Starting phenix.real_space_refine on Wed Mar 4 00:45:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nbf_0410/03_2026/6nbf_0410.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nbf_0410/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6nbf_0410/03_2026/6nbf_0410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nbf_0410/03_2026/6nbf_0410.map" model { file = "/net/cci-nas-00/data/ceres_data/6nbf_0410/03_2026/6nbf_0410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nbf_0410/03_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-dev-5986/lib/python3.9/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: 2.12, per 1000 atoms: 0.22 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: 0.66 Conformation dependent library (CDL) restraints added in 281.3 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: 0.25 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: 1.44 Time building geometry restraints manager: 0.92 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: 5669 14.18 - 28.37: 262 28.37 - 42.55: 55 42.55 - 56.74: 23 56.74 - 70.92: 3 Dihedral angle restraints: 6012 sinusoidal: 2673 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 6009 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: 1.170 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.200 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:7.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 9.167 70.921 3834 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 covalent geometry : bond 0.00474 ( 9640) covalent geometry : angle 0.90192 (13060) SS BOND : bond 0.00251 ( 6) SS BOND : angle 1.72845 ( 12) hydrogen bonds : bond 0.13358 ( 452) hydrogen bonds : angle 6.81163 ( 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 : 0.328 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: 0.5174 time to fit residues: 112.9721 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 : 0.279 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4275 r_free = 0.4275 target = 0.187415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.133525 restraints weight = 10548.200| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.73 r_work: 0.3625 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9646 Z= 0.172 Angle : 0.566 6.456 13072 Z= 0.301 Chirality : 0.043 0.153 1450 Planarity : 0.004 0.054 1621 Dihedral : 6.976 51.506 1710 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.36 % Allowed : 8.95 % 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: 0.15 (0.25), residues: 1124 helix: 1.46 (0.25), residues: 439 sheet: -0.36 (0.31), residues: 233 loop : -0.97 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 389 TYR 0.028 0.002 TYR R 191 PHE 0.018 0.002 PHE B 222 TRP 0.019 0.002 TRP R 298 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9640) covalent geometry : angle 0.56593 (13060) SS BOND : bond 0.00200 ( 6) SS BOND : angle 0.68142 ( 12) hydrogen bonds : bond 0.04458 ( 452) hydrogen bonds : angle 4.78593 ( 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 183 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.301 Fit side-chains REVERT: R 423 VAL cc_start: 0.8560 (t) cc_final: 0.8334 (m) REVERT: A 24 LYS cc_start: 0.7196 (mttt) cc_final: 0.6788 (mmmt) REVERT: A 31 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7779 (tp-100) REVERT: A 314 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7945 (pt0) REVERT: B 42 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.5631 (mmt180) REVERT: B 181 THR cc_start: 0.8933 (p) cc_final: 0.8657 (p) REVERT: B 220 GLN cc_start: 0.8188 (mt0) cc_final: 0.7740 (mt0) REVERT: B 254 ASP cc_start: 0.8417 (t70) cc_final: 0.8086 (t0) REVERT: N 46 GLU cc_start: 0.8273 (pt0) cc_final: 0.7968 (pt0) REVERT: N 53 GLN cc_start: 0.8119 (mp10) cc_final: 0.7640 (mp10) outliers start: 33 outliers final: 12 residues processed: 163 average time/residue: 0.5420 time to fit residues: 94.2340 Evaluate side-chains 138 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 392 THR 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 285 LEU 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 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: 2.9990 chunk 