Starting phenix.real_space_refine on Sat Aug 23 05:03:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8haf_34587/08_2025/8haf_34587.cif Found real_map, /net/cci-nas-00/data/ceres_data/8haf_34587/08_2025/8haf_34587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8haf_34587/08_2025/8haf_34587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8haf_34587/08_2025/8haf_34587.map" model { file = "/net/cci-nas-00/data/ceres_data/8haf_34587/08_2025/8haf_34587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8haf_34587/08_2025/8haf_34587.cif" } resolution = 3.25 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= 0.028 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 6258 2.51 5 N 1635 2.21 5 O 1730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9681 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} 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: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "P" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 301 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "R" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3029 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 11, 'TRANS': 357} Chain breaks: 3 Chain: "R" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 366 Unusual residues: {'CLR': 6, 'PLM': 11} Classifications: {'undetermined': 17} Link IDs: {None: 16} Time building chain proxies: 2.18, per 1000 atoms: 0.23 Number of scatterers: 9681 At special positions: 0 Unit cell: (103.824, 130.192, 140.08, 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 1730 8.00 N 1635 7.00 C 6258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 354.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 41.8% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 removed outlier: 4.267A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 235 through 241 removed outlier: 4.311A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 241 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.525A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.539A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.544A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) 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 removed outlier: 4.217A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.643A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 32 Processing helix chain 'P' and resid 33 through 36 Processing helix chain 'R' and resid 33 through 51 removed outlier: 3.596A pdb=" N PHE R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 172 removed outlier: 3.758A pdb=" N VAL R 171 " --> pdb=" O TYR R 167 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS R 172 " --> pdb=" O SER R 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 167 through 172' Processing helix chain 'R' and resid 178 through 212 removed outlier: 3.553A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 244 removed outlier: 3.735A pdb=" N ALA R 242 " --> pdb=" O PHE R 238 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU R 244 " --> pdb=" O LYS R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 311 removed outlier: 3.653A pdb=" N GLY R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 319 Processing helix chain 'R' and resid 320 through 347 removed outlier: 4.052A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.581A pdb=" N ALA R 347 " --> pdb=" O ARG R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 393 Proline residue: R 366 - end of helix removed outlier: 3.971A pdb=" N ILE R 371 " --> pdb=" O ILE R 367 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL R 372 " --> pdb=" O LEU R 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 414 removed outlier: 3.769A pdb=" N ARG R 404 " --> pdb=" O ARG R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.088A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 480 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.711A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N HIS A 34 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N PHE A 222 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A 36 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG A 35 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE A 245 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 37 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A 247 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A 39 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ASP A 249 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.772A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.684A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.306A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.004A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.999A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.632A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.507A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.526A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG