Starting phenix.real_space_refine on Wed Mar 4 00:55:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f16_31405/03_2026/7f16_31405_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f16_31405/03_2026/7f16_31405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f16_31405/03_2026/7f16_31405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f16_31405/03_2026/7f16_31405.map" model { file = "/net/cci-nas-00/data/ceres_data/7f16_31405/03_2026/7f16_31405_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f16_31405/03_2026/7f16_31405_neut.cif" } resolution = 2.8 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= 0.001 sd= 0.023 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 6106 2.51 5 N 1619 2.21 5 O 1705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 9488 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3072 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 10, 'TRANS': 365} Chain breaks: 3 Chain: "P" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 282 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1905 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} 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: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Unusual residues: {'CLR': 4, 'PLM': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 2.49, per 1000 atoms: 0.26 Number of scatterers: 9488 At special positions: 0 Unit cell: (74.195, 101.365, 172.425, 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 1705 8.00 N 1619 7.00 C 6106 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 72 " distance=2.03 Simple disulfide: pdb=" SG CYS R 63 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS R 86 " - pdb=" SG CYS R 125 " distance=2.04 Simple disulfide: pdb=" SG CYS R 236 " - pdb=" SG CYS R 306 " 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: 0.75 Conformation dependent library (CDL) restraints added in 344.6 milliseconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 44.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'R' and resid 33 through 57 removed outlier: 3.882A pdb=" N THR R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN R 55 " --> pdb=" O ASN R 51 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN R 57 " --> pdb=" O THR R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 169 removed outlier: 3.871A pdb=" N ASP R 132 " --> pdb=" O PHE R 128 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU R 159 " --> pdb=" O SER R 155 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.561A pdb=" N ILE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 267 removed outlier: 4.167A pdb=" N LYS R 237 " --> pdb=" O TYR R 233 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA R 248 " --> pdb=" O ILE R 244 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN R 263 " --> pdb=" O LEU R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 302 Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 315 through 347 Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 354 through 373 Processing helix chain 'R' and resid 373 through 381 removed outlier: 4.172A pdb=" N ILE R 377 " --> pdb=" O GLY R 373 " (cutoff:3.500A) Processing helix chain 'R' and resid 389 through 414 removed outlier: 4.489A pdb=" N GLY R 406 " --> pdb=" O ASN R 402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE R 407 " --> pdb=" O SER R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 434 Processing helix chain 'P' and resid 4 through 34 Processing helix chain 'A' and resid 12 through 40 removed outlier: 4.265A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.512A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.949A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.776A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.396A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.545A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.613A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.556A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.936A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 81 through 85 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.609A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 7.063A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.868A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.294A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.497A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.696A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.657A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.543A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.996A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1425 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: 1.40 Time building geometry restraints manager: 1.04 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: 3030 1.34 - 1.47: 2348 1.47 - 1.59: 4242 1.59 - 1.71: 0 1.71 - 1.83: 80 Bond restraints: 9700 Sorted by residual: bond pdb=" C PHE R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.58e+00 bond pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.32e-02 5.74e+03 3.30e+00 bond pdb=" C5 CLR R 503 " pdb=" C6 CLR R 503 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C ALA R 320 " pdb=" N PRO R 321 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.39e+00 bond pdb=" C5 CLR R 502 " pdb=" C6 CLR R 502 " ideal model delta sigma weight residual 1.332 1.302 