78 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 0.0470 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4299 r_free = 0.4299 target = 0.190422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136649 restraints weight = 10299.571| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.75 r_work: 0.3605 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9646 Z= 0.103 Angle : 0.481 5.911 13072 Z= 0.254 Chirality : 0.040 0.170 1450 Planarity : 0.004 0.049 1621 Dihedral : 6.473 55.561 1707 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.34 % Allowed : 13.12 % Favored : 84.54 % 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: 0.72 (0.25), residues: 1124 helix: 2.13 (0.25), residues: 433 sheet: -0.09 (0.32), residues: 233 loop : -0.81 (0.28), residues: 458 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 0.011 0.001 PHE B 222 TRP 0.014 0.001 TRP R 298 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9640) covalent geometry : angle 0.48097 (13060) SS BOND : bond 0.00157 ( 6) SS BOND : angle 0.55709 ( 12) hydrogen bonds : bond 0.03618 ( 452) hydrogen bonds : angle 4.31543 ( 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 161 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: R 181 ARG cc_start: 0.7039 (ttm170) cc_final: 0.6750 (ttp80) REVERT: R 214 ARG cc_start: 0.6739 (mtt180) cc_final: 0.6422 (ptm160) REVERT: A 31 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7704 (tp-100) REVERT: A 239 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8636 (p0) REVERT: A 283 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7457 (mtt90) REVERT: A 314 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7877 (pt0) REVERT: A 344 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7955 (tp30) REVERT: A 378 ASP cc_start: 0.7752 (m-30) cc_final: 0.7445 (m-30) REVERT: B 19 ARG cc_start: 0.6774 (ttp-110) cc_final: 0.6449 (mtp85) REVERT: B 181 THR cc_start: 0.8766 (p) cc_final: 0.8561 (p) REVERT: B 198 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8200 (mt) REVERT: B 214 ARG cc_start: 0.8079 (ttm170) cc_final: 0.7856 (mtt180) REVERT: B 217 MET cc_start: 0.8008 (pmt) cc_final: 0.7208 (pmm) REVERT: B 219 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7513 (mtp85) REVERT: B 254 ASP cc_start: 0.8242 (t70) cc_final: 0.7833 (t0) REVERT: G 46 LYS cc_start: 0.8113 (mptt) cc_final: 0.7776 (pptt) REVERT: N 53 GLN cc_start: 0.8129 (mp10) cc_final: 0.7624 (mp10) outliers start: 23 outliers final: 13 residues processed: 148 average time/residue: 0.5406 time to fit residues: 85.6251 Evaluate side-chains 135 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 35 ASN 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: 0.0980 chunk 18 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4186 r_free = 0.4186 target = 0.181023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127282 restraints weight = 10723.529| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.75 r_work: 0.3578 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9646 Z= 0.183 Angle : 0.542 7.660 13072 Z= 0.287 Chirality : 0.042 0.153 1450 Planarity : 0.004 0.044 1621 Dihedral : 6.615 57.878 1705 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.46 % Allowed : 13.02 % Favored : 83.52 % 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: 2.08 (0.25), residues: 437 sheet: -0.05 (0.32), residues: 229 loop : -0.78 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.024 0.002 TYR R 191 PHE 0.027 0.002 PHE A 238 TRP 0.015 0.002 TRP R 298 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9640) covalent geometry : angle 0.54218 (13060) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.61203 ( 12) hydrogen bonds : bond 0.04355 ( 452) hydrogen bonds : angle 4.33981 ( 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 164 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.299 Fit side-chains REVERT: R 214 ARG cc_start: 0.6873 (mtt180) cc_final: 0.6561 (ptm160) REVERT: A 24 LYS cc_start: 0.7245 (mttt) cc_final: 0.6779 (tptt) REVERT: A 31 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7811 (tp-100) REVERT: A 283 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7798 (mtt90) REVERT: A 314 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8007 (pt0) REVERT: A 356 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7208 (ttp80) REVERT: A 378 ASP cc_start: 0.7917 (m-30) cc_final: 0.7620 (m-30) REVERT: A 381 ASP cc_start: 0.8335 (t70) cc_final: 0.8014 (t0) REVERT: B 44 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6497 (mm-40) REVERT: B 45 MET cc_start: 0.8295 (mtt) cc_final: 0.7917 (mtt) REVERT: B 46 ARG cc_start: 0.7259 (tpt170) cc_final: 0.6631 (ttm-80) REVERT: B 172 GLU cc_start: 0.8035 (tp30) cc_final: 0.7571 (pm20) REVERT: B 217 MET cc_start: 0.7973 (pmt) cc_final: 0.7340 (pmm) REVERT: B 219 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7668 (mtp85) REVERT: G 38 MET cc_start: 0.7242 (ttp) cc_final: 0.6855 (tpp) REVERT: N 53 GLN cc_start: 0.8207 (mp10) cc_final: 0.7608 (mp10) REVERT: N 91 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7852 (t) outliers start: 34 outliers final: 18 residues processed: 148 average time/residue: 0.5473 time to fit residues: 86.3943 Evaluate side-chains 146 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 412 VAL 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: 0.6980 chunk 92 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.182672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129155 restraints weight = 10718.268| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.76 r_work: 0.3603 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9646 Z= 0.132 Angle : 0.495 7.660 13072 Z= 0.262 Chirality : 0.041 0.266 1450 Planarity : 0.004 0.038 1621 Dihedral : 6.259 54.098 1705 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.05 % Allowed : 14.04 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.96 (0.25), residues: 1124 helix: 2.31 (0.25), residues: 431 sheet: 0.11 (0.32), residues: 228 loop : -0.69 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.022 0.001 TYR R 191 PHE 0.022 0.001 PHE N 29 TRP 0.013 0.001 TRP R 298 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9640) covalent geometry : angle 0.49536 (13060) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.52573 ( 12) hydrogen bonds : bond 0.03795 ( 452) hydrogen bonds : angle 4.15548 ( 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 160 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: R 214 ARG cc_start: 0.6865 (mtt180) cc_final: 0.6527 (ptm160) REVERT: A 24 LYS cc_start: 0.7219 (mttt) cc_final: 0.6752 (tptt) REVERT: A 31 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7513 (tp-100) REVERT: A 283 ARG cc_start: 0.8177 (mtm180) cc_final: 0.7784 (mtt90) REVERT: A 314 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7924 (pt0) REVERT: A 356 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7320 (ttp80) REVERT: B 44 GLN cc_start: 0.7797 (mt0) cc_final: 0.6662 (mm-40) REVERT: B 45 MET cc_start: 0.8352 (mtt) cc_final: 0.7939 (mtt) REVERT: B 46 ARG cc_start: 0.7228 (tpt170) cc_final: 0.6619 (ttm-80) REVERT: B 172 GLU cc_start: 0.7980 (tp30) cc_final: 0.7511 (pm20) REVERT: B 214 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7923 (mpt180) REVERT: B 217 MET cc_start: 0.7854 (pmt) cc_final: 0.7338 (pmm) REVERT: B 219 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7644 (mtp85) REVERT: G 38 MET cc_start: 0.7037 (ttp) cc_final: 0.6734 (tpp) REVERT: G 46 LYS cc_start: 0.8092 (mptt) cc_final: 0.7870 (ttmp) REVERT: N 38 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7881 (ptm160) REVERT: N 53 GLN cc_start: 0.8124 (mp10) cc_final: 0.7491 (mp10) REVERT: N 89 GLU cc_start: 0.7444 (pp20) cc_final: 0.7202 (pp20) REVERT: N 91 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8088 (t) outliers start: 30 outliers final: 15 residues processed: 148 average time/residue: 0.5569 time to fit residues: 87.8272 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 : 0.330 ------------------------------------------------------------------------------- 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 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 29 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 0.0270 chunk 80 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 295 