N 38 " --> pdb=" O GLU N 46 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1284 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: 1.54 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3073 1.35 - 1.46: 2394 1.46 - 1.58: 4348 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9897 Sorted by residual: bond pdb=" C1 PLM R1507 " pdb=" C2 PLM R1507 " ideal model delta sigma weight residual 1.542 1.573 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 PLM R1501 " pdb=" C2 PLM R1501 " ideal model delta sigma weight residual 1.542 1.572 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 PLM R1511 " pdb=" C2 PLM R1511 " ideal model delta sigma weight residual 1.542 1.571 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 PLM R1504 " pdb=" C2 PLM R1504 " ideal model delta sigma weight residual 1.542 1.571 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 PLM R1503 " pdb=" C2 PLM R1503 " ideal model delta sigma weight residual 1.542 1.571 -0.029 2.00e-02 2.50e+03 2.05e+00 ... (remaining 9892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.48: 13355 6.48 - 12.96: 7 12.96 - 19.44: 5 19.44 - 25.92: 0 25.92 - 32.39: 2 Bond angle restraints: 13369 Sorted by residual: angle pdb=" C17 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C18 CLR R1515 " ideal model delta sigma weight residual 110.18 77.79 32.39 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C12 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C18 CLR R1515 " ideal model delta sigma weight residual 111.01 78.96 32.05 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C4 CLR R1512 " pdb=" C3 CLR R1512 " pdb=" O1 CLR R1512 " ideal model delta sigma weight residual 111.96 130.39 -18.43 3.00e+00 1.11e-01 3.77e+01 angle pdb=" C12 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C17 CLR R1515 " ideal model delta sigma weight residual 116.52 133.93 -17.41 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C14 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C18 CLR R1515 " ideal model delta sigma weight residual 112.24 95.10 17.14 3.00e+00 1.11e-01 3.27e+01 ... (remaining 13364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 5993 35.92 - 71.83: 176 71.83 - 107.75: 2 107.75 - 143.67: 2 143.67 - 179.58: 5 Dihedral angle restraints: 6178 sinusoidal: 2782 harmonic: 3396 Sorted by residual: dihedral pdb=" CB CYS R 131 " pdb=" SG CYS R 131 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 153.39 -60.39 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" C18 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C14 CLR R1515 " pdb=" C8 CLR R1515 " ideal model delta sinusoidal sigma weight residual 62.65 -116.93 179.58 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C15 CLR R1515 " pdb=" C13 CLR R1515 " pdb=" C14 CLR R1515 " pdb=" C18 CLR R1515 " ideal model delta sinusoidal sigma weight residual 69.18 -111.99 -178.83 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 6175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 1468 0.349 - 0.699: 1 0.699 - 1.048: 1 1.048 - 1.397: 0 1.397 - 1.746: 1 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C13 CLR R1515 " pdb=" C12 CLR R1515 " pdb=" C14 CLR R1515 " pdb=" C17 CLR R1515 " both_signs ideal model delta sigma weight residual False -2.93 -1.19 -1.75 2.00e-01 2.50e+01 7.62e+01 chirality pdb=" C3 CLR R1512 " pdb=" C2 CLR R1512 " pdb=" C4 CLR R1512 " pdb=" O1 CLR R1512 " both_signs ideal model delta sigma weight residual False -2.46 -1.41 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" C3 CLR R1515 " pdb=" C2 CLR R1515 " pdb=" C4 CLR R1515 " pdb=" O1 CLR R1515 " both_signs ideal model delta sigma weight residual False -2.46 -3.00 0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 1468 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 164 " -0.024 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP R 164 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP R 164 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP R 164 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 164 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 164 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 164 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 164 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 164 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP R 164 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 137 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C ASP R 137 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP R 137 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE R 138 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG P 21 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C ARG P 21 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG P 21 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE P 22 " -0.013 2.00e-02 2.50e+03 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 8 2.32 - 2.96: 4397 2.96 - 3.61: 13918 3.61 - 4.25: 21038 4.25 - 4.90: 36186 Nonbonded interactions: 75547 Sorted by model distance: nonbonded pdb=" O1 CLR R1512 " pdb=" O1 CLR R1515 " model vdw 1.671 2.432 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.043 3.040 nonbonded pdb=" O1 CLR R1512 " pdb=" C2 CLR R1515 " model vdw 2.061 2.752 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.170 3.040 nonbonded pdb=" C4 CLR R1512 " pdb=" O1 CLR R1515 " model vdw 2.236 2.752 ... (remaining 75542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.160 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 : 0.003 0.040 9903 Z= 0.152 Angle : 0.821 32.394 13377 Z= 0.376 Chirality : 0.068 1.746 1471 Planarity : 0.004 0.052 1652 Dihedral : 16.056 179.584 3972 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.40 % Allowed : 17.96 % Favored : 81.64 % 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 aren not related in a simple way. whole: 0.83 (0.26), residues: 1147 helix: 2.05 (0.25), residues: 460 sheet: 0.92 (0.42), residues: 175 loop : -1.03 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 43 TYR 0.032 0.001 TYR R 191 PHE 0.017 0.001 PHE R 39 TRP 0.058 0.001 TRP R 164 HIS 0.004 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9897) covalent geometry : angle 0.82135 (13369) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.93401 ( 8) hydrogen bonds : bond 0.19147 ( 449) hydrogen bonds : angle 5.88251 ( 1284) Misc. bond : bond 0.01743 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6267 (tmm) cc_final: 0.5877 (tmm) REVERT: A 208 PHE cc_start: 0.8405 (m-80) cc_final: 0.8202 (m-80) REVERT: A 211 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7885 (mttt) REVERT: A 283 ARG cc_start: 0.7362 (ptt180) cc_final: 0.6982 (ptp-170) REVERT: A 342 ARG cc_start: 0.7316 (ttp-170) cc_final: 0.7096 (ttt-90) REVERT: B 188 MET cc_start: 0.7690 (mmm) cc_final: 0.7372 (mmm) REVERT: B 217 MET cc_start: 0.6992 (ppp) cc_final: 0.6234 (ppp) REVERT: B 289 TYR cc_start: 0.7813 (m-80) cc_final: 0.6921 (m-80) REVERT: B 295 ASN cc_start: 0.8242 (m-40) cc_final: 0.8003 (m-40) REVERT: N 34 MET cc_start: 0.8015 (mmm) cc_final: 0.7501 (mmm) REVERT: N 49 SER cc_start: 0.8222 (p) cc_final: 0.7787 (t) REVERT: R 240 LYS cc_start: 0.7317 (tmmt) cc_final: 0.7086 (ttpt) REVERT: R 342 VAL cc_start: 0.7439 (t) cc_final: 0.7113 (p) REVERT: R 404 ARG cc_start: 0.7230 (mtt90) cc_final: 0.7021 (mtt90) REVERT: R 413 LEU cc_start: 0.7112 (tp) cc_final: 0.6834 (tp) outliers start: 4 outliers final: 3 residues processed: 217 average time/residue: 0.1265 time to fit residues: 35.4037 Evaluate side-chains 192 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 135 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 271 ASN A 362 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 220 GLN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115108 restraints weight = 13156.185| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.80 r_work: 0.3285 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9903 Z= 0.199 Angle : 0.834 32.592 13377 Z= 0.371 Chirality : 0.070 1.660 1471 Planarity : 0.005 0.044 1652 Dihedral : 12.626 179.857 1833 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.30 % Allowed : 17.07 % Favored : 80.64 % 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 aren not related in a simple way. whole: 0.90 (0.25), residues: 1147 helix: 2.18 (0.25), residues: 452 sheet: 0.67 (0.37), residues: 206 loop : -0.98 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 31 TYR 0.026 0.002 TYR R 191 PHE 0.025 0.002 PHE R 335 TRP 0.017 0.002 TRP B 339 HIS 0.006 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 9897) covalent geometry : angle 0.83417 (13369) SS BOND : bond 0.00212 ( 4) SS BOND : angle 0.92204 ( 8) hydrogen bonds : bond 0.04640 ( 449) hydrogen bonds : angle 4.04921 ( 1284) Misc. bond : bond 0.01759 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6654 (tmm) cc_final: 0.6290 (tmm) REVERT: A 314 GLU cc_start: 0.7448 (mp0) cc_final: 0.7189 (mp0) REVERT: A 346 LEU cc_start: 0.7794 (mm) cc_final: 0.7477 (mt) REVERT: B 188 MET cc_start: 0.8172 (mmm) cc_final: 0.7841 (mmm) REVERT: B 217 MET cc_start: 0.7814 (ppp) cc_final: 0.7022 (ppp) REVERT: B 219 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7589 (mtp85) REVERT: B 221 THR cc_start: 0.8017 (m) cc_final: 0.7688 (t) REVERT: B 275 SER cc_start: 0.7919 (t) cc_final: 0.7621 (t) REVERT: B 316 SER cc_start: 0.8348 (t) cc_final: 0.8043 (p) REVERT: B 317 CYS cc_start: 0.7952 (p) cc_final: 0.7729 (p) REVERT: N 60 TYR cc_start: 0.8408 (m-80) cc_final: 0.8191 (m-80) REVERT: N 108 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: R 36 GLU