Starting phenix.real_space_refine on Wed Apr 30 14:54:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nbf_0410/04_2025/6nbf_0410.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nbf_0410/04_2025/6nbf_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_0410/04_2025/6nbf_0410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nbf_0410/04_2025/6nbf_0410.map" model { file = "/net/cci-nas-00/data/ceres_data/6nbf_0410/04_2025/6nbf_0410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nbf_0410/04_2025/6nbf_0410.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.03, per 1000 atoms: 0.64 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: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.04 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: 2.82 Time building geometry restraints manager: 3.07 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: 1.380 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 25.270 Find NCS groups from input model: 0.110 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (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 TRP 0.026 0.003 TRP B 99 HIS 0.013 0.002 HIS A 220 PHE 0.018 0.002 PHE B 199 TYR 0.030 0.002 TYR R 297 ARG 0.005 0.000 ARG P 11 Details of bonding type rmsd hydrogen bonds : bond 0.13358 ( 452) hydrogen bonds : angle 6.81163 ( 1287) SS BOND : bond 0.00251 ( 6) SS BOND : angle 1.72845 ( 12) covalent geometry : bond 0.00474 ( 9640) covalent geometry : angle 0.90192 (13060) *********************** 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 : 0.923 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) REVERT: N 53 GLN cc_start: 0.7796 (mp10) cc_final: 0.7546 (mp10) outliers start: 1 outliers final: 2 residues processed: 204 average time/residue: 1.1322 time to fit residues: 248.3611 Evaluate side-chains 126 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.0670 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 100 optimal weight: 0.0050 overall best weight: 1.0136 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.186694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.131842 restraints weight = 10474.593| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.79 r_work: 0.3647 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9646 Z= 0.141 Angle : 0.538 6.272 13072 Z= 0.287 Chirality : 0.042 0.154 1450 Planarity : 0.004 0.051 1621 Dihedral : 6.902 50.059 1710 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.95 % Allowed : 9.97 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1124 helix: 1.50 (0.25), residues: 441 sheet: -0.33 (0.31), residues: 233 loop : -1.00 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 298 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.002 PHE B 222 TYR 0.028 0.001 TYR R 191 ARG 0.003 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 452) hydrogen bonds : angle 4.74100 ( 1287) SS BOND : bond 0.00192 ( 6) SS BOND : angle 0.65099 ( 12) covalent geometry : bond 0.00322 ( 9640) covalent geometry : angle 0.53742 (13060) *********************** 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 : 0.925 Fit side-chains REVERT: R 312 MET cc_start: 0.4943 (mpt) cc_final: 0.4724 (mpt) REVERT: A 31 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7724 (tp-100) REVERT: A 314 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7880 (pt0) REVERT: B 146 LEU cc_start: 0.8799 (tp) cc_final: 0.8421 (mm) REVERT: B 160 SER cc_start: 0.8952 (t) cc_final: 0.8565 (p) REVERT: B 181 THR cc_start: 0.8902 (p) cc_final: 0.8619 (p) REVERT: B 220 GLN cc_start: 0.8072 (mt0) cc_final: 0.7654 (mt0) REVERT: B 254 ASP cc_start: 0.8359 (t70) cc_final: 0.7998 (t0) REVERT: N 46 GLU cc_start: 0.8150 (pt0) cc_final: 0.7881 (pt0) REVERT: N 53 GLN cc_start: 0.7930 (mp10) cc_final: 0.7345 (mp10) REVERT: N 59 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7559 (p) outliers start: 29 outliers final: 12 residues processed: 161 average time/residue: 1.1969 time to fit residues: 206.1929 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 : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR 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 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 85 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.185904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132041 restraints weight = 10541.975| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.77 r_work: 0.3643 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9646 Z= 0.120 Angle : 0.497 6.394 13072 Z= 0.262 Chirality : 0.041 0.153 1450 Planarity : 0.003 0.042 1621 Dihedral : 6.531 59.975 1707 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.75 % Allowed : 13.02 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1124 helix: 2.08 (0.26), residues: 432 sheet: -0.09 (0.32), residues: 233 loop : -0.82 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 222 TYR 