0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 9695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 12467 1.77 - 3.54: 544 3.54 - 5.31: 81 5.31 - 7.07: 22 7.07 - 8.84: 3 Bond angle restraints: 13117 Sorted by residual: angle pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " pdb=" CG TYR R 148 " ideal model delta sigma weight residual 113.90 121.73 -7.83 1.80e+00 3.09e-01 1.89e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 124.31 130.25 -5.94 1.67e+00 3.59e-01 1.27e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 127.49 -4.75 1.44e+00 4.82e-01 1.09e+01 angle pdb=" N GLY B 116 " pdb=" CA GLY B 116 " pdb=" C GLY B 116 " ideal model delta sigma weight residual 111.27 116.50 -5.23 1.67e+00 3.59e-01 9.82e+00 angle pdb=" C MET R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.14 115.67 5.47 1.75e+00 3.27e-01 9.78e+00 ... (remaining 13112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 5777 18.02 - 36.04: 127 36.04 - 54.05: 35 54.05 - 72.07: 3 72.07 - 90.09: 3 Dihedral angle restraints: 5945 sinusoidal: 2570 harmonic: 3375 Sorted by residual: dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 72 " pdb=" CB CYS R 72 " ideal model delta sinusoidal sigma weight residual -86.00 -176.09 90.09 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CA TYR R 233 " pdb=" C TYR R 233 " pdb=" N ILE R 234 " pdb=" CA ILE R 234 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ARG A 231 " pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 5942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1295 0.090 - 0.180: 131 0.180 - 0.270: 9 0.270 - 0.360: 4 0.360 - 0.451: 4 Chirality restraints: 1443 Sorted by residual: chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C14 CLR R 501 " pdb=" C13 CLR R 501 " pdb=" C15 CLR R 501 " pdb=" C8 CLR R 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 1440 not shown) Planarity restraints: 1639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 242 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C MET R 242 " -0.049 2.00e-02 2.50e+03 pdb=" O MET R 242 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE R 243 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO A 332 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.92e+00 pdb=" N PRO A 361 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.036 5.00e-02 4.00e+02 ... (remaining 1636 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1343 2.77 - 3.30: 8742 3.30 - 3.84: 15530 3.84 - 4.37: 17916 4.37 - 4.90: 31547 Nonbonded interactions: 75078 Sorted by model distance: nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.240 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.301 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.307 3.040 ... (remaining 75073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.350 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9706 Z= 0.212 Angle : 0.848 8.843 13129 Z= 0.471 Chirality : 0.060 0.451 1443 Planarity : 0.006 0.068 1639 Dihedral : 8.872 77.994 3747 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.51 (0.22), residues: 1141 helix: 1.29 (0.20), residues: 464 sheet: 0.82 (0.36), residues: 211 loop : -0.84 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 314 TYR 0.024 0.002 TYR R 178 PHE 0.032 0.003 PHE R 290 TRP 0.027 0.003 TRP A 281 HIS 0.022 0.003 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9700) covalent geometry : angle 0.84436 (13117) SS BOND : bond 0.00241 ( 6) SS BOND : angle 2.58627 ( 12) hydrogen bonds : bond 0.10641 ( 496) hydrogen bonds : angle 5.73090 ( 1425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 33 THR cc_start: 0.8198 (m) cc_final: 0.6785 (m) REVERT: R 70 LEU cc_start: 0.8501 (tp) cc_final: 0.8227 (pt) REVERT: R 86 CYS cc_start: 0.3613 (m) cc_final: 0.3144 (m) REVERT: R 371 VAL cc_start: 0.8306 (t) cc_final: 0.7946 (p) REVERT: R 410 SER cc_start: 0.8490 (t) cc_final: 0.8212 (p) REVERT: A 221 MET cc_start: 0.7304 (ttp) cc_final: 0.7027 (ttp) REVERT: A 344 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7064 (tp30) REVERT: B 155 ASN cc_start: 0.7406 (m-40) cc_final: 0.7162 (t0) REVERT: B 280 LYS cc_start: 0.8534 (tttp) cc_final: 0.8268 (tttp) REVERT: N 11 LEU cc_start: 0.8565 (tp) cc_final: 0.8222 (tm) REVERT: N 73 ASP cc_start: 0.7387 (t0) cc_final: 0.6774 (t0) REVERT: N 78 THR cc_start: 0.6547 (m) cc_final: 0.6237 (m) REVERT: N 95 TYR cc_start: 0.8595 (m-10) cc_final: 0.8372 (m-80) outliers start: 0 outliers final: 1 residues processed: 340 average time/residue: 0.5699 time to fit residues: 206.8104 Evaluate side-chains 204 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN R 204 HIS R 250 ASN R 396 HIS A 59 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS B 91 HIS B 155 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.145117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.106018 restraints weight = 15215.079| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.96 r_work: 0.3305 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9706 Z= 0.202 Angle : 0.628 7.269 13129 Z= 0.338 Chirality : 0.044 0.274 1443 Planarity : 0.005 0.061 1639 Dihedral : 6.823 57.210 1615 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.64 % Allowed : 15.77 % Favored : 80.59 % 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: 1.42 (0.24), residues: 1141 helix: 2.27 (0.22), residues: 459 sheet: 0.49 (0.34), residues: 235 loop : -0.17 