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 = 0.4235 r_free = 0.4235 target = 0.186101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132017 restraints weight = 10493.460| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.77 r_work: 0.3568 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9646 Z= 0.099 Angle : 0.460 8.394 13072 Z= 0.243 Chirality : 0.040 0.237 1450 Planarity : 0.003 0.039 1621 Dihedral : 5.964 53.626 1705 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.34 % Allowed : 14.95 % Favored : 82.71 % 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 (0.26), residues: 1124 helix: 2.54 (0.25), residues: 432 sheet: 0.27 (0.33), residues: 226 loop : -0.61 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.021 0.001 TYR R 191 PHE 0.019 0.001 PHE N 29 TRP 0.011 0.001 TRP R 298 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9640) covalent geometry : angle 0.46010 (13060) SS BOND : bond 0.00127 ( 6) SS BOND : angle 0.48352 ( 12) hydrogen bonds : bond 0.03350 ( 452) hydrogen bonds : angle 3.99755 ( 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 146 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: R 214 ARG cc_start: 0.6797 (mtt180) cc_final: 0.6431 (ptm160) REVERT: R 414 MET cc_start: 0.7592 (mtp) cc_final: 0.7286 (mtt) REVERT: A 31 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7664 (tp-100) REVERT: A 34 LYS cc_start: 0.7379 (ttpt) cc_final: 0.7150 (ttpt) REVERT: A 283 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7531 (mtt90) REVERT: A 314 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7839 (pt0) REVERT: A 381 ASP cc_start: 0.8265 (t70) cc_final: 0.7912 (t0) REVERT: B 19 ARG cc_start: 0.6927 (ttp-110) cc_final: 0.6618 (mtp85) REVERT: B 44 GLN cc_start: 0.7454 (mt0) cc_final: 0.6400 (mm-40) REVERT: B 45 MET cc_start: 0.8451 (mtt) cc_final: 0.8033 (mtt) REVERT: B 46 ARG cc_start: 0.7122 (tpt170) cc_final: 0.6432 (ttm-80) REVERT: B 172 GLU cc_start: 0.7964 (tp30) cc_final: 0.7422 (pm20) REVERT: B 214 ARG cc_start: 0.8354 (mtt180) cc_final: 0.7894 (mpt180) REVERT: B 217 MET cc_start: 0.7751 (pmt) cc_final: 0.7212 (pmm) REVERT: B 219 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7663 (mtp85) REVERT: B 220 GLN cc_start: 0.8468 (mt0) cc_final: 0.8090 (mt0) REVERT: B 340 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7446 (t0) REVERT: G 38 MET cc_start: 0.6799 (ttp) cc_final: 0.6534 (tpp) REVERT: G 58 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7361 (tm-30) REVERT: N 38 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7546 (ptm160) REVERT: N 53 GLN cc_start: 0.8052 (mp10) cc_final: 0.7437 (mp10) REVERT: N 89 GLU cc_start: 0.7474 (pp20) cc_final: 0.7222 (pp20) REVERT: N 91 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7967 (t) outliers start: 23 outliers final: 13 residues processed: 137 average time/residue: 0.5701 time to fit residues: 83.2678 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 : 0.254 ------------------------------------------------------------------------------- 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 349 SER Chi-restraints excluded: chain B residue 29 THR 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 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 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: 0.0770 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 87 optimal weight: 0.1980 chunk 4 optimal weight: 40.0000 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4218 r_free = 0.4218 target = 0.186251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133943 restraints weight = 10534.685| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.72 r_work: 0.3521 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9646 Z= 0.099 Angle : 0.465 8.507 13072 Z= 0.243 Chirality : 0.041 0.216 1450 Planarity : 0.003 0.041 1621 Dihedral : 5.842 53.767 1705 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.54 % Allowed : 15.06 % Favored : 82.40 % 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: 1.31 (0.26), residues: 1124 helix: 2.64 (0.25), residues: 432 sheet: 0.19 (0.33), residues: 233 loop : -0.49 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.020 