (ttp) cc_final: 0.7640 (ttp) REVERT: A 31 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7774 (tp-100) REVERT: A 239 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8708 (p0) REVERT: A 283 ARG cc_start: 0.7973 (mtm180) cc_final: 0.7589 (mtt90) REVERT: A 314 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7953 (pt0) REVERT: A 344 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8059 (tp30) REVERT: A 378 ASP cc_start: 0.7806 (m-30) cc_final: 0.7569 (m-30) REVERT: B 181 THR cc_start: 0.8808 (p) cc_final: 0.8589 (p) REVERT: B 197 ARG cc_start: 0.7086 (mmm160) cc_final: 0.6783 (mmm160) REVERT: B 198 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8304 (mt) REVERT: B 254 ASP cc_start: 0.8326 (t70) cc_final: 0.7957 (t0) REVERT: G 46 LYS cc_start: 0.8172 (mptt) cc_final: 0.7841 (pptt) REVERT: N 53 GLN cc_start: 0.8147 (mp10) cc_final: 0.7649 (mp10) outliers start: 27 outliers final: 12 residues processed: 152 average time/residue: 0.4876 time to fit residues: 79.7992 Evaluate side-chains 136 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 32 HIS A 239 ASN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.185046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.131261 restraints weight = 10636.312| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.73 r_work: 0.3532 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9646 Z= 0.175 Angle : 0.541 7.738 13072 Z= 0.286 Chirality : 0.042 0.153 1450 Planarity : 0.004 0.042 1621 Dihedral : 5.322 52.421 1369 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.66 % Allowed : 13.12 % Favored : 83.21 % 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: 0.74 (0.25), residues: 1124 helix: 2.10 (0.25), residues: 437 sheet: -0.08 (0.33), residues: 227 loop : -0.78 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.024 0.002 TYR R 191 PHE 0.030 0.002 PHE A 238 TRP 0.015 0.002 TRP R 298 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 9640) covalent geometry : angle 0.54098 / 0.29 (13060) SS BOND : bond 0.00169 / 0.11 ( 6) SS BOND : angle 0.59819 / 0.35 ( 12) hydrogen bonds : bond 0.04328 / 2.87 ( 452) hydrogen bonds : angle 4.33045 / 3.09 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.363 Fit side-chains REVERT: A 24 LYS cc_start: 0.7099 (mttt) cc_final: 0.6679 (tptt) REVERT: A 31 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7751 (tp-100) REVERT: A 239 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8603 (p0) REVERT: A 283 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7695 (mtt90) REVERT: A 314 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7960 (pt0) REVERT: A 344 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8082 (tp30) REVERT: A 356 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7168 (ttp80) REVERT: A 378 ASP cc_start: 0.7830 (m-30) cc_final: 0.7530 (m-30) REVERT: A 381 ASP cc_start: 0.8245 (t70) cc_final: 0.7909 (t0) REVERT: B 44 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6417 (mm-40) REVERT: B 45 MET cc_start: 0.8262 (mtt) cc_final: 0.7868 (mtt) REVERT: B 46 ARG cc_start: 0.7164 (tpt170) cc_final: 0.6459 (ttm-80) REVERT: B 219 ARG cc_start: 0.7419 (mtt180) cc_final: 0.7004 (mtt-85) REVERT: B 220 GLN cc_start: 0.8225 (mt0) cc_final: 0.7982 (mt0) REVERT: B 312 ASP cc_start: 0.8193 (t70) cc_final: 0.7827 (t0) REVERT: G 38 MET cc_start: 0.7077 (ttp) cc_final: 0.6725 (tpp) REVERT: N 53 GLN cc_start: 0.8136 (mp10) cc_final: 0.7460 (mp10) REVERT: N 91 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7739 (t) outliers start: 36 outliers final: 17 residues processed: 146 average time/residue: 0.5196 time to fit residues: 81.2529 Evaluate side-chains 143 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 94 optimal weight: 0.1980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 32 HIS A 59 GLN A 239 ASN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.189173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134693 restraints weight = 