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.027 0.002 TYR P 29 PHE 0.033 0.002 PHE R 290 TRP 0.033 0.002 TRP A 281 HIS 0.008 0.002 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9700) covalent geometry : angle 0.62564 (13117) SS BOND : bond 0.00338 ( 6) SS BOND : angle 1.94297 ( 12) hydrogen bonds : bond 0.04111 ( 496) hydrogen bonds : angle 4.57703 ( 1425) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8530 (mp0) cc_final: 0.8039 (pm20) REVERT: R 93 PHE cc_start: 0.8910 (m-80) cc_final: 0.8621 (m-80) REVERT: R 168 TYR cc_start: 0.8844 (t80) cc_final: 0.8624 (t80) REVERT: R 281 LEU cc_start: 0.8275 (tm) cc_final: 0.8019 (tm) REVERT: R 397 CYS cc_start: 0.8423 (m) cc_final: 0.8210 (m) REVERT: R 416 CYS cc_start: 0.8260 (t) cc_final: 0.7960 (m) REVERT: P 20 LEU cc_start: 0.8934 (mt) cc_final: 0.8632 (mt) REVERT: A 33 ASP cc_start: 0.8306 (t70) cc_final: 0.7806 (m-30) REVERT: A 35 GLN cc_start: 0.8062 (mt0) cc_final: 0.7511 (mm-40) REVERT: A 38 ARG cc_start: 0.8917 (mmt90) cc_final: 0.8593 (mmm-85) REVERT: A 54 ASN cc_start: 0.8487 (m-40) cc_final: 0.8215 (p0) REVERT: A 209 GLU cc_start: 0.7681 (tt0) cc_final: 0.7444 (tm-30) REVERT: A 221 MET cc_start: 0.8645 (ttp) cc_final: 0.8399 (ttp) REVERT: A 280 LYS cc_start: 0.8364 (pttt) cc_final: 0.8145 (pttm) REVERT: A 283 ARG cc_start: 0.7762 (mtm180) cc_final: 0.7479 (mtp-110) REVERT: A 336 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7152 (ttm-80) REVERT: A 390 GLN cc_start: 0.9026 (mt0) cc_final: 0.8819 (mt0) REVERT: B 155 ASN cc_start: 0.8211 (m110) cc_final: 0.7761 (t0) REVERT: B 172 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7802 (mm-30) REVERT: B 220 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: B 226 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 230 ASN cc_start: 0.8715 (m-40) cc_final: 0.8432 (m110) REVERT: B 273 ILE cc_start: 0.8717 (mt) cc_final: 0.8440 (mp) REVERT: B 280 LYS cc_start: 0.8744 (tttp) cc_final: 0.8459 (tttp) REVERT: B 303 ASP cc_start: 0.7229 (p0) cc_final: 0.6996 (p0) REVERT: G 21 MET cc_start: 0.6691 (tmm) cc_final: 0.6265 (tmm) REVERT: N 11 LEU cc_start: 0.8351 (tp) cc_final: 0.8124 (tm) REVERT: N 73 ASP cc_start: 0.7466 (t0) cc_final: 0.6547 (t0) REVERT: N 80 TYR cc_start: 0.7219 (m-80) cc_final: 0.6874 (m-80) REVERT: N 82 GLN cc_start: 0.7825 (tp-100) cc_final: 0.7345 (tp40) REVERT: N 95 TYR cc_start: 0.8294 (m-10) cc_final: 0.8052 (m-80) REVERT: N 105 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7441 (mtp85) outliers start: 36 outliers final: 12 residues processed: 240 average time/residue: 0.5428 time to fit residues: 139.6394 Evaluate side-chains 193 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 60 optimal weight: 0.0020 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN R 396 HIS A 387 HIS B 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.148526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.109852 restraints weight = 14940.835| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.00 r_work: 0.3309 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9706 Z= 0.126 Angle : 0.559 7.477 13129 Z= 0.300 Chirality : 0.041 0.240 1443 Planarity : 0.004 0.038 1639 Dihedral : 6.469 59.354 1613 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.54 % Allowed : 18.91 % Favored : 77.55 % 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: 1.49 (0.24), residues: 1141 helix: 2.45 (0.23), residues: 460 sheet: 0.42 (0.34), residues: 228 loop : -0.20 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 228 TYR 0.025 0.002 TYR P 29 PHE 0.027 0.002 PHE R 290 TRP 0.012 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9700) covalent geometry : angle 0.55824 (13117) SS BOND : bond 0.00134 ( 6) SS BOND : angle 1.26516 ( 12) hydrogen bonds : bond 0.03636 ( 496) hydrogen bonds : angle 4.40902 ( 1425) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: R 33 THR cc_start: 0.8318 (m) cc_final: 0.7877 (m) REVERT: R 35 GLU cc_start: 0.8578 (mp0) cc_final: 0.8126 (pm20) REVERT: R 233 TYR cc_start: 0.7753 (m-80) cc_final: 0.7346 (m-80) REVERT: R 273 THR cc_start: 0.7913 (m) cc_final: 0.7670 (t) REVERT: R 309 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7772 (mm) REVERT: R 357 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7551 (pp30) REVERT: R 416 CYS cc_start: 0.8238 (t) cc_final: 0.7987 (m) REVERT: P 20 LEU cc_start: 0.8972 (mt) cc_final: 0.8598 (mt) REVERT: A 14 ASN cc_start: 0.9178 (m110) cc_final: 0.8843 (p0) REVERT: A 33 ASP cc_start: 0.8309 (t70) cc_final: 0.7958 (m-30) REVERT: A 35 GLN cc_start: 0.8154 (mt0) cc_final: 0.7643 (mm-40) REVERT: A 336 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7478 (ptm160) REVERT: A 346 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7389 (mm) REVERT: A 390 GLN cc_start: 0.9049 (mt0) cc_final: 0.8844 (mt0) REVERT: B 155 ASN cc_start: 0.8280 (m110) cc_final: 0.7779 (t0) REVERT: B 172 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7901 (mm-30) REVERT: B 230 ASN cc_start: 0.8663 (m-40) cc_final: 0.8433 (m110) REVERT: B 259 GLN cc_start: 0.8418 (pt0) cc_final: 0.7960 (pm20) REVERT: B 267 ASP cc_start: 0.8852 (m-30) cc_final: 0.8632 (m-30) REVERT: B 280 LYS cc_start: 0.8861 (tttp) cc_final: 0.8600 (tttp) REVERT: B 292 PHE cc_start: 0.8076 (m-80) cc_final: 0.7519 (m-80) REVERT: B 312 ASP cc_start: 0.8582 (p0) cc_final: 0.8248 (p0) REVERT: G 21 MET cc_start: 0.6663 (tmm) cc_final: 0.6247 (tmm) REVERT: N 11 LEU cc_start: 0.8434 (tp) cc_final: 0.8184 (tm) REVERT: N 18 LEU cc_start: 0.7744 (tp) cc_final: 0.7536 (tt) REVERT: N 34 MET cc_start: 0.8183 (mtp) cc_final: 0.7663 (mtp) REVERT: N 39 GLN cc_start: 0.8943 (tt0) cc_final: 0.8704 (tt0) REVERT: N 73 ASP cc_start: 0.7749 (t0) cc_final: 0.6939 (t0) REVERT: N 76 LYS cc_start: 0.8845 (ttmm) cc_final: 0.8541 (ttmm) REVERT: N 80 TYR cc_start: 0.7252 (m-80) cc_final: 0.6985 (m-80) REVERT: N 82 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7511 (tp40) REVERT: N 89 GLU cc_start: 0.8882 (pp20) cc_final: 0.8342 (tm-30) REVERT: N 95 TYR cc_start: 0.8648 (m-80) cc_final: 0.8156 (m-80) REVERT: N 105 ARG cc_start: 0.8377 (mtm180) cc_final: 0.7681 (mtp85) outliers start: 35 outliers final: 6 residues processed: 214 average time/residue: 0.5791 time to fit residues: 132.1091 Evaluate side-chains 185 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 357 GLN Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 303 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 9 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN R 396 HIS A 59 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.143683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103720 restraints weight = 15016.797| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.90 r_work: 0.3215 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9706 Z= 0.184 Angle : 0.563 7.455 13129 Z= 0.302 Chirality : 0.042 0.228 1443 Planarity : 0.004 0.040 1639 Dihedral : 6.368 58.492 1613 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.54 % Allowed : 19.41 % Favored : 77.05 % 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: 1.39 (0.24), residues: 1141 helix: 2.48 (0.23), residues: 457 sheet: 0.07 (0.33), residues: 235 loop : -0.20 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.022 0.002 TYR R 148 PHE 0.023 0.002 PHE R 290 TRP 0.020 0.002 TRP R 431 HIS 0.007 0.001 HIS P 31 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9700) covalent geometry : angle 0.56147 (13117) SS BOND : bond 0.00188 ( 6) SS BOND : angle 1.39776 ( 12) hydrogen bonds : bond 0.03703 ( 496) hydrogen bonds : angle 4.37617 ( 1425) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 319 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7911 (tp40) REVERT: R 416 CYS cc_start: 0.8322 (t) cc_final: 0.8118 (m) REVERT: P 20 LEU cc_start: 0.9024 (mt) cc_final: 0.8632 (mt) REVERT: P 31 HIS cc_start: 0.8468 (p-80) cc_final: 0.8193 (p90) REVERT: A 14 ASN cc_start: 0.9133 (m110) cc_final: 0.8837 (p0) REVERT: A 33 ASP cc_start: 0.8394 (t70) cc_final: 0.8131 (m-30) REVERT: A 35 GLN cc_start: 0.8279 (mt0) cc_final: 0.7808 (mm-40) REVERT: A 346 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7930 (mm) REVERT: A 365 CYS cc_start: 0.8342 (m) cc_final: 0.8124 (m) REVERT: B 155 ASN cc_start: 0.8393 (m110) cc_final: 0.7983 (t0) REVERT: B 172 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8177 (mm-30) REVERT: B 267 ASP cc_start: 0.8814 (m-30) cc_final: 0.8602 (m-30) REVERT: B 292 PHE cc_start: 0.8453 (m-10) cc_final: 0.8006 (m-80) REVERT: G 21 MET cc_start: 0.6781 (tmm) cc_final: 0.6442 (tmm) REVERT: G 38 MET cc_start: 0.8046 (mtm) cc_final: 0.7657 (mtt) REVERT: N 34 MET cc_start: 0.8299 (mtp) cc_final: 0.8037 (mtp) REVERT: N 46 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8514 (pt0) REVERT: N 73 ASP cc_start: 0.7857 (t0) cc_final: 0.7195 (t0) REVERT: N 89 GLU cc_start: 0.8864 (pp20) cc_final: 0.8319 (tm-30) REVERT: N 105 ARG cc_start: 0.8432 (mtm180) cc_final: 0.8082 (mtm-85) outliers start: 35 outliers final: 17 residues processed: 196 average time/residue: 0.5494 time to fit residues: 115.3172 Evaluate side-chains 177 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 319 GLN Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN R 396 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 44 GLN B 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.144997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104777 restraints weight = 14956.487| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.92 r_work: 0.3222 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9706 Z= 0.142 Angle : 0.544 7.399 13129 Z= 0.290 Chirality : 0.041 0.204 1443 Planarity : 0.004 0.046 1639 Dihedral : 6.212 59.208 1613 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.94 % Allowed : 19.72 % Favored : 76.34 % 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: 1.38 (0.25), residues: 1141 helix: 2.53 (0.23), residues: 457 sheet: -0.03 (0.33), residues: 235 loop : -0.21 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 19 TYR 0.027 0.002 TYR P 29 PHE 0.029 0.002 PHE R 169 TRP 0.017 0.001 TRP R 119 HIS 0.005 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9700) covalent geometry : angle 0.54198 (13117) SS BOND : bond 0.00642 ( 6) SS BOND : angle 1.53326 ( 12) hydrogen bonds : bond 0.03534 ( 496) hydrogen bonds : angle 4.38970 ( 1425) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 33 THR cc_start: 0.8139 (m) cc_final: 0.7865 (m) REVERT: R 35 GLU cc_start: 0.8448 (mp0) cc_final: 0.8043 (pm20) REVERT: R 233 TYR cc_start: 0.7585 (m-80) cc_final: 0.7212 (m-80) REVERT: R 357 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7654 (pp30) REVERT: R 416 CYS cc_start: 0.8456 (t) cc_final: 0.8250 (m) REVERT: R 431 TRP cc_start: 0.7802 (t-100) cc_final: 0.7373 (t60) REVERT: P 20 LEU cc_start: 