cc_start: 0.7141 (tp30) cc_final: 0.6929 (tp30) REVERT: R 181 ARG cc_start: 0.7119 (mmm-85) cc_final: 0.6766 (mmm-85) REVERT: R 342 VAL cc_start: 0.7905 (t) cc_final: 0.7587 (p) REVERT: R 360 LYS cc_start: 0.8371 (ttpp) cc_final: 0.7776 (ptpp) REVERT: R 408 LYS cc_start: 0.8434 (tmtt) cc_final: 0.8211 (tptp) REVERT: R 443 TYR cc_start: 0.8428 (t80) cc_final: 0.8197 (t80) outliers start: 23 outliers final: 14 residues processed: 224 average time/residue: 0.1045 time to fit residues: 31.3189 Evaluate side-chains 202 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 420 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 54 HIS R 364 GLN R 380 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113816 restraints weight = 13139.398| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.81 r_work: 0.3268 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9903 Z= 0.182 Angle : 0.779 32.644 13377 Z= 0.342 Chirality : 0.069 1.684 1471 Planarity : 0.004 0.039 1652 Dihedral : 12.336 178.949 1824 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.49 % Allowed : 17.37 % Favored : 79.14 % 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 aren not related in a simple way. whole: 0.95 (0.26), residues: 1147 helix: 2.21 (0.25), residues: 456 sheet: 0.61 (0.38), residues: 198 loop : -0.90 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 390 TYR 0.025 0.002 TYR R 191 PHE 0.029 0.002 PHE R 335 TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9897) covalent geometry : angle 0.77946 (13369) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.69198 ( 8) hydrogen bonds : bond 0.04588 ( 449) hydrogen bonds : angle 3.93307 ( 1284) Misc. bond : bond 0.01742 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6669 (tmm) cc_final: 0.6286 (tmm) REVERT: A 309 GLU cc_start: 0.7827 (mp0) cc_final: 0.7435 (mp0) REVERT: A 314 GLU cc_start: 0.7522 (mp0) cc_final: 0.7189 (mp0) REVERT: A 346 LEU cc_start: 0.7884 (mm) cc_final: 0.7456 (mt) REVERT: B 188 MET cc_start: 0.8185 (mmm) cc_final: 0.7903 (mmm) REVERT: B 217 MET cc_start: 0.7850 (ppp) cc_final: 0.6972 (ppp) REVERT: B 219 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7579 (mtp85) REVERT: B 221 THR cc_start: 0.8009 (m) cc_final: 0.7627 (t) REVERT: B 275 SER cc_start: 0.7876 (t) cc_final: 0.7621 (t) REVERT: B 289 TYR cc_start: 0.8648 (m-80) cc_final: 0.8369 (m-80) REVERT: B 298 ASP cc_start: 0.7671 (t0) cc_final: 0.7318 (t0) REVERT: B 316 SER cc_start: 0.8334 (t) cc_final: 0.7948 (p) REVERT: B 317 CYS cc_start: 0.7961 (p) cc_final: 0.7712 (p) REVERT: N 108 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: R 36 GLU cc_start: 0.7202 (tp30) cc_final: 0.6986 (tp30) REVERT: R 181 ARG cc_start: 0.7033 (mmm-85) cc_final: 0.6672 (mmm-85) REVERT: R 321 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7699 (tt) REVERT: R 342 VAL cc_start: 0.7944 (t) cc_final: 0.7607 (p) REVERT: R 360 LYS cc_start: 0.8360 (ttpp) cc_final: 0.7867 (ptpp) outliers start: 35 outliers final: 23 residues processed: 210 average time/residue: 0.1283 time to fit residues: 35.0977 Evaluate side-chains 209 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 420 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.139291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114378 restraints weight = 13256.027| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.82 r_work: 0.3264 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9903 Z= 0.152 Angle : 0.762 32.495 13377 Z= 0.329 Chirality : 0.069 1.692 1471 Planarity : 0.004 0.037 1652 Dihedral : 12.214 177.967 1824 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.89 % Allowed : 19.06 % Favored : 78.04 % 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 aren not related in a simple way. whole: 0.99 (0.26), residues: 1147 helix: 2.35 (0.25), residues: 451 sheet: 0.53 (0.37), residues: 196 loop : -0.91 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 383 TYR 0.023 0.001 TYR R 191 PHE 0.023 0.002 PHE R 335 TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9897) covalent geometry : angle 0.76228 (13369) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.67714 ( 8) hydrogen bonds : bond 0.04129 ( 449) hydrogen bonds : angle 3.83797 ( 1284) Misc. bond : bond 0.01745 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6674 (tmm) cc_final: 0.6286 (tmm) REVERT: A 25 LYS cc_start: 0.8373 (ttmm) cc_final: 0.7997 (ttmm) REVERT: A 309 GLU cc_start: 0.7823 (mp0) cc_final: 0.7437 (mp0) REVERT: A 314 GLU cc_start: 0.7541 (mp0) cc_final: 0.7157 (mp0) REVERT: A 343 ASP cc_start: 0.7668 (t0) cc_final: 0.7403 (m-30) REVERT: A 344 GLU cc_start: 0.7928 (tp30) cc_final: 0.7411 (tp30) REVERT: A 346 LEU cc_start: 0.7903 (mm) cc_final: 0.7380 (mt) REVERT: B 188 MET cc_start: 0.8174 (mmm) cc_final: 0.7901 (mmm) REVERT: B 217 MET cc_start: 0.7843 (ppp) cc_final: 0.7030 (ppp) REVERT: B 219 