0.026 0.001 TYR R 191 ARG 0.003 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 452) hydrogen bonds : angle 4.32565 ( 1287) SS BOND : bond 0.00142 ( 6) SS BOND : angle 0.57265 ( 12) covalent geometry : bond 0.00274 ( 9640) covalent geometry : angle 0.49694 (13060) *********************** 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 170 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: R 214 ARG cc_start: 0.6770 (mtt180) cc_final: 0.6344 (ptm160) REVERT: R 471 LYS cc_start: 0.6438 (mttt) cc_final: 0.6119 (mttp) REVERT: P 8 MET cc_start: 0.7850 (ttp) cc_final: 0.7623 (ttp) REVERT: A 31 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7745 (tp-100) REVERT: A 239 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8688 (p0) REVERT: A 310 ASP cc_start: 0.7823 (t0) cc_final: 0.7601 (t0) REVERT: A 314 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7924 (pt0) REVERT: A 378 ASP cc_start: 0.7833 (m-30) cc_final: 0.7577 (m-30) REVERT: B 44 GLN cc_start: 0.7524 (mt0) cc_final: 0.6326 (mm-40) REVERT: B 146 LEU cc_start: 0.8830 (tp) cc_final: 0.8548 (mm) REVERT: B 181 THR cc_start: 0.8816 (p) cc_final: 0.8583 (p) REVERT: B 198 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8275 (mt) REVERT: B 214 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7913 (mtt180) REVERT: B 217 MET cc_start: 0.7873 (pmt) cc_final: 0.7194 (pmm) REVERT: B 219 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7639 (mtp85) REVERT: B 220 GLN cc_start: 0.8210 (mt0) cc_final: 0.7912 (mt0) REVERT: B 254 ASP cc_start: 0.8287 (t70) cc_final: 0.7925 (t0) REVERT: B 312 ASP cc_start: 0.7996 (t70) cc_final: 0.7661 (t70) REVERT: G 46 LYS cc_start: 0.8171 (mptt) cc_final: 0.7816 (pptt) REVERT: N 46 GLU cc_start: 0.8046 (pt0) cc_final: 0.7836 (pt0) REVERT: N 53 GLN cc_start: 0.8144 (mp10) cc_final: 0.7506 (mp10) outliers start: 27 outliers final: 16 residues processed: 157 average time/residue: 1.1530 time to fit residues: 194.3810 Evaluate side-chains 146 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 B residue 161 SER Chi-restraints excluded: chain B residue 173 THR 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 66 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 80 optimal weight: 0.7980 chunk 110 optimal weight: 0.4980 chunk 5 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 390 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.183726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.129961 restraints weight = 10545.758| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.75 r_work: 0.3632 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9646 Z= 0.136 Angle : 0.499 7.150 13072 Z= 0.263 Chirality : 0.041 0.250 1450 Planarity : 0.004 0.047 1621 Dihedral : 6.273 50.250 1705 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.36 % Allowed : 13.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1124 helix: 2.22 (0.25), residues: 431 sheet: -0.01 (0.32), residues: 235 loop : -0.67 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.004 0.001 HIS A 357 PHE 0.020 0.002 PHE A 238 TYR 0.022 0.001 TYR R 191 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 452) hydrogen bonds : angle 4.18642 ( 1287) SS BOND : bond 0.00146 ( 6) SS BOND : angle 0.55760 ( 12) covalent geometry : bond 0.00318 ( 9640) covalent geometry : angle 0.49856 (13060) *********************** 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 168 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.937 Fit side-chains REVERT: R 214 ARG cc_start: 0.6899 (mtt180) cc_final: 0.6399 (ptm160) REVERT: A 24 LYS cc_start: 0.7193 (mttt) cc_final: 0.6778 (tptt) REVERT: A 31 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7807 (tp-100) REVERT: A 239 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8689 (p0) REVERT: A 283 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7804 (mtt90) REVERT: A 314 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7979 (pt0) REVERT: A 356 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7223 (ttp80) REVERT: A 378 ASP cc_start: 0.7866 (m-30) cc_final: 0.7561 (m-30) REVERT: A 381 ASP cc_start: 0.8330 (t70) cc_final: 0.8023 (t0) REVERT: B 44 GLN cc_start: 0.7581 (mt0) cc_final: 0.6430 (mm-40) REVERT: B 46 ARG cc_start: 0.7157 (tpt170) cc_final: 0.6424 (tpp-160) REVERT: B 181 THR cc_start: 0.8807 (p) cc_final: 0.8590 (p) REVERT: B 217 MET cc_start: 0.7884 (pmt) cc_final: 0.7310 (pmm) REVERT: B 219 ARG cc_start: 0.7954 (mtp85) cc_final: 0.7332 (mmm160) REVERT: N 53 GLN cc_start: 0.8238 (mp10) cc_final: 0.7593 (mp10) REVERT: N 91 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7704 (t) outliers start: 33 outliers final: 16 residues processed: 152 average time/residue: 1.1982 time to fit residues: 195.1950 Evaluate side-chains 144 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 446 LEU 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 