0.9012 (mt) cc_final: 0.8625 (mt) REVERT: P 31 HIS cc_start: 0.8545 (p-80) cc_final: 0.8259 (p90) REVERT: A 14 ASN cc_start: 0.9128 (m110) cc_final: 0.8832 (p0) REVERT: A 33 ASP cc_start: 0.8351 (t70) cc_final: 0.8127 (m-30) REVERT: A 35 GLN cc_start: 0.8308 (mt0) cc_final: 0.7818 (mm-40) REVERT: A 38 ARG cc_start: 0.8915 (mmt90) cc_final: 0.8609 (mmt-90) REVERT: A 209 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7225 (tm-30) REVERT: A 294 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7730 (mm110) REVERT: A 336 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7417 (ttt-90) REVERT: A 342 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7494 (tmm-80) REVERT: A 346 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7916 (mm) REVERT: A 365 CYS cc_start: 0.8391 (m) cc_final: 0.7587 (t) REVERT: B 46 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.6066 (mtm180) REVERT: B 155 ASN cc_start: 0.8403 (m110) cc_final: 0.7946 (t0) REVERT: B 172 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8313 (mm-30) REVERT: B 217 MET cc_start: 0.8839 (pmm) cc_final: 0.8615 (pmm) REVERT: B 264 TYR cc_start: 0.9025 (m-80) cc_final: 0.8725 (m-80) REVERT: B 292 PHE cc_start: 0.8515 (m-10) cc_final: 0.8042 (m-80) REVERT: G 21 MET cc_start: 0.6714 (tmm) cc_final: 0.6279 (tmm) REVERT: G 38 MET cc_start: 0.7949 (mtm) cc_final: 0.7532 (mtt) REVERT: G 42 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7907 (mm-30) REVERT: N 34 MET cc_start: 0.8236 (mtp) cc_final: 0.7870 (mtp) REVERT: N 46 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8614 (pt0) REVERT: N 73 ASP cc_start: 0.7922 (t0) cc_final: 0.7308 (t0) REVERT: N 89 GLU cc_start: 0.8935 (pp20) cc_final: 0.8279 (tm-30) outliers start: 39 outliers final: 12 residues processed: 195 average time/residue: 0.5767 time to fit residues: 120.2169 Evaluate side-chains 177 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 357 GLN Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN R 396 HIS ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.141055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099877 restraints weight = 14961.080| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.93 r_work: 0.3189 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9706 Z= 0.147 Angle : 0.549 7.732 13129 Z= 0.293 Chirality : 0.041 0.167 1443 Planarity : 0.004 0.051 1639 Dihedral : 6.099 58.503 1613 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.44 % Allowed : 20.93 % Favored : 75.63 % 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: 1.41 (0.24), residues: 1141 helix: 2.59 (0.23), residues: 455 sheet: -0.00 (0.33), residues: 230 loop : -0.23 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 19 TYR 0.027 0.002 TYR P 29 PHE 0.022 0.001 PHE R 290 TRP 0.013 0.001 TRP R 119 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9700) covalent geometry : angle 0.54707 (13117) SS BOND : bond 0.00288 ( 6) SS BOND : angle 1.48231 ( 12) hydrogen bonds : bond 0.03529 ( 496) hydrogen bonds : angle 4.37605 ( 1425) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8492 (mp0) cc_final: 0.8012 (pm20) REVERT: R 357 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7616 (pp30) REVERT: R 416 CYS cc_start: 0.8437 (t) cc_final: 0.8214 (m) REVERT: R 431 TRP cc_start: 0.7790 (t-100) cc_final: 0.7252 (t60) REVERT: P 20 LEU cc_start: 0.8962 (mt) cc_final: 0.8590 (mt) REVERT: P 21 GLU cc_start: 0.8512 (pp20) cc_final: 0.8172 (pp20) REVERT: P 31 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.8281 (p90) REVERT: A 14 ASN cc_start: 0.9183 (m110) cc_final: 0.8827 (OUTLIER) REVERT: A 33 ASP cc_start: 0.8188 (t70) cc_final: 0.7915 (m-30) REVERT: A 35 GLN cc_start: 0.8234 (mt0) cc_final: 0.7744 (mm-40) REVERT: A 294 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8113 (mm110) REVERT: A 336 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7209 (ttt-90) REVERT: A 365 CYS cc_start: 0.8557 (m) cc_final: 0.7517 (p) REVERT: B 45 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8665 (mtm) REVERT: B 46 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5774 (mtm180) REVERT: B 155 ASN cc_start: 0.8403 (m110) cc_final: 0.7819 (t0) REVERT: B 172 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8358 (mm-30) REVERT: B 264 TYR cc_start: 0.8922 (m-80) cc_final: 0.8530 (m-80) REVERT: B 267 ASP cc_start: 0.8972 (m-30) cc_final: 0.8739 (m-30) REVERT: B 292 PHE cc_start: 0.8643 (m-10) cc_final: 0.8062 (m-80) REVERT: B 312 ASP cc_start: 0.8684 (p0) cc_final: 0.8442 (p0) REVERT: G 21 MET cc_start: 0.6639 (tmm) cc_final: 0.6200 (tmm) REVERT: G 38 MET cc_start: 0.7784 (mtm) cc_final: 0.7535 (mtt) REVERT: G 42 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8113 (mp0) REVERT: N 34 MET cc_start: 0.8227 (mtp) cc_final: 0.7837 (mtp) REVERT: N 46 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8505 (pt0) REVERT: N 73 ASP cc_start: 0.7874 (t0) cc_final: 0.7219 (t0) REVERT: N 85 SER cc_start: 0.9093 (m) cc_final: 0.8753 (p) REVERT: N 89 GLU cc_start: 0.9047 (pp20) cc_final: 0.8320 (tm-30) REVERT: N 105 ARG cc_start: 0.8380 (mtm180) cc_final: 0.7951 (mtm180) outliers start: 34 outliers final: 16 residues processed: 187 average time/residue: 0.5871 time to fit residues: 117.1759 Evaluate side-chains 178 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 357 GLN Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 31 