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7580 (mtp85) REVERT: B 221 THR cc_start: 0.7959 (m) cc_final: 0.7570 (t) REVERT: B 262 MET cc_start: 0.7414 (pmm) cc_final: 0.7157 (ptp) REVERT: B 275 SER cc_start: 0.7842 (t) cc_final: 0.7572 (t) REVERT: B 289 TYR cc_start: 0.8658 (m-80) cc_final: 0.8371 (m-80) REVERT: B 298 ASP cc_start: 0.7646 (t0) cc_final: 0.7300 (t0) REVERT: B 316 SER cc_start: 0.8341 (t) cc_final: 0.7945 (p) REVERT: B 317 CYS cc_start: 0.7951 (p) cc_final: 0.7698 (p) REVERT: N 13 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: N 108 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: R 36 GLU cc_start: 0.7173 (tp30) cc_final: 0.6968 (tp30) REVERT: R 181 ARG cc_start: 0.7045 (mmm-85) cc_final: 0.6688 (mmm-85) REVERT: R 321 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7668 (tt) REVERT: R 342 VAL cc_start: 0.7941 (t) cc_final: 0.7615 (p) REVERT: R 360 LYS cc_start: 0.8359 (ttpp) cc_final: 0.7970 (pttm) REVERT: R 368 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7837 (mp) outliers start: 29 outliers final: 18 residues processed: 211 average time/residue: 0.1084 time to fit residues: 29.8376 Evaluate side-chains 207 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 420 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112676 restraints weight = 13160.230| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.80 r_work: 0.3239 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9903 Z= 0.194 Angle : 0.780 32.334 13377 Z= 0.342 Chirality : 0.070 1.709 1471 Planarity : 0.004 0.035 1652 Dihedral : 12.139 176.789 1824 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.49 % Allowed : 17.96 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.26), residues: 1147 helix: 2.24 (0.25), residues: 451 sheet: 0.42 (0.36), residues: 206 loop : -0.89 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 383 TYR 0.022 0.002 TYR R 191 PHE 0.025 0.002 PHE R 335 TRP 0.012 0.002 TRP B 339 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 9897) covalent geometry : angle 0.78000 (13369) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.71941 ( 8) hydrogen bonds : bond 0.04471 ( 449) hydrogen bonds : angle 3.90956 ( 1284) Misc. bond : bond 0.01745 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6645 (tmm) cc_final: 0.6258 (tmm) REVERT: A 300 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8088 (ttmt) REVERT: A 309 GLU cc_start: 0.7828 (mp0) cc_final: 0.7453 (mp0) REVERT: A 314 GLU cc_start: 0.7541 (mp0) cc_final: 0.7185 (mp0) REVERT: A 343 ASP cc_start: 0.7783 (t0) cc_final: 0.7510 (m-30) REVERT: A 344 GLU cc_start: 0.7967 (tp30) cc_final: 0.7508 (tp30) REVERT: A 346 LEU cc_start: 0.7993 (mm) cc_final: 0.7491 (mt) REVERT: B 171 ILE cc_start: 0.7115 (mm) cc_final: 0.6899 (mm) REVERT: B 188 MET cc_start: 0.8168 (mmm) cc_final: 0.7905 (mmm) REVERT: B 217 MET cc_start: 0.7880 (ppp) cc_final: 0.7145 (ppp) REVERT: B 219 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7518 (mtt-85) REVERT: B 221 THR cc_start: 0.8005 (m) cc_final: 0.7613 (t) REVERT: B 275 SER cc_start: 0.7862 (t) cc_final: 0.7629 (t) REVERT: B 316 SER cc_start: 0.8332 (t) cc_final: 0.7911 (p) REVERT: B 317 CYS cc_start: 0.7856 (p) cc_final: 0.7612 (p) REVERT: N 13 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8031 (mp10) REVERT: N 108 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: R 35 GLU cc_start: 0.7330 (mp0) cc_final: 0.6655 (mp0) REVERT: R 36 GLU cc_start: 0.7273 (tp30) cc_final: 0.7058 (tp30) REVERT: R 181 ARG cc_start: 0.7077 (mmm-85) cc_final: 0.6735 (mmm-85) REVERT: R 321 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7637 (tt) REVERT: R 342 VAL cc_start: 0.8010 (t) cc_final: 0.7688 (p) REVERT: R 360 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7997 (pttm) REVERT: R 368 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7843 (mp) outliers start: 45 outliers final: 28 residues processed: 222 average time/residue: 0.1058 time to fit residues: 31.3024 Evaluate side-chains 217 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113694 restraints weight = 13089.624| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.81 r_work: 0.3259 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9903 Z= 0.156 Angle : 0.759 32.285 13377 Z= 0.329 Chirality : 0.069 1.714 1471 Planarity : 0.004 0.033 1652 Dihedral : 12.031 176.557 1824 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.29 % Allowed : 19.66 % Favored : 76.05 % 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 aren not related in a simple way. whole: 0.97 (0.25), residues: 1147 helix: 2.35 (0.25), residues: 451 sheet: 0.47 (0.36), residues: 202 loop : -0.92 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 389 TYR 0.023 0.001 TYR R 191 PHE 0.022 0.002 PHE R 335 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9897) covalent geometry : angle 0.75861 (13369) SS