10546.349| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.81 r_work: 0.3560 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9646 Z= 0.103 Angle : 0.471 7.339 13072 Z= 0.249 Chirality : 0.040 0.247 1450 Planarity : 0.003 0.038 1621 Dihedral : 4.781 51.065 1369 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.54 % Allowed : 14.95 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1124 helix: 2.43 (0.25), residues: 431 sheet: 0.09 (0.33), residues: 230 loop : -0.64 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.022 0.001 TYR R 191 PHE 0.016 0.001 PHE N 29 TRP 0.012 0.001 TRP R 298 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 9640) covalent geometry : angle 0.47082 / 0.25 (13060) SS BOND : bond 0.00160 / 0.09 ( 6) SS BOND : angle 0.48388 / 0.28 ( 12) hydrogen bonds : bond 0.03551 / 2.34 ( 452) hydrogen bonds : angle 4.11409 / 2.94 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: R 414 MET cc_start: 0.7549 (mtp) cc_final: 0.7185 (mtt) REVERT: A 31 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7659 (tp-100) REVERT: A 239 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8585 (p0) REVERT: A 283 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7632 (mtt90) REVERT: A 314 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7884 (pt0) REVERT: A 356 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7177 (ttp80) REVERT: B 44 GLN cc_start: 0.7749 (mt0) cc_final: 0.6484 (mm-40) REVERT: B 45 MET cc_start: 0.8277 (mtt) cc_final: 0.7851 (mtt) REVERT: B 46 ARG cc_start: 0.7053 (tpt170) cc_final: 0.6215 (tpp-160) REVERT: B 214 ARG cc_start: 0.8315 (mtt180) cc_final: 0.7776 (mpt180) REVERT: B 219 ARG cc_start: 0.7357 (mtt180) cc_final: 0.7010 (mtp85) REVERT: G 38 MET cc_start: 0.6967 (ttp) cc_final: 0.6610 (tpp) REVERT: N 38 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7680 (ptm160) REVERT: N 53 GLN cc_start: 0.8147 (mp10) cc_final: 0.7506 (mp10) REVERT: N 89 GLU cc_start: 0.7366 (pp20) cc_final: 0.7108 (pp20) REVERT: N 91 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7863 (t) outliers start: 25 outliers final: 12 residues processed: 143 average time/residue: 0.5307 time to fit residues: 81.2722 Evaluate side-chains 138 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 32 HIS A 239 ASN B 340 ASN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.181493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128939 restraints weight = 10643.605| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.70 r_work: 0.3497 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9646 Z= 0.178 Angle : 0.545 8.489 13072 Z= 0.285 Chirality : 0.043 0.236 1450 Planarity : 0.004 0.039 1621 Dihedral : 5.077 54.957 1369 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.95 % Allowed : 14.04 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.25), residues: 1124 helix: 2.24 (0.25), residues: 438 sheet: 0.05 (0.33), residues: 230 loop : -0.67 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.022 0.002 TYR R 191 PHE 0.017 0.002 PHE N 29 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 9640) covalent geometry : angle 0.54540 / 0.29 (13060) SS BOND : bond 0.00170 / 0.11 ( 6) SS BOND : angle 0.60880 / 0.33 ( 12) hydrogen bonds : bond 0.04210 / 2.77 ( 452) hydrogen bonds : angle 4.23626 / 3.03 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7209 (mttt) cc_final: 0.6720 (tptt) REVERT: A 31 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7521 (tp-100) REVERT: A 314 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7988 (pt0) REVERT: A 356 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7288 (ttp80) REVERT: A 381 ASP cc_start: 0.8388 (t70) cc_final: 0.8082 (t0) REVERT: B 19 ARG cc_start: 0.7030 (ttp-110) cc_final: 0.6654 (mtp85) REVERT: B 44 GLN cc_start: 0.7803 (mt0) cc_final: 0.6769 (mm-40) REVERT: B 45 MET cc_start: 0.8438 (mtt) cc_final: 0.8121 (mtt) REVERT: B 46 ARG cc_start: 0.7312 (tpt170) cc_final: 0.6710 (ttm-80) REVERT: G 38 MET cc_start: 0.7075 (ttp) cc_final: 