HIS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 63 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 HIS R 319 GLN R 396 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.140713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099977 restraints weight = 14937.690| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.94 r_work: 0.3185 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9706 Z= 0.140 Angle : 0.547 6.839 13129 Z= 0.294 Chirality : 0.041 0.161 1443 Planarity : 0.004 0.048 1639 Dihedral : 6.021 58.019 1613 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.24 % Allowed : 21.74 % Favored : 75.03 % 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: 1.46 (0.25), residues: 1141 helix: 2.62 (0.23), residues: 457 sheet: 0.02 (0.32), residues: 228 loop : -0.19 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 19 TYR 0.028 0.002 TYR P 29 PHE 0.021 0.001 PHE R 290 TRP 0.011 0.001 TRP R 253 HIS 0.006 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9700) covalent geometry : angle 0.54559 (13117) SS BOND : bond 0.00249 ( 6) SS BOND : angle 1.46270 ( 12) hydrogen bonds : bond 0.03509 ( 496) hydrogen bonds : angle 4.37314 ( 1425) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8532 (mp0) cc_final: 0.8029 (pm20) REVERT: R 169 PHE cc_start: 0.6547 (m-10) cc_final: 0.6288 (m-80) REVERT: R 357 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7640 (pp30) REVERT: R 416 CYS cc_start: 0.8411 (t) cc_final: 0.8173 (m) REVERT: R 431 TRP cc_start: 0.7788 (t-100) cc_final: 0.7260 (t60) REVERT: P 20 LEU cc_start: 0.8975 (mt) cc_final: 0.8594 (mt) REVERT: P 31 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.8279 (p90) REVERT: A 14 ASN cc_start: 0.9174 (m110) cc_final: 0.8836 (OUTLIER) REVERT: A 33 ASP cc_start: 0.8114 (t70) cc_final: 0.7884 (m-30) REVERT: A 35 GLN cc_start: 0.8243 (mt0) cc_final: 0.7763 (mm-40) REVERT: A 294 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7531 (mm110) REVERT: A 336 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7095 (ttt-90) REVERT: A 344 GLU cc_start: 0.7696 (tt0) cc_final: 0.7421 (mt-10) REVERT: A 365 CYS cc_start: 0.8553 (m) cc_final: 0.7532 (p) REVERT: B 45 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8671 (mtm) REVERT: B 46 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.5907 (mtm180) REVERT: B 155 ASN cc_start: 0.8397 (m110) cc_final: 0.7815 (t0) REVERT: B 172 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8333 (mm-30) REVERT: B 230 ASN cc_start: 0.8749 (m-40) cc_final: 0.8385 (m110) REVERT: B 264 TYR cc_start: 0.8975 (m-80) cc_final: 0.8537 (m-80) REVERT: B 267 ASP cc_start: 0.8979 (m-30) cc_final: 0.8738 (m-30) REVERT: B 292 PHE cc_start: 0.8653 (m-10) cc_final: 0.8064 (m-80) REVERT: B 312 ASP cc_start: 0.8618 (p0) cc_final: 0.8392 (p0) REVERT: G 21 MET cc_start: 0.6681 (tmm) cc_final: 0.6238 (tmm) REVERT: G 38 MET cc_start: 0.7831 (mtm) cc_final: 0.7592 (mtt) REVERT: G 42 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8087 (mp0) REVERT: N 34 MET cc_start: 0.8210 (mtp) cc_final: 0.7890 (mtp) REVERT: N 46 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8559 (pt0) REVERT: N 73 ASP cc_start: 0.7906 (t0) cc_final: 0.7249 (t0) REVERT: N 85 SER cc_start: 0.9104 (m) cc_final: 0.8773 (p) REVERT: N 89 GLU cc_start: 0.9047 (pp20) cc_final: 0.8241 (tm-30) REVERT: N 105 ARG cc_start: 0.8397 (mtm180) cc_final: 0.7636 (mtp85) outliers start: 32 outliers final: 15 residues processed: 186 average time/residue: 0.5467 time to fit residues: 108.7969 Evaluate side-chains 178 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 357 GLN Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 31 HIS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 396 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.140839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.099919 restraints weight = 14868.559| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.90 r_work: 0.3183 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9706 Z= 0.145 Angle : 0.559 8.265 13129 Z= 0.299 Chirality : 0.041 0.150 1443 Planarity : 0.004 0.050 1639 Dihedral : 5.923 57.478 1613 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.73 % Allowed : 22.04 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.45 (0.25), residues: 1141 helix: 2.63 (0.23), residues: 457 sheet: -0.03 (0.33), residues: 227 loop : -0.19 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.027 0.002 TYR P 29 PHE 0.022 0.001 PHE R 290 TRP 0.012 0.001 TRP R 253 HIS 0.006 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9700) covalent geometry : angle 0.55760 (13117) SS BOND : bond 0.00226 ( 6) SS BOND : angle 1.43182 ( 12) hydrogen bonds : bond 0.03510 ( 496) hydrogen bonds : angle 4.36865 ( 1425) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 169 PHE cc_start: 0.6392 (m-10) cc_final: 0.6089 (m-80) REVERT: R 233 TYR cc_start: 0.7700 (m-80) cc_final: 0.7424 (m-10) REVERT: R 273 THR cc_start: 0.8556 (p) cc_final: 0.8044 (t) REVERT: R 357 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7617 (pp30) REVERT: R 431 TRP cc_start: 0.7878 (t-100) cc_final: 0.7325 (t60) REVERT: P 20 LEU cc_start: 0.8953 (mt) cc_final: 0.8599 (mt) REVERT: P 21 GLU cc_start: 0.8595 (pp20) cc_final: 0.8265 (pp20) REVERT: P 31 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.8291 (p90) REVERT: A 14 ASN cc_start: 0.9165 (m110) cc_final: 0.8816 (OUTLIER) REVERT: A 33 ASP cc_start: 