BOND : bond 0.00180 ( 4) SS BOND : angle 0.61221 ( 8) hydrogen bonds : bond 0.04164 ( 449) hydrogen bonds : angle 3.81217 ( 1284) Misc. bond : bond 0.01745 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6610 (tmm) cc_final: 0.6239 (tmm) REVERT: A 309 GLU cc_start: 0.7869 (mp0) cc_final: 0.7511 (mp0) REVERT: A 314 GLU cc_start: 0.7545 (mp0) cc_final: 0.7214 (mp0) REVERT: A 343 ASP cc_start: 0.7751 (t0) cc_final: 0.7452 (m-30) REVERT: A 344 GLU cc_start: 0.7901 (tp30) cc_final: 0.7465 (tp30) REVERT: B 19 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7387 (ttp80) REVERT: B 188 MET cc_start: 0.8160 (mmm) cc_final: 0.7902 (mmm) REVERT: B 217 MET cc_start: 0.7901 (ppp) cc_final: 0.7154 (ppp) REVERT: B 219 ARG cc_start: 0.8100 (mtp85) cc_final: 0.7528 (mtt-85) REVERT: B 221 THR cc_start: 0.7983 (m) cc_final: 0.7602 (t) REVERT: B 275 SER cc_start: 0.7914 (t) cc_final: 0.7659 (t) REVERT: B 316 SER cc_start: 0.8322 (t) cc_final: 0.7939 (p) REVERT: B 317 CYS cc_start: 0.7875 (p) cc_final: 0.7603 (p) REVERT: N 13 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: N 108 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: R 35 GLU cc_start: 0.7337 (mp0) cc_final: 0.6654 (mp0) REVERT: R 181 ARG cc_start: 0.7022 (mmm-85) cc_final: 0.6679 (mmm-85) REVERT: R 321 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7646 (tt) REVERT: R 342 VAL cc_start: 0.8019 (t) cc_final: 0.7701 (p) REVERT: R 360 LYS cc_start: 0.8316 (ttpp) cc_final: 0.8027 (pttm) REVERT: R 368 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7830 (mp) REVERT: R 414 MET cc_start: 0.7960 (ttp) cc_final: 0.7717 (ttm) outliers start: 43 outliers final: 28 residues processed: 223 average time/residue: 0.1126 time to fit residues: 33.2709 Evaluate side-chains 223 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.139224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113786 restraints weight = 13128.712| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.84 r_work: 0.3261 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9903 Z= 0.146 Angle : 0.757 32.250 13377 Z= 0.327 Chirality : 0.069 1.717 1471 Planarity : 0.004 0.044 1652 Dihedral : 11.959 176.445 1824 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.99 % Allowed : 20.86 % Favored : 75.15 % 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 aren not related in a simple way. whole: 1.01 (0.26), residues: 1147 helix: 2.40 (0.25), residues: 451 sheet: 0.49 (0.36), residues: 202 loop : -0.93 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 31 TYR 0.024 0.001 TYR R 191 PHE 0.022 0.001 PHE R 335 TRP 0.009 0.001 TRP B 169 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9897) covalent geometry : angle 0.75713 (13369) SS BOND : bond 0.00186 ( 4) SS BOND : angle 0.62529 ( 8) hydrogen bonds : bond 0.04050 ( 449) hydrogen bonds : angle 3.77292 ( 1284) Misc. bond : bond 0.01743 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6600 (tmm) cc_final: 0.6234 (tmm) REVERT: A 248 VAL cc_start: 0.8876 (t) cc_final: 0.8655 (p) REVERT: A 300 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8051 (ttmt) REVERT: A 309 GLU cc_start: 0.7870 (mp0) cc_final: 0.7527 (mp0) REVERT: A 314 GLU cc_start: 0.7532 (mp0) cc_final: 0.7215 (mp0) REVERT: A 317 ARG cc_start: 0.8511 (ptp90) cc_final: 0.8300 (ptp90) REVERT: A 343 ASP cc_start: 0.7760 (t0) cc_final: 0.7457 (m-30) REVERT: A 344 GLU cc_start: 0.7904 (tp30) cc_final: 0.7452 (tp30) REVERT: B 188 MET cc_start: 0.8114 (mmm) cc_final: 0.7878 (mmm) REVERT: B 217 MET cc_start: 0.7852 (ppp) cc_final: 0.7144 (ppp) REVERT: B 221 THR cc_start: 0.7950 (m) cc_final: 0.7547 (t) REVERT: B 275 SER cc_start: 0.7928 (t) cc_final: 0.7676 (t) REVERT: B 316 SER cc_start: 0.8343 (t) cc_final: 0.7932 (p) REVERT: B 317 CYS cc_start: 0.7880 (p) cc_final: 0.7587 (p) REVERT: N 13 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: N 108 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: P 13 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7807 (ttmm) REVERT: R 35 GLU cc_start: 0.7342 (mp0) cc_final: 0.6707 (mp0) REVERT: R 181 ARG cc_start: 0.7001 (mmm-85) cc_final: 0.6654 (mmm-85) REVERT: R 226 LEU cc_start: 0.8115 (tp) cc_final: 0.7809 (tp) REVERT: R 321 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7649 (tt) REVERT: R 342 VAL cc_start: 0.8037 (t) cc_final: 0.7710 (p) REVERT: R 360 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8024 (pttm) REVERT: R 414 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7764 (ttm) outliers start: 40 outliers final: 28 residues processed: 220 average time/residue: 0.1122 time to fit residues: 32.4911 Evaluate side-chains 228 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113162 restraints weight = 13180.600| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.82 r_work: 0.3261 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9903 Z= 0.162 