0.001 TYR R 191 PHE 0.017 0.001 PHE N 29 TRP 0.010 0.001 TRP R 298 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9640) covalent geometry : angle 0.46505 (13060) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.42925 ( 12) hydrogen bonds : bond 0.03356 ( 452) hydrogen bonds : angle 3.93852 ( 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 150 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: R 214 ARG cc_start: 0.6807 (mtt180) cc_final: 0.6522 (ptm160) REVERT: R 414 MET cc_start: 0.7658 (mtp) cc_final: 0.7352 (mtt) REVERT: A 31 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7755 (tp-100) REVERT: A 34 LYS cc_start: 0.7670 (ttpt) cc_final: 0.7445 (ttpt) REVERT: A 239 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8763 (p0) REVERT: A 314 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7931 (pt0) REVERT: A 356 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7304 (ttp80) REVERT: A 381 ASP cc_start: 0.8393 (t70) cc_final: 0.8079 (t0) REVERT: B 19 ARG cc_start: 0.7110 (ttp-110) cc_final: 0.6720 (mtp85) REVERT: B 44 GLN cc_start: 0.7575 (mt0) cc_final: 0.6649 (mm-40) REVERT: B 45 MET cc_start: 0.8394 (mtt) cc_final: 0.7945 (mtt) REVERT: B 46 ARG cc_start: 0.7300 (tpt170) cc_final: 0.6721 (ttm-80) REVERT: B 172 GLU cc_start: 0.7964 (tp30) cc_final: 0.7584 (pm20) REVERT: B 198 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8193 (mt) REVERT: B 214 ARG cc_start: 0.8413 (mtt180) cc_final: 0.8012 (mpt180) REVERT: B 217 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7402 (pmm) REVERT: B 219 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7829 (mtp85) REVERT: B 220 GLN cc_start: 0.8562 (mt0) cc_final: 0.8074 (mt0) REVERT: B 340 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7150 (t0) REVERT: G 38 MET cc_start: 0.7022 (ttp) cc_final: 0.6761 (tpp) REVERT: G 58 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7510 (tm-30) REVERT: N 38 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7715 (ptm160) REVERT: N 53 GLN cc_start: 0.8006 (mp10) cc_final: 0.7344 (mp10) REVERT: N 91 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8084 (t) outliers start: 25 outliers final: 15 residues processed: 138 average time/residue: 0.5595 time to fit residues: 82.4937 Evaluate side-chains 139 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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 29 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 139 ASN A 239 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.185648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133302 restraints weight = 10580.144| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.72 r_work: 0.3544 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9646 Z= 0.105 Angle : 0.472 9.794 13072 Z= 0.246 Chirality : 0.040 0.212 1450 Planarity : 0.003 0.042 1621 Dihedral : 5.800 54.177 1705 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.85 % Allowed : 15.56 % Favored : 81.59 % 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: 1.37 (0.26), residues: 1124 helix: 2.68 (0.25), residues: 432 sheet: 0.29 (0.33), residues: 228 loop : -0.49 (0.29), residues: 464 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 0.014 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 covalent geometry : bond 0.00240 ( 9640) covalent geometry : angle 0.47195 (13060) SS BOND : bond 0.00127 ( 6) SS BOND : angle 0.43675 ( 12) hydrogen bonds : bond 0.03367 ( 452) hydrogen bonds : angle 3.89028 ( 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 151 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: R 414 MET cc_start: 0.7634 (mtp) cc_final: 0.7331 (mtt) REVERT: A 31 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7771 (tp-100) REVERT: A 34 LYS cc_start: 0.7703 (ttpt) cc_final: 0.7479 (ttpt) REVERT: A 229 ASP cc_start: 0.7612 (t0) cc_final: 0.7070 (t0) REVERT: A 314 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7918 (pt0) REVERT: A 356 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7268 (ttp80) REVERT: A 381 ASP cc_start: 0.8403 (t70) cc_final: 0.8093 (t0) REVERT: B 19 ARG cc_start: 0.7150 (ttp-110) cc_final: 0.6778 (mtp85) REVERT: B 44 