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 35 ASN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 0.0670 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.186309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.131650 restraints weight = 10494.087| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.78 r_work: 0.3580 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9646 Z= 0.101 Angle : 0.460 7.327 13072 Z= 0.242 Chirality : 0.040 0.147 1450 Planarity : 0.003 0.039 1621 Dihedral : 5.971 49.068 1705 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.54 % Allowed : 15.16 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1124 helix: 2.46 (0.25), residues: 431 sheet: 0.17 (0.32), residues: 228 loop : -0.67 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 298 HIS 0.003 0.001 HIS A 357 PHE 0.019 0.001 PHE A 238 TYR 0.022 0.001 TYR R 191 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 452) hydrogen bonds : angle 4.01156 ( 1287) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.49044 ( 12) covalent geometry : bond 0.00227 ( 9640) covalent geometry : angle 0.45978 (13060) *********************** 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 157 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: R 214 ARG cc_start: 0.6792 (mtt180) cc_final: 0.6280 (ptm160) REVERT: R 289 LEU cc_start: 0.7995 (pp) cc_final: 0.7777 (mp) REVERT: A 31 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7633 (tp-100) REVERT: A 266 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7109 (mt) REVERT: A 283 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7640 (mtt90) REVERT: A 314 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7871 (pt0) REVERT: B 44 GLN cc_start: 0.7545 (mt0) cc_final: 0.6350 (mm-40) REVERT: B 46 ARG cc_start: 0.7049 (tpt170) cc_final: 0.6208 (tpp-160) REVERT: B 214 ARG cc_start: 0.8385 (mtt180) cc_final: 0.7839 (mpt180) REVERT: B 217 MET cc_start: 0.7745 (pmt) cc_final: 0.7214 (pmm) REVERT: B 219 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7494 (mtp85) REVERT: N 38 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7693 (ptm160) REVERT: N 53 GLN cc_start: 0.8095 (mp10) cc_final: 0.7355 (mp10) REVERT: N 89 GLU cc_start: 0.7235 (pp20) cc_final: 0.6994 (pp20) REVERT: N 91 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7688 (t) outliers start: 25 outliers final: 13 residues processed: 143 average time/residue: 1.2575 time to fit residues: 192.7486 Evaluate side-chains 141 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 346 LEU 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 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 35 ASN Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.187266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133025 restraints weight = 10394.033| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.77 r_work: 0.3590 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9646 Z= 0.097 Angle : 0.452 8.274 13072 Z= 0.237 Chirality : 0.040 0.251 1450 Planarity : 0.003 0.039 1621 Dihedral : 5.800 47.949 1705 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1124 helix: 2.61 (0.25), residues: 432 sheet: 0.32 (0.33), residues: 228 loop : -0.60 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 298 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE N 29 TYR 0.021 0.001 TYR R 191 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 452) hydrogen bonds : angle 3.92671 ( 1287) SS BOND : bond 0.00138 ( 6) SS BOND : angle 0.49719 ( 12) covalent geometry : bond 0.00217 ( 9640) covalent geometry : angle 0.45208 (13060) *********************** 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 153 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: R 214 ARG cc_start: 0.6862 (mtt180) cc_final: 0.6335 (ptm160) REVERT: A 31 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7649 (tp-100) REVERT: A 283 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7671 (mtt90) REVERT: A 314 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7892 (pt0) REVERT: A 356 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7234 (ttp80) REVERT: A 381 ASP cc_start: 0.8279 (t70) cc_final: 0.7935 (t0) REVERT: B 19 ARG cc_start: 0.6923 (ttp-110) cc_final: 0.6597 (mtp85) REVERT: B 44 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6350 (mm-40) REVERT: B 46 ARG cc_start: 0.7074 (tpt170) cc_final: 0.6357 (ttm-80) REVERT: B 172 GLU cc_start: 0.7947 (tp30) cc_final: 0.7473 (pm20) REVERT: B 198 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8059 (mt) REVERT: B 214 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7926 (mpt180) REVERT: B 217 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7293 (pmm) REVERT: B 219 ARG cc_start: 0.7923 (mtp85) cc_final: 0.7599 (mtp85) REVERT: G 38 MET cc_start: 0.7004 (ttp) cc_final: 0.6699 (tpp) REVERT: N 38 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7673 (ptm160) REVERT: N 53 GLN cc_start: 0.8068 (mp10) cc_final: 0.7369 (mp10) REVERT: N 89 GLU cc_start: 0.7467 (pp20) cc_final: 0.7239 (pp20) REVERT: N 91 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7847 (t) outliers start: 25 outliers final: 15 residues processed: 141 average time/residue: 1.2049 time to fit residues: 182.3473 Evaluate side-chains 145 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 446 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 44 GLN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 106 optimal weight: 0.0980 chunk 83 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 139 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.185952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.133177 restraints weight = 10635.612| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.73 r_work: 0.3533 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9646 Z= 0.112 Angle : 0.461 7.667 13072 Z= 0.244 Chirality : 0.041 0.234 1450 Planarity : 0.003 0.041 1621 Dihedral : 5.758 47.972 1705 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.15 % Allowed : 14.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1124 helix: 2.68 (0.25), residues: 432 sheet: 0.25 (0.33), residues: 233 loop : -0.52 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 298 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE N 29 TYR 0.023 0.001 TYR R 191 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 452) hydrogen bonds : angle 3.94581 ( 1287) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.45087 ( 12) covalent geometry : bond 0.00260 ( 9640) covalent geometry : angle 0.46067 (13060) *********************** 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 160 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: R 181 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7092 (ttp80) REVERT: R 214 ARG cc_start: 0.6977 (mtt180) cc_final: 0.6427 (ptm160) REVERT: R 414 MET cc_start: 0.7814 (mtp) cc_final: 0.7470 (mtt) REVERT: A 31 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7798 (tp-100) REVERT: A 229 ASP cc_start: 0.7564 (t0) cc_final: 0.7011 (t0) REVERT: A 283 ARG cc_start: 0.8175 (mtm180) cc_final: 0.7817 (mtt90) REVERT: A 314 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7995 (pt0) REVERT: A 356 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7356 (ttp80) REVERT: A 378 ASP cc_start: 0.7775 (m-30) cc_final: 0.7481 (m-30) REVERT: A 381 ASP cc_start: 0.8449 (t70) cc_final: 0.8175 (t0) REVERT: B 44 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6596 (mm-40) REVERT: B 46 ARG cc_start: 0.7301 (tpt170) cc_final: 0.6779 (ttm-80) REVERT: B 172 GLU cc_start: 0.7961 (tp30) cc_final: 0.7541 (pm20) REVERT: B 198 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8306 (mt) REVERT: B 214 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8084 (mpt180) REVERT: B 217 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7525 (pmm) REVERT: B 219 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7844 (mtp85) REVERT: B 220 GLN cc_start: 0.8589 (mt0) cc_final: 0.8246 (mt0) REVERT: B 262 MET cc_start: 0.8478 (mtp) cc_final: 0.8010 (mtp) REVERT: G 38 MET cc_start: 0.7309 (ttp) cc_final: 0.6921 (tpp) REVERT: G 58 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7344 (tm-30) REVERT: N 38 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7959 (ptm160) REVERT: N 53 GLN cc_start: 0.8187 (mp10) cc_final: 0.7542 (mp10) REVERT: N 91 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8096 (t) outliers start: 31 outliers final: 17 residues processed: 144 average time/residue: 1.2371 time to fit residues: 192.2985 Evaluate side-chains 147 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 ARG Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 446 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 44 GLN 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 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 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 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 4 optimal weight: 40.0000 chunk 43 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.184755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132081 restraints weight = 10738.297| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.73 r_work: 0.3537 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9646 Z= 0.121 Angle : 0.479 10.856 13072 Z= 0.251 Chirality : 0.040 0.225 1450 Planarity : 0.003 0.040 1621 Dihedral : 5.746 49.359 1705 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.85 % Allowed : 15.36 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1124 helix: 2.57 (0.24), residues: 438 sheet: 0.26 (0.33), residues: 233 loop : -0.45 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 298 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE N 29 TYR 0.019 0.001 TYR R 191 ARG 0.008 