Angle : 0.768 32.218 13377 Z= 0.334 Chirality : 0.069 1.720 1471 Planarity : 0.004 0.039 1652 Dihedral : 11.916 176.335 1824 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.09 % Allowed : 21.06 % Favored : 74.85 % 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 aren not related in a simple way. whole: 0.98 (0.25), residues: 1147 helix: 2.38 (0.25), residues: 451 sheet: 0.49 (0.36), residues: 202 loop : -0.95 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 31 TYR 0.024 0.002 TYR R 191 PHE 0.023 0.002 PHE R 335 TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9897) covalent geometry : angle 0.76773 (13369) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.59924 ( 8) hydrogen bonds : bond 0.04136 ( 449) hydrogen bonds : angle 3.74482 ( 1284) Misc. bond : bond 0.01741 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6586 (tmm) cc_final: 0.6236 (tmm) REVERT: A 25 LYS cc_start: 0.8398 (ttmm) cc_final: 0.8179 (ttmm) REVERT: A 248 VAL cc_start: 0.8895 (t) cc_final: 0.8683 (p) REVERT: A 300 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8084 (ttmt) REVERT: A 309 GLU cc_start: 0.7864 (mp0) cc_final: 0.7532 (mp0) REVERT: A 314 GLU cc_start: 0.7551 (mp0) cc_final: 0.7248 (mp0) REVERT: A 317 ARG cc_start: 0.8544 (ptp90) cc_final: 0.8325 (ptp90) REVERT: A 343 ASP cc_start: 0.7774 (t0) cc_final: 0.7490 (m-30) REVERT: A 344 GLU cc_start: 0.7894 (tp30) cc_final: 0.7455 (tp30) REVERT: B 217 MET cc_start: 0.7851 (ppp) cc_final: 0.7151 (ppp) REVERT: B 221 THR cc_start: 0.7953 (m) cc_final: 0.7545 (t) REVERT: B 275 SER cc_start: 0.7939 (t) cc_final: 0.7684 (t) REVERT: B 316 SER cc_start: 0.8350 (t) cc_final: 0.7913 (p) REVERT: B 317 CYS cc_start: 0.7846 (p) cc_final: 0.7575 (p) REVERT: N 13 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: N 108 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: P 13 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7890 (ttmm) REVERT: R 35 GLU cc_start: 0.7376 (mp0) cc_final: 0.6775 (mp0) REVERT: R 181 ARG cc_start: 0.7017 (mmm-85) cc_final: 0.6680 (mmm-85) REVERT: R 321 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7655 (tt) REVERT: R 342 VAL cc_start: 0.8082 (t) cc_final: 0.7746 (p) REVERT: R 360 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8021 (pttm) outliers start: 41 outliers final: 29 residues processed: 218 average time/residue: 0.1060 time to fit residues: 30.7509 Evaluate side-chains 228 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.0050 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 358 ASN R 364 GLN R 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113415 restraints weight = 13210.511| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.80 r_work: 0.3272 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9903 Z= 0.141 Angle : 0.758 32.200 13377 Z= 0.327 Chirality : 0.069 1.721 1471 Planarity : 0.004 0.041 1652 Dihedral : 11.842 176.377 1824 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.89 % Allowed : 21.46 % Favored : 74.65 % 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 aren not related in a simple way. whole: 1.08 (0.26), residues: 1147 helix: 2.48 (0.25), residues: 453 sheet: 0.54 (0.36), residues: 206 loop : -0.95 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 31 TYR 0.023 0.001 TYR R 191 PHE 0.022 0.001 PHE R 335 TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9897) covalent geometry : angle 0.75789 (13369) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.59723 ( 8) hydrogen bonds : bond 0.03932 ( 449) hydrogen bonds : angle 3.68440 ( 1284) Misc. bond : bond 0.01738 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6537 (tmm) cc_final: 0.6200 (tmm) REVERT: A 25 LYS cc_start: 0.8383 (ttmm) cc_final: 0.8182 (ttmm) REVERT: A 248 VAL cc_start: 0.8893 (t) cc_final: 0.8679 (p) REVERT: A 300 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8045 (ttmt) REVERT: A 309 GLU cc_start: 0.7855 (mp0) cc_final: 0.7524 (mp0) REVERT: A 314 GLU cc_start: 0.7527 (mp0) cc_final: 0.7229 (mp0) REVERT: A 317 ARG cc_start: 0.8525 (ptp90) cc_final: 0.8300 (ptp90) REVERT: A 343 ASP cc_start: 0.7775 (t0) cc_final: 0.7484 (m-30) REVERT: A 344 GLU cc_start: 0.7882 (tp30) cc_final: 0.7451 (tp30) REVERT: B 78 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8071 (mtmm) REVERT: B 90 VAL cc_start: 0.8455 (m) cc_final: 0.8245 (t) REVERT: B 217 MET cc_start: 0.7845 (ppp) cc_final: 0.7154 (ppp) REVERT: B 221 THR cc_start: 0.7952 (m) cc_final: 0.7527 (t) REVERT: B 275 SER cc_start: 0.7927 (t) cc_final: 0.7683 (t) REVERT: B 316 SER cc_start: 0.8374 (t) cc_final: 0.7926 (p) REVERT: B 317 CYS cc_start: 0.7825 (p) cc_final: 0.7529 (p) REVERT: N 13 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: N 108 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: P 13 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7895 (ttmm) REVERT: R 35 GLU