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6659 (mm-40) REVERT: B 45 MET cc_start: 0.8432 (mtt) cc_final: 0.8024 (mtt) REVERT: B 46 ARG cc_start: 0.7309 (tpt170) cc_final: 0.6725 (ttm-80) REVERT: B 172 GLU cc_start: 0.7991 (tp30) cc_final: 0.7574 (pm20) REVERT: B 198 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8160 (mt) REVERT: B 214 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8007 (mmt180) REVERT: B 217 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7429 (pmm) REVERT: B 219 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7821 (mtp85) REVERT: B 220 GLN cc_start: 0.8703 (mt0) cc_final: 0.8274 (mt0) REVERT: G 38 MET cc_start: 0.7099 (ttp) cc_final: 0.6785 (tpp) REVERT: G 58 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7547 (tm-30) REVERT: N 38 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7750 (ptm160) REVERT: N 53 GLN cc_start: 0.8044 (mp10) cc_final: 0.7367 (mp10) REVERT: N 91 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8094 (t) REVERT: N 111 THR cc_start: 0.8207 (m) cc_final: 0.7960 (p) outliers start: 28 outliers final: 16 residues processed: 138 average time/residue: 0.5316 time to fit residues: 78.6185 Evaluate side-chains 141 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 138 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 94 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.185642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133063 restraints weight = 10584.555| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.75 r_work: 0.3559 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9646 Z= 0.105 Angle : 0.475 10.519 13072 Z= 0.247 Chirality : 0.040 0.215 1450 Planarity : 0.003 0.044 1621 Dihedral : 5.709 55.517 1705 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.44 % Allowed : 16.07 % Favored : 81.49 % 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: 1.42 (0.26), residues: 1124 helix: 2.75 (0.24), residues: 432 sheet: 0.19 (0.33), residues: 236 loop : -0.41 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.020 0.001 TYR R 191 PHE 0.012 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 covalent geometry : bond 0.00241 ( 9640) covalent geometry : angle 0.47462 (13060) SS BOND : bond 0.00135 ( 6) SS BOND : angle 0.42422 ( 12) hydrogen bonds : bond 0.03371 ( 452) hydrogen bonds : angle 3.86818 ( 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 145 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 414 MET cc_start: 0.7659 (mtp) cc_final: 0.7365 (mtt) REVERT: R 423 VAL cc_start: 0.8705 (t) cc_final: 0.8465 (m) REVERT: A 31 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7697 (tp-100) REVERT: A 229 ASP cc_start: 0.7642 (t0) cc_final: 0.7123 (t0) REVERT: A 314 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7946 (pt0) REVERT: A 356 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7247 (ttp80) REVERT: A 381 ASP cc_start: 0.8420 (t70) cc_final: 0.8111 (t0) REVERT: B 19 ARG cc_start: 0.7165 (ttp-110) cc_final: 0.6760 (mtp85) REVERT: B 44 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6785 (mm-40) REVERT: B 45 MET cc_start: 0.8344 (mtt) cc_final: 0.7960 (mtt) REVERT: B 46 ARG cc_start: 0.7346 (tpt170) cc_final: 0.6773 (ttm-80) REVERT: B 59 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: B 172 GLU cc_start: 0.8006 (tp30) cc_final: 0.7610 (pm20) REVERT: B 198 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8169 (mt) REVERT: B 214 ARG cc_start: 0.8437 (mtt180) cc_final: 0.8024 (mmt180) REVERT: B 217 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7407 (pmm) REVERT: B 220 GLN cc_start: 0.8737 (mt0) cc_final: 0.8284 (mt0) REVERT: G 38 MET cc_start: 0.7160 (ttp) cc_final: 0.6838 (tpp) REVERT: G 58 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7527 (tm-30) REVERT: N 38 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7776 (ptm160) REVERT: N 53 GLN cc_start: 0.7998 (mp10) cc_final: 0.7317 (mp10) REVERT: N 91 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8131 (t) REVERT: N 110 VAL cc_start: 0.7664 (t) cc_final: 0.7450 (p) REVERT: N 111 THR cc_start: 0.8222 (m) cc_final: 0.7991 (p) outliers start: 24 outliers final: 15 residues processed: 135 average time/residue: 0.5385 time to fit residues: 77.7406 Evaluate side-chains 138 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 198 LEU Chi-restraints excluded: chain B residue 217 MET 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: 7.