0.6792 (tpp) REVERT: G 58 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7364 (tm-30) REVERT: N 38 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7957 (ptm160) REVERT: N 53 GLN cc_start: 0.8218 (mp10) cc_final: 0.7513 (mp10) REVERT: N 89 GLU cc_start: 0.7546 (pp20) cc_final: 0.7335 (pp20) REVERT: N 91 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8154 (t) outliers start: 29 outliers final: 15 residues processed: 148 average time/residue: 0.5287 time to fit residues: 83.8344 Evaluate side-chains 143 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 0.0570 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.184876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132174 restraints weight = 10562.510| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.72 r_work: 0.3517 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9646 Z= 0.109 Angle : 0.482 8.920 13072 Z= 0.252 Chirality : 0.041 0.235 1450 Planarity : 0.003 0.040 1621 Dihedral : 4.816 54.738 1369 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.64 % Allowed : 14.75 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.26), residues: 1124 helix: 2.52 (0.25), residues: 432 sheet: 0.06 (0.32), residues: 238 loop : -0.53 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.021 0.001 TYR R 191 PHE 0.017 0.001 PHE N 29 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9640) covalent geometry : angle 0.48170 / 0.25 (13060) SS BOND : bond 0.00140 / 0.08 ( 6) SS BOND : angle 0.46356 / 0.26 ( 12) hydrogen bonds : bond 0.03570 / 2.35 ( 452) hydrogen bonds : angle 4.04087 / 2.89 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 414 MET cc_start: 0.7669 (mtp) cc_final: 0.7321 (mtt) REVERT: A 24 LYS cc_start: 0.7201 (mttt) cc_final: 0.6738 (tptt) REVERT: A 31 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7786 (tp-100) REVERT: A 239 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8715 (p0) REVERT: A 314 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7921 (pt0) REVERT: A 381 ASP cc_start: 0.8396 (t70) cc_final: 0.8071 (t0) REVERT: B 19 ARG cc_start: 0.7085 (ttp-110) cc_final: 0.6722 (mtp85) REVERT: B 44 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6628 (mm-40) REVERT: B 45 MET cc_start: 0.8422 (mtt) cc_final: 0.8153 (mtt) REVERT: B 46 ARG cc_start: 0.7337 (tpt170) cc_final: 0.6650 (ttm-80) REVERT: B 59 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: B 340 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7348 (t0) REVERT: G 38 MET cc_start: 0.7020 (ttp) cc_final: 0.6763 (tpp) REVERT: G 58 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7440 (tm-30) REVERT: N 38 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7762 (ptm160) REVERT: N 53 GLN cc_start: 0.8186 (mp10) cc_final: 0.7456 (mp10) REVERT: N 89 GLU cc_start: 0.7561 (pp20) cc_final: 0.7324 (pp20) REVERT: N 91 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8087 (t) outliers start: 26 outliers final: 12 residues processed: 139 average time/residue: 0.5149 time to fit residues: 77.0558 Evaluate side-chains 139 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 104 optimal weight: 0.0870 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 139 ASN A 239 ASN B 295 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.185560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.132708 restraints weight = 10579.316| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.74 r_work: 0.3555 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9646 Z= 0.106 Angle : 0.473 9.218 13072 Z= 0.249 Chirality : 0.040 0.218 1450 Planarity : 0.003 0.041 1621 Dihedral : 4.673 55.533 1369 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.85 % Allowed : 15.06 % Favored : 82.10 % 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: 1.25 (0.26), residues: 1124 helix: 2.59 (0.25), residues: 432 sheet: 0.01 (0.32), residues: 243 loop : -0.43 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.021 0.001 TYR R 191 PHE 0.016 0.001 PHE N 29 