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 452) hydrogen bonds : angle 3.90086 ( 1287) SS BOND : bond 0.00139 ( 6) SS BOND : angle 0.43304 ( 12) covalent geometry : bond 0.00283 ( 9640) covalent geometry : angle 0.47943 (13060) *********************** 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 155 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 181 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6906 (ttp80) REVERT: R 214 ARG cc_start: 0.6998 (mtt180) cc_final: 0.6419 (ptm160) REVERT: R 289 LEU cc_start: 0.8053 (pp) cc_final: 0.7813 (mp) REVERT: R 414 MET cc_start: 0.7765 (mtp) cc_final: 0.7410 (mtt) REVERT: A 31 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7766 (tp-100) REVERT: A 229 ASP cc_start: 0.7580 (t0) cc_final: 0.7078 (t0) REVERT: A 314 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7969 (pt0) REVERT: A 356 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7299 (ttp80) REVERT: A 378 ASP cc_start: 0.7814 (m-30) cc_final: 0.7532 (m-30) REVERT: A 381 ASP cc_start: 0.8409 (t70) cc_final: 0.8104 (t0) REVERT: B 19 ARG cc_start: 0.7010 (ttp-110) cc_final: 0.6652 (mtp85) REVERT: B 44 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6602 (mm-40) REVERT: B 46 ARG cc_start: 0.7243 (tpt170) cc_final: 0.6706 (ttm-80) REVERT: B 172 GLU cc_start: 0.7949 (tp30) cc_final: 0.7513 (pm20) REVERT: B 214 ARG cc_start: 0.8435 (mtt180) cc_final: 0.8056 (mpt180) REVERT: B 217 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7515 (pmm) REVERT: B 219 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7778 (mtp85) REVERT: G 38 MET cc_start: 0.7102 (ttp) cc_final: 0.6792 (tpp) REVERT: G 58 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7355 (tm-30) REVERT: N 38 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7811 (ptm160) REVERT: N 53 GLN cc_start: 0.8136 (mp10) cc_final: 0.7392 (mp10) REVERT: N 91 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8091 (t) outliers start: 28 outliers final: 18 residues processed: 142 average time/residue: 1.2092 time to fit residues: 183.9840 Evaluate side-chains 150 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 ARG Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain R residue 446 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 161 SER 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 78 THR 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 63 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.182295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129605 restraints weight = 10609.704| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.70 r_work: 0.3512 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9646 Z= 0.156 Angle : 0.523 10.010 13072 Z= 0.272 Chirality : 0.042 0.231 1450 Planarity : 0.003 0.041 1621 Dihedral : 5.933 52.835 1705 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.64 % Allowed : 15.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1124 helix: 2.61 (0.24), residues: 432 sheet: 0.16 (0.33), residues: 236 loop : -0.48 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE N 29 TYR 0.020 0.001 TYR R 191 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 452) hydrogen bonds : angle 4.02108 ( 1287) SS BOND : bond 0.00153 ( 6) SS BOND : angle 0.51114 ( 12) covalent geometry : bond 0.00372 ( 9640) covalent geometry : angle 0.52273 (13060) *********************** 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 151 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: R 181 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6928 (ttp80) REVERT: R 214 ARG cc_start: 0.7168 (mtt180) cc_final: 0.6812 (ttp80) REVERT: R 414 MET cc_start: 0.7808 (mtp) cc_final: 0.7446 (mtt) REVERT: A 24 LYS cc_start: 0.7224 (mttt) cc_final: 0.6745 (tptt) REVERT: A 31 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7797 (tp-100) REVERT: A 229 ASP cc_start: 0.7753 (t0) cc_final: 0.7096 (t0) REVERT: A 314 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7953 (pt0) REVERT: A 356 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7309 (ttp80) REVERT: A 378 ASP cc_start: 0.7860 (m-30) cc_final: 0.7569 (m-30) REVERT: A 381 ASP cc_start: 0.8425 (t70) cc_final: 0.8120 (t0) REVERT: B 19 ARG cc_start: 0.7092 (ttp-110) cc_final: 0.6720 (mtp85) REVERT: B 44 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6677 (mm-40) REVERT: B 46 ARG cc_start: 0.7399 (tpt170) cc_final: 0.6844 (ttm-80) REVERT: B 172 GLU cc_start: 0.7934 (tp30) cc_final: 0.7567 (pm20) REVERT: B 214 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8056 (mpt180) REVERT: B 217 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7510 (pmm) REVERT: B 220 GLN cc_start: 0.8582 (mt0) cc_final: 0.8244 (mt0) REVERT: B 340 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7473 (t0) REVERT: G 38 MET cc_start: 0.7200 (ttp) cc_final: 0.6909 (tpp) REVERT: G 58 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7486 (tm-30) REVERT: N 38 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7883 (ptm160) REVERT: N 53 GLN cc_start: 0.8173 (mp10) cc_final: 0.7452 (mp10) REVERT: N 91 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8184 (t) outliers start: 26 outliers final: 18 residues processed: 139 average time/residue: 1.2232 time to fit residues: 182.3116 Evaluate side-chains 146 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 ARG 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 R residue 446 LEU 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 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 78 THR 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 62 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 87 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.184623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132368 restraints weight = 10612.831| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.70 r_work: 0.3529 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3656 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= 0.114 Angle : 0.485 9.513 13072 Z= 0.253 Chirality : 0.041 0.239 1450 Planarity : 0.003 0.042 1621 Dihedral : 5.767 53.280 1705 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.24 % Allowed : 16.79 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1124 helix: 2.62 (0.24), residues: 438 sheet: 0.15 (0.33), residues: 231 loop : -0.44 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE N 29 TYR 0.020 0.001 TYR R 191 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 452) hydrogen bonds : angle 3.91762 ( 1287) SS BOND : bond 0.00129 ( 6) SS BOND : angle 0.44174 ( 12) covalent geometry : bond 0.00264 ( 9640) covalent geometry : angle 0.48551 (13060) ********************** 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 142 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: R 181 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6894 (ttp80) REVERT: R 214 ARG cc_start: 0.7018 (mtt180) cc_final: 0.6663 (ttp80) REVERT: R 414 MET cc_start: 0.7744 (mtp) cc_final: 0.7383 (mtt) REVERT: A 31 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7794 (tp-100) REVERT: A 314 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7937 (pt0) REVERT: A 356 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7293 (ttp80) REVERT: A 378 ASP cc_start: 0.7792 (m-30) cc_final: 0.7505 (m-30) REVERT: A 381 ASP cc_start: 0.8423 (t70) cc_final: 0.8117 (t0) REVERT: B 19 ARG cc_start: 0.7097 (ttp-110) cc_final: 0.6715 (mtp85) REVERT: B 44 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6756 (mm-40) REVERT: B 46 ARG cc_start: 0.7289 (tpt170) cc_final: 0.6753 (ttm-80) REVERT: B 172 GLU cc_start: 0.7932 (tp30) cc_final: 0.7524 (pm20) REVERT: B 214 ARG cc_start: 0.8425 (mtt180) cc_final: 0.8052 (mpt180) REVERT: B 217 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7489 (pmm) REVERT: B 220 GLN cc_start: 0.8685 (mt0) cc_final: 0.8329 (mt0) REVERT: B 340 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6958 (t0) REVERT: G 38 MET cc_start: 0.7182 (ttp) cc_final: 0.6917 (tpp) REVERT: G 58 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7542 (tm-30) REVERT: N 38 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7739 (ptm160) REVERT: N 53 GLN cc_start: 0.8141 (mp10) cc_final: 0.7640 (mp10) REVERT: N 91 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8171 (t) outliers start: 22 outliers final: 15 residues processed: 131 average time/residue: 1.1875 time to fit residues: 167.1671 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 : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 ARG 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 446 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 3 optimal weight: 40.0000 chunk 76 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.184095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.131480 restraints weight = 10586.472| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.71 r_work: 0.3498 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3720 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 : 0.500 11.233 13072 Z= 0.259 Chirality : 0.041 0.229 1450 Planarity : 0.003 0.042 1621 Dihedral : 5.777 55.014 1705 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.44 % Allowed : 16.58 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1124 helix: 2.65 (0.24), residues: 438 sheet: 0.11 (0.33), residues: 231 loop : -0.46 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE N 29 TYR 0.020 0.001 TYR R 191 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 452) hydrogen bonds : angle 3.94446 ( 1287) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.44035 ( 12) covalent geometry : bond 0.00298 ( 9640) covalent geometry : angle 0.50022 (13060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6657.79 seconds wall clock time: 114 minutes 53.22 seconds (6893.22 seconds total)