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.182771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130256 restraints weight = 10643.749| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.71 r_work: 0.3501 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9646 Z= 0.145 Angle : 0.521 12.437 13072 Z= 0.270 Chirality : 0.042 0.247 1450 Planarity : 0.003 0.042 1621 Dihedral : 5.903 59.621 1705 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.03 % Allowed : 16.58 % Favored : 81.38 % 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: 1.28 (0.25), residues: 1124 helix: 2.63 (0.24), residues: 432 sheet: 0.09 (0.33), residues: 236 loop : -0.46 (0.30), residues: 456 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 0.014 0.001 PHE N 29 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9640) covalent geometry : angle 0.52142 (13060) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.46228 ( 12) hydrogen bonds : bond 0.03871 ( 452) hydrogen bonds : angle 4.00723 ( 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 145 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: R 414 MET cc_start: 0.7667 (mtp) cc_final: 0.7298 (mtt) REVERT: A 24 LYS cc_start: 0.7205 (mttt) cc_final: 0.6767 (tptt) REVERT: A 31 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7803 (tp-100) REVERT: A 229 ASP cc_start: 0.7690 (t0) cc_final: 0.7093 (t0) REVERT: A 314 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7975 (pt0) REVERT: A 356 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7258 (ttp80) REVERT: A 381 ASP cc_start: 0.8411 (t70) cc_final: 0.8093 (t0) REVERT: B 19 ARG cc_start: 0.7101 (ttp-110) cc_final: 0.6729 (mtp85) REVERT: B 44 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6830 (mm-40) REVERT: B 45 MET cc_start: 0.8390 (mtt) cc_final: 0.8018 (mtt) REVERT: B 46 ARG cc_start: 0.7450 (tpt170) cc_final: 0.6924 (ttm-80) REVERT: B 59 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7301 (m-80) REVERT: B 172 GLU cc_start: 0.8003 (tp30) cc_final: 0.7586 (pm20) REVERT: B 214 ARG cc_start: 0.8424 (mtt180) cc_final: 0.8017 (mpt180) REVERT: B 217 MET cc_start: 0.8013 (pmt) cc_final: 0.7333 (pmm) REVERT: B 220 GLN cc_start: 0.8740 (mt0) cc_final: 0.8292 (mt0) REVERT: G 58 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7537 (tm-30) REVERT: N 38 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7792 (ptm160) REVERT: N 53 GLN cc_start: 0.8094 (mp10) cc_final: 0.7387 (mp10) REVERT: N 91 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8179 (t) outliers start: 20 outliers final: 15 residues processed: 138 average time/residue: 0.5472 time to fit residues: 80.7421 Evaluate side-chains 143 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 30.0000 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 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.183456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.131218 restraints weight = 10555.953| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.70 r_work: 0.3505 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9646 Z= 0.124 Angle : 0.494 9.303 13072 Z= 0.258 Chirality : 0.041 0.233 1450 Planarity : 0.003 0.043 1621 Dihedral : 5.795 58.856 1705 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.14 % Allowed : 16.58 % Favored : 81.28 % 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: 1.30 (0.25), residues: 1124 helix: 2.60 (0.24), residues: 438 sheet: 0.07 (0.33), residues: 236 loop : -0.42 (0.30), residues: 450 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 0.013 0.001 PHE N 29 TRP 0.011 0.001 TRP R 352 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9640) covalent geometry : angle 0.49398 (13060) SS BOND : bond 0.00111 ( 6) SS BOND : angle 0.48844 ( 12) hydrogen bonds : bond 0.03613 ( 452) hydrogen bonds : angle 3.94722 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3049.75 seconds wall clock time: 52 minutes 38.60 seconds (3158.60 seconds total)