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9640) covalent geometry : angle 0.47270 / 0.25 (13060) SS BOND : bond 0.00133 / 0.08 ( 6) SS BOND : angle 0.43281 / 0.24 ( 12) hydrogen bonds : bond 0.03512 / 2.30 ( 452) hydrogen bonds : angle 3.99438 / 2.86 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7781 (tp-100) REVERT: A 314 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7940 (pt0) REVERT: A 356 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7230 (ttp80) REVERT: A 378 ASP cc_start: 0.7792 (m-30) cc_final: 0.7496 (m-30) REVERT: A 381 ASP cc_start: 0.8401 (t70) cc_final: 0.8103 (t0) REVERT: B 19 ARG cc_start: 0.7124 (ttp-110) cc_final: 0.6731 (mtp85) REVERT: B 44 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6821 (mm-40) REVERT: B 45 MET cc_start: 0.8310 (mtt) cc_final: 0.7876 (mtt) REVERT: B 46 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6755 (ttm-80) REVERT: B 59 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: B 218 CYS cc_start: 0.8574 (p) cc_final: 0.8092 (t) REVERT: B 220 GLN cc_start: 0.7932 (mt0) cc_final: 0.7524 (mt0) REVERT: B 340 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.6842 (t0) REVERT: G 38 MET cc_start: 0.7142 (ttp) cc_final: 0.6842 (tpp) REVERT: G 58 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7536 (tm-30) REVERT: N 38 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7749 (ptm160) REVERT: N 53 GLN cc_start: 0.8201 (mp10) cc_final: 0.7461 (mp10) REVERT: N 91 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8101 (t) REVERT: N 110 VAL cc_start: 0.7685 (t) cc_final: 0.7482 (p) REVERT: N 111 THR cc_start: 0.8222 (m) cc_final: 0.7945 (p) outliers start: 28 outliers final: 14 residues processed: 137 average time/residue: 0.4974 time to fit residues: 73.6152 Evaluate side-chains 137 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 69 optimal weight: 0.0370 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.183768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.131317 restraints weight = 10574.973| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.71 r_work: 0.3532 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9646 Z= 0.126 Angle : 0.510 10.923 13072 Z= 0.264 Chirality : 0.041 0.226 1450 Planarity : 0.003 0.042 1621 Dihedral : 4.786 57.695 1369 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.34 % Allowed : 15.46 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.25), residues: 1124 helix: 2.59 (0.24), residues: 432 sheet: -0.03 (0.32), residues: 238 loop : -0.49 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.021 0.001 TYR R 191 PHE 0.017 0.001 PHE N 29 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9640) covalent geometry : angle 0.51006 / 0.26 (13060) SS BOND : bond 0.00149 / 0.09 ( 6) SS BOND : angle 0.45368 / 0.26 ( 12) hydrogen bonds : bond 0.03678 / 2.42 ( 452) hydrogen bonds : angle 4.00671 / 2.87 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 414 MET cc_start: 0.7720 (mtp) cc_final: 0.7359 (mtt) REVERT: A 31 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7765 (tp-100) REVERT: A 229 ASP cc_start: 0.7649 (t0) cc_final: 0.7099 (t0) REVERT: A 314 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7951 (pt0) REVERT: A 356 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7244 (ttp80) REVERT: A 381 ASP cc_start: 0.8430 (t70) cc_final: 0.8116 (t0) REVERT: B 19 ARG cc_start: 0.7122 (ttp-110) cc_final: 0.6733 (mtp85) REVERT: B 44 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6825 (mm-40) REVERT: B 45 MET cc_start: 0.8448 (mtt) cc_final: 0.8079 (mtt) REVERT: B 46 ARG cc_start: 0.7378 (tpt170) cc_final: 0.6802 (ttm-80) REVERT: B 218 CYS cc_start: 0.8532 (p) cc_final: 0.8080 (t) REVERT: G 38 MET cc_start: 0.7175 (ttp) cc_final: 0.6868 (tpp) REVERT: G 58 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7533 (tm-30) REVERT: N 38 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7776 (ptm160) REVERT: N 53 GLN cc_start: 0.8248 (mp10) cc_final: 0.7494 (mp10) REVERT: N 91 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8142 (t) REVERT: N 111 THR cc_start: 0.8258 (m) cc_final: 0.7997 (p) outliers start: 23 outliers final: 16 residues processed: 132 average time/residue: 0.5280 time to fit residues: 75.0211 Evaluate side-chains 137 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.183798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.131311 restraints weight = 10618.538| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.72 r_work: 0.3525 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9646 Z= 0.126 Angle : 0.506 12.500 13072 Z= 0.262 Chirality : 0.041 0.217 1450 Planarity : 0.003 0.042 1621 Dihedral : 4.817 59.737 1369 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.14 % Allowed : 15.67 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.25), residues: 1124 helix: 2.62 (0.24), residues: 432 sheet: -0.08 (0.32), residues: 238 loop : -0.49 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.021 0.001 TYR R 191 PHE 0.017 0.001 PHE N 29 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9640) covalent geometry : angle 0.50616 / 0.26 (13060) SS BOND : bond 0.00155 / 0.10 ( 6) SS BOND : angle 0.42596 / 0.25 ( 12) hydrogen bonds : bond 0.03688 / 2.42 ( 452) hydrogen bonds : angle 4.02231 / 2.88 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 414 MET cc_start: 0.7798 (mtp) cc_final: 0.7450 (mtt) REVERT: R 423 VAL cc_start: 0.8697 (t) cc_final: 0.8460 (m) REVERT: A 31 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7773 (tp-100) REVERT: A 229 ASP cc_start: 0.7659 (t0) cc_final: 0.7085 (t0) REVERT: A 314 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7970 (pt0) REVERT: A 356 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7254 (ttp80) REVERT: A 381 ASP cc_start: 0.8420 (t70) cc_final: 0.8102 (t0) REVERT: B 19 ARG cc_start: 0.7128 (ttp-110) cc_final: 0.6729 (mtp85) REVERT: B 44 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6815 (mm-40) REVERT: B 45 MET cc_start: 0.8362 (mtt) cc_final: 0.7968 (mtt) REVERT: B 46 ARG cc_start: 0.7424 (tpt170) cc_final: 0.6868 (ttm-80) REVERT: B 59 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: B 218 CYS cc_start: 0.8472 (p) cc_final: 0.8097 (t) REVERT: B 340 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8227 (t0) REVERT: G 58 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7494 (tm-30) REVERT: N 38 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7761 (ptm160) REVERT: N 53 GLN cc_start: 0.8202 (mp10) cc_final: 0.7480 (mp10) REVERT: N 91 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8192 (t) REVERT: N 111 THR cc_start: 0.8254 (m) cc_final: 0.8039 (p) outliers start: 21 outliers final: 15 residues processed: 130 average time/residue: 0.5286 time to fit residues: 73.6226 Evaluate side-chains 138 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.178704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125622 restraints weight = 10675.410| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.77 r_work: 0.3447 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 9646 Z= 0.232 Angle : 0.607 10.637 13072 Z= 0.316 Chirality : 0.045 0.231 1450 Planarity : 0.004 0.041 1621 Dihedral : 5.481 54.866 1369 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.54 % Allowed : 15.36 % Favored : 82.10 % 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 (0.25), residues: 1124 helix: 2.23 (0.24), residues: 438 sheet: -0.22 (0.32), residues: 238 loop : -0.60 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.022 0.002 TYR A 339 PHE 0.019 0.002 PHE N 29 TRP 0.014 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.23 ( 9640) covalent geometry : angle 0.60669 / 0.32 (13060) SS BOND : bond 0.00194 / 0.13 ( 6) SS BOND : angle 0.58202 / 0.33 ( 12) hydrogen bonds : bond 0.04658 / 3.08 ( 452) hydrogen bonds : angle 4.31451 / 3.09 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3012.03 seconds wall clock time: 52 minutes 2.65 seconds (3122.65 seconds total)