0.8048 (t70) cc_final: 0.7816 (m-30) REVERT: A 35 GLN cc_start: 0.8189 (mt0) cc_final: 0.7713 (mm-40) REVERT: A 294 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7811 (mm110) REVERT: A 336 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7183 (ttt-90) REVERT: A 344 GLU cc_start: 0.7709 (tt0) cc_final: 0.7445 (mt-10) REVERT: A 365 CYS cc_start: 0.8597 (m) cc_final: 0.7525 (p) REVERT: B 45 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8679 (mtm) REVERT: B 46 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.5936 (mtm180) REVERT: B 155 ASN cc_start: 0.8413 (m110) cc_final: 0.7785 (t0) REVERT: B 172 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8281 (mm-30) REVERT: B 230 ASN cc_start: 0.8690 (m-40) cc_final: 0.8334 (m110) REVERT: B 264 TYR cc_start: 0.8929 (m-80) cc_final: 0.8499 (m-80) REVERT: B 267 ASP cc_start: 0.8971 (m-30) cc_final: 0.8706 (m-30) REVERT: B 292 PHE cc_start: 0.8680 (m-10) cc_final: 0.8064 (m-80) REVERT: B 312 ASP cc_start: 0.8630 (p0) cc_final: 0.8348 (p0) REVERT: G 21 MET cc_start: 0.6711 (tmm) cc_final: 0.6245 (tmm) REVERT: G 38 MET cc_start: 0.7801 (mtm) cc_final: 0.7564 (mtt) REVERT: G 42 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8089 (mp0) REVERT: N 34 MET cc_start: 0.8210 (mtp) cc_final: 0.7902 (mtp) REVERT: N 46 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8528 (pt0) REVERT: N 73 ASP cc_start: 0.7895 (t0) cc_final: 0.7214 (t0) REVERT: N 76 LYS cc_start: 0.9082 (ttmm) cc_final: 0.8857 (ttmm) REVERT: N 85 SER cc_start: 0.9133 (m) cc_final: 0.8793 (p) REVERT: N 105 ARG cc_start: 0.8395 (mtm180) cc_final: 0.7612 (mtp85) outliers start: 27 outliers final: 16 residues processed: 182 average time/residue: 0.5454 time to fit residues: 106.2441 Evaluate side-chains 173 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 357 GLN Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 31 HIS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 0.0370 chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 396 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.141036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.100590 restraints weight = 14869.583| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.91 r_work: 0.3200 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9706 Z= 0.132 Angle : 0.574 7.986 13129 Z= 0.307 Chirality : 0.041 0.186 1443 Planarity : 0.004 0.047 1639 Dihedral : 5.824 57.304 1613 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.33 % Allowed : 23.15 % Favored : 74.52 % 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: 1.45 (0.25), residues: 1141 helix: 2.61 (0.23), residues: 457 sheet: 0.01 (0.32), residues: 225 loop : -0.21 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.031 0.002 TYR N 95 PHE 0.022 0.001 PHE R 290 TRP 0.011 0.001 TRP R 253 HIS 0.006 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9700) covalent geometry : angle 0.57262 (13117) SS BOND : bond 0.00243 ( 6) SS BOND : angle 1.36967 ( 12) hydrogen bonds : bond 0.03499 ( 496) hydrogen bonds : angle 4.40698 ( 1425) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8435 (mp0) cc_final: 0.8127 (mp0) REVERT: R 169 PHE cc_start: 0.6185 (m-10) cc_final: 0.5852 (m-80) REVERT: R 233 TYR cc_start: 0.7840 (m-80) cc_final: 0.7628 (m-10) REVERT: R 273 THR cc_start: 0.8557 (p) cc_final: 0.8050 (t) REVERT: R 421 GLN cc_start: 0.8155 (mt0) cc_final: 0.7941 (mt0) REVERT: R 431 TRP cc_start: 0.7840 (t-100) cc_final: 0.7301 (t60) REVERT: P 20 LEU cc_start: 0.8932 (mt) cc_final: 0.8594 (mt) REVERT: P 21 GLU cc_start: 0.8530 (pp20) cc_final: 0.8202 (pp20) REVERT: P 31 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.8297 (p90) REVERT: A 14 ASN cc_start: 0.9172 (m110) cc_final: 0.8817 (OUTLIER) REVERT: A 33 ASP cc_start: 0.7999 (t70) cc_final: 0.7747 (m-30) REVERT: A 35 GLN cc_start: 0.8166 (mt0) cc_final: 0.7693 (mm-40) REVERT: A 209 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: A 294 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7588 (mm110) REVERT: A 336 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6949 (ttt-90) REVERT: A 344 GLU cc_start: 0.7700 (tt0) cc_final: 0.7441 (mt-10) REVERT: A 365 CYS cc_start: 0.8577 (m) cc_final: 0.7464 (p) REVERT: B 46 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5884 (mtm180) REVERT: B 155 ASN cc_start: 0.8421 (m110) cc_final: 0.7712 (t0) REVERT: B 172 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8245 (mm-30) REVERT: B 226 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8072 (mt-10) REVERT: B 230 ASN cc_start: 0.8651 (m-40) cc_final: 0.8329 (m110) REVERT: B 264 TYR cc_start: 0.8929 (m-80) cc_final: 0.8533 (m-80) REVERT: B 267 ASP cc_start: 0.8981 (m-30) cc_final: 0.8727 (m-30) REVERT: B 292 PHE cc_start: 0.8634 (m-10) cc_final: 0.7967 (m-80) REVERT: B 308 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8589 (mt) REVERT: B 312 ASP cc_start: 0.8585 (p0) cc_final: 0.8238 (p0) REVERT: G 21 MET cc_start: 0.6660 (tmm) cc_final: 0.6186 (tmm) REVERT: G 38 MET cc_start: 0.7737 (mtm) cc_final: 0.7482 (mtt) REVERT: G 42 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7993 (mp0) REVERT: N 34 MET cc_start: 0.8147 (mtp) cc_final: 0.7838 (mtp) REVERT: N 46 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8472 (pt0) REVERT: N 73 ASP cc_start: 0.7829 (t0) cc_final: 0.7131 (t0) REVERT: N 76 LYS cc_start: 0.9119 (ttmm) cc_final: 0.8869 (ttmm) REVERT: N 85 SER cc_start: 0.9162 (m) cc_final: 0.8779 (p) outliers start: 23 outliers final: 12 residues processed: 176 average time/residue: 0.6050 time to fit residues: 113.5608 Evaluate side-chains 166 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 31 HIS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 4 optimal weight: 40.0000 chunk 66 optimal weight: 0.0010 chunk 75 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 396 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.141428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100672 restraints weight = 14914.594| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.95 r_work: 0.3220 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9706 Z= 0.128 Angle : 0.595 9.196 13129 Z= 0.316 Chirality : 0.041 0.184 1443 Planarity : 0.004 0.047 1639 Dihedral : 5.739 57.174 1613 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.82 % Allowed : 23.36 % Favored : 74.82 % 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: 1.47 (0.25), residues: 1141 helix: 2.69 (0.23), residues: 457 sheet: -0.00 (0.32), residues: 223 loop : -0.24 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.027 0.002 TYR P 29 PHE 0.023 0.001 PHE R 290 TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9700) covalent geometry : angle 0.59410 (13117) SS BOND : bond 0.00201 ( 6) SS BOND : angle 1.31905 ( 12) hydrogen bonds : bond 0.03473 ( 496) hydrogen bonds : angle 4.37364 ( 1425) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8417 (mp0) cc_final: 0.8048 (mp0) REVERT: R 70 LEU cc_start: 0.8429 (pt) cc_final: 0.8138 (tm) REVERT: R 273 THR cc_start: 0.8542 (p) cc_final: 0.8035 (t) REVERT: R 431 TRP cc_start: 0.7843 (t-100) cc_final: 0.7303 (t60) REVERT: P 20 LEU cc_start: 0.8947 (mt) cc_final: 0.8615 (mt) REVERT: P 21 GLU cc_start: 0.8545 (pp20) cc_final: 0.8217 (pp20) REVERT: P 31 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8324 (p90) REVERT: A 14 ASN cc_start: 0.9171 (m110) cc_final: 0.8848 (OUTLIER) REVERT: A 33 ASP cc_start: 0.8011 (t70) cc_final: 0.7775 (m-30) REVERT: A 35 GLN cc_start: 0.8184 (mt0) cc_final: 0.7717 (mm-40) REVERT: A 209 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: A 294 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7896 (mm110) REVERT: A 336 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7071 (ttt-90) REVERT: A 344 GLU cc_start: 0.7688 (tt0) cc_final: 0.7398 (mt-10) REVERT: A 365 CYS cc_start: 0.8545 (m) cc_final: 0.7496 (p) REVERT: B 46 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5923 (mtm180) REVERT: B 155 ASN cc_start: 0.8432 (m110) cc_final: 0.7733 (t0) REVERT: B 172 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8147 (mm-30) REVERT: B 226 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 230 ASN cc_start: 0.8689 (m-40) cc_final: 0.8418 (m110) REVERT: B 259 GLN cc_start: 0.8361 (pt0) cc_final: 0.8088 (pt0) REVERT: B 262 MET cc_start: 0.7652 (mtt) cc_final: 0.7409 (mtp) REVERT: B 267 ASP cc_start: 0.8944 (m-30) cc_final: 0.8687 (m-30) REVERT: B 292 PHE cc_start: 0.8627 (m-10) cc_final: 0.7965 (m-80) REVERT: B 308 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8559 (mt) REVERT: B 312 ASP cc_start: 0.8553 (p0) cc_final: 0.8136 (p0) REVERT: G 21 MET cc_start: 0.6703 (tmm) cc_final: 0.6229 (tmm) REVERT: G 38 MET cc_start: 0.7735 (mtm) cc_final: 0.7489 (mtt) REVERT: G 42 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7998 (mp0) REVERT: N 3 GLN cc_start: 0.8299 (tt0) cc_final: 0.8039 (tt0) REVERT: N 34 MET cc_start: 0.8157 (mtp) cc_final: 0.7832 (mtp) REVERT: N 46 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8515 (pt0) REVERT: N 73 ASP cc_start: 0.7886 (t0) cc_final: 0.7173 (t0) REVERT: N 76 LYS cc_start: 0.9113 (ttmm) cc_final: 0.8856 (ttmm) REVERT: N 85 SER cc_start: 0.9152 (m) cc_final: 0.8772 (p) outliers start: 18 outliers final: 10 residues processed: 169 average time/residue: 0.5936 time to fit residues: 107.1369 Evaluate side-chains 165 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain R residue 423 GLU Chi-restraints excluded: chain P residue 31 HIS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain N residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 88 optimal weight: 0.0770 chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 396 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.140807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.099928 restraints weight = 14856.563| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.95 r_work: 0.3189 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9706 Z= 0.139 Angle : 0.592 8.638 13129 Z= 0.315 Chirality : 0.041 0.179 1443 Planarity : 0.004 0.049 1639 Dihedral : 5.729 56.702 1613 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.92 % Allowed : 24.06 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.25), residues: 1141 helix: 2.67 (0.23), residues: 457 sheet: -0.06 (0.32), residues: 220 loop : -0.23 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 389 TYR 0.026 0.002 TYR P 29 PHE 0.022 0.001 PHE R 290 TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9700) covalent geometry : angle 0.59032 (13117) SS BOND : bond 0.00182 ( 6) SS BOND : angle 1.37973 ( 12) hydrogen bonds : bond 0.03503 ( 496) hydrogen bonds : angle 4.39068 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3602.99 seconds wall clock time: 62 minutes 3.82 seconds (3723.82 seconds total)