cc_start: 0.7380 (mp0) cc_final: 0.6793 (mp0) REVERT: R 181 ARG cc_start: 0.6988 (mmm-85) cc_final: 0.6689 (mmm-85) REVERT: R 195 TYR cc_start: 0.8217 (m-80) cc_final: 0.7975 (m-80) REVERT: R 226 LEU cc_start: 0.8182 (tp) cc_final: 0.7869 (tp) REVERT: R 321 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7638 (tt) REVERT: R 342 VAL cc_start: 0.8069 (t) cc_final: 0.7738 (p) REVERT: R 360 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8026 (pttm) REVERT: R 429 TYR cc_start: 0.8127 (m-10) cc_final: 0.7890 (m-10) outliers start: 39 outliers final: 26 residues processed: 225 average time/residue: 0.1039 time to fit residues: 31.0562 Evaluate side-chains 231 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 0.5980 chunk 81 optimal weight: 0.0020 chunk 43 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 358 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113701 restraints weight = 13093.278| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.78 r_work: 0.3272 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9903 Z= 0.146 Angle : 0.762 32.164 13377 Z= 0.329 Chirality : 0.069 1.724 1471 Planarity : 0.004 0.042 1652 Dihedral : 11.794 176.601 1824 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.59 % Allowed : 22.06 % Favored : 74.35 % 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 aren not related in a simple way. whole: 1.08 (0.26), residues: 1147 helix: 2.61 (0.25), residues: 446 sheet: 0.53 (0.35), residues: 213 loop : -1.06 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 31 TYR 0.022 0.001 TYR R 191 PHE 0.024 0.002 PHE R 454 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9897) covalent geometry : angle 0.76255 (13369) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.54831 ( 8) hydrogen bonds : bond 0.03957 ( 449) hydrogen bonds : angle 3.69469 ( 1284) Misc. bond : bond 0.01735 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6544 (tmm) cc_final: 0.6214 (tmm) REVERT: A 25 LYS cc_start: 0.8375 (ttmm) cc_final: 0.8174 (ttmm) REVERT: A 248 VAL cc_start: 0.8898 (t) cc_final: 0.8686 (p) REVERT: A 300 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8065 (ttmt) REVERT: A 309 GLU cc_start: 0.7870 (mp0) cc_final: 0.7537 (mp0) REVERT: A 314 GLU cc_start: 0.7524 (mp0) cc_final: 0.7225 (mp0) REVERT: A 317 ARG cc_start: 0.8527 (ptp90) cc_final: 0.8296 (ptp90) REVERT: A 343 ASP cc_start: 0.7755 (t0) cc_final: 0.7474 (m-30) REVERT: A 344 GLU cc_start: 0.7873 (tp30) cc_final: 0.7470 (tp30) REVERT: B 78 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8039 (mtmm) REVERT: B 90 VAL cc_start: 0.8452 (m) cc_final: 0.8250 (t) REVERT: B 217 MET cc_start: 0.7833 (ppp) cc_final: 0.7159 (ppp) REVERT: B 221 THR cc_start: 0.7961 (m) cc_final: 0.7527 (t) REVERT: B 275 SER cc_start: 0.7888 (t) cc_final: 0.7661 (t) REVERT: B 316 SER cc_start: 0.8410 (t) cc_final: 0.7921 (p) REVERT: B 317 CYS cc_start: 0.7860 (p) cc_final: 0.7562 (p) REVERT: N 13 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: N 108 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: R 35 GLU cc_start: 0.7406 (mp0) cc_final: 0.6824 (mp0) REVERT: R 181 ARG cc_start: 0.6979 (mmm-85) cc_final: 0.6692 (mmm-85) REVERT: R 195 TYR cc_start: 0.8219 (m-80) cc_final: 0.7965 (m-80) REVERT: R 226 LEU cc_start: 0.8194 (tp) cc_final: 0.7873 (tp) REVERT: R 321 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7643 (tt) REVERT: R 342 VAL cc_start: 0.8072 (t) cc_final: 0.7743 (p) outliers start: 36 outliers final: 27 residues processed: 224 average time/residue: 0.1061 time to fit residues: 31.2465 Evaluate side-chains 230 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 22 PHE Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 358 ASN ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112876 restraints weight = 13218.543| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.77 r_work: 0.3251 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9903 Z= 0.186 Angle : 0.784 32.167 13377 Z= 0.343 Chirality : 0.070 1.721 1471 Planarity : 0.004 0.041 1652 Dihedral : 11.788 176.533 1824 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.49 % Allowed : 22.16 % Favored : 74.35 % 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 aren not related in a simple way. whole: 1.00 (0.25), residues: 1147 helix: 2.48 (0.25), residues: 445 sheet: 0.52 (0.35), residues: 213 loop : -1.05 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 31 TYR 0.024 0.002 TYR R 191 PHE 0.028 0.002 PHE R 335 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 9897) covalent geometry : angle 0.78428 (13369) SS BOND : bond 0.00264 ( 4) SS BOND : angle 0.62064 ( 8) hydrogen bonds : bond 0.04294 ( 449) hydrogen bonds : angle 3.78975 ( 1284) Misc. bond : bond 0.01738 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.34 seconds wall clock time: 41 minutes 39.35 seconds (2499.35 seconds total)