Starting phenix.real_space_refine on Wed Apr 30 20:17:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8haf_34587/04_2025/8haf_34587.cif Found real_map, /net/cci-nas-00/data/ceres_data/8haf_34587/04_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_34587/04_2025/8haf_34587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8haf_34587/04_2025/8haf_34587.map" model { file = "/net/cci-nas-00/data/ceres_data/8haf_34587/04_2025/8haf_34587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8haf_34587/04_2025/8haf_34587.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.69, per 1000 atoms: 0.79 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: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.15 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: 3.37 Time building geometry restraints manager: 3.18 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: 42.770 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: 1.440 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 27.840 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.130 ------------------------------------------------------------------------------- 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 : 7.15 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (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 TRP 0.058 0.001 TRP R 164 HIS 0.004 0.001 HIS R 420 PHE 0.017 0.001 PHE R 39 TYR 0.032 0.001 TYR R 191 ARG 0.012 0.001 ARG R 43 Details of bonding type rmsd hydrogen bonds : bond 0.19147 ( 449) hydrogen bonds : angle 5.88251 ( 1284) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.93401 ( 8) covalent geometry : bond 0.00304 ( 9897) covalent geometry : angle 0.82135 (13369) 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 : 1.053 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: 0.3146 time to fit residues: 88.3136 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 : 1.015 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.142459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117808 restraints weight = 13142.041| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.78 r_work: 0.3330 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9903 Z= 0.182 Angle : 0.810 32.582 13377 Z= 0.356 Chirality : 0.069 1.665 1471 Planarity : 0.004 0.045 1652 Dihedral : 12.630 179.937 1833 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.10 % Allowed : 16.87 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1147 helix: 2.31 (0.25), residues: 454 sheet: 0.81 (0.38), residues: 205 loop : -0.97 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 164 HIS 0.008 0.001 HIS A 362 PHE 0.020 0.002 PHE R 335 TYR 0.025 0.002 TYR R 191 ARG 0.008 0.001 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.04768 ( 449) hydrogen bonds : angle 4.06772 ( 1284) SS BOND : bond 0.00177 ( 4) SS BOND : angle 0.82531 ( 8) covalent geometry : bond 0.00421 ( 9897) covalent geometry : angle 0.80978 (13369) 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 224 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6625 (tmm) cc_final: 0.6273 (tmm) REVERT: A 280 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.7375 (ttm-80) REVERT: A 314 GLU cc_start: 0.7440 (mp0) cc_final: 0.7179 (mp0) REVERT: A 346 LEU cc_start: 0.7710 (mm) cc_final: 0.7432 (mt) REVERT: B 55 LEU cc_start: 0.8561 (mt) cc_final: 0.8330 (mp) REVERT: B 78 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8282 (mtmm) REVERT: B 79 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7871 (mt) REVERT: B 84 SER cc_start: 0.7979 (m) cc_final: 0.7779 (p) REVERT: B 111 TYR cc_start: 0.8559 (m-80) cc_final: 0.8333 (m-80) REVERT: B 188 MET cc_start: 0.8138 (mmm) cc_final: 0.7792 (mmm) REVERT: B 217 MET cc_start: 0.7745 (ppp) cc_final: 0.6926 (ppp) REVERT: B 219 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7512 (mtp85) REVERT: B 262 MET cc_start: 0.7415 (pmm) cc_final: 0.6643 (pmm) REVERT: B 275 SER cc_start: 0.7902 (t) cc_final: 0.7611 (t) REVERT: B 289 TYR cc_start: 0.8394 (m-80) cc_final: 0.8178 (m-80) REVERT: B 316 SER cc_start: 0.8266 (t) cc_final: 0.8046 (p) REVERT: B 317 CYS cc_start: 0.8035 (p) cc_final: 0.7817 (p) REVERT: N 13 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: N 59 SER cc_start: 0.8025 (m) cc_final: 0.7725 (t) REVERT: N 108 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: R 36 GLU cc_start: 0.7100 (tp30) cc_final: 0.6896 (tp30) REVERT: R 181 ARG cc_start: 0.7066 (mmm-85) cc_final: 0.6715 (mmm-85) REVERT: R 342 VAL cc_start: 0.7822 (t) cc_final: 0.7513 (p) REVERT: R 360 LYS cc_start: 0.8354 (ttpp) cc_final: 0.8151 (ptpp) REVERT: R 404 ARG cc_start: 0.7726 (mtt90) cc_final: 0.7475 (mtt90) REVERT: R 431 GLU cc_start: 0.7098 (mp0) cc_final: 0.6892 (mp0) outliers start: 21 outliers final: 11 residues processed: 218 average time/residue: 0.2737 time to fit residues: 79.2265 Evaluate side-chains 210 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU 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 48 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114899 restraints weight = 13322.471| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.83 r_work: 0.3290 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9903 Z= 0.151 Angle : 0.760 32.468 13377 Z= 0.331 Chirality : 0.069 1.691 1471 Planarity : 0.004 0.039 1652 Dihedral : 12.209 177.430 1824 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.19 % Allowed : 17.27 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1147 helix: 2.33 (0.25), residues: 456 sheet: 0.76 (0.38), residues: 206 loop : -0.90 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS R 420 PHE 0.022 0.002 PHE R 335 TYR 0.024 0.002 TYR R 191 ARG 0.006 0.001 ARG R 390 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 449) hydrogen bonds : angle 3.82964 ( 1284) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.70113 ( 8) covalent geometry : bond 0.00344 ( 9897) covalent geometry : angle 0.76038 (13369) Misc. bond : bond 0.01744 ( 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 228 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6640 (tmm) cc_final: 0.6318 (tmm) REVERT: A 309 GLU cc_start: 0.7790 (mp0) cc_final: 0.7412 (mp0) REVERT: A 314 GLU cc_start: 0.7510 (mp0) cc_final: 0.7189 (mp0) REVERT: B 78 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8194 (mtmm) REVERT: B 188 MET cc_start: 0.8176 (mmm) cc_final: 0.7871 (mmm) REVERT: B 212 ASP cc_start: 0.7918 (t0) cc_final: 0.7716 (t70) REVERT: B 217 MET cc_start: 0.7808 (ppp) cc_final: 0.7095 (ppp) REVERT: B 275 SER cc_start: 0.7872 (t) cc_final: 0.7611 (t) REVERT: B 289 TYR cc_start: 0.8598 (m-80) cc_final: 0.8371 (m-80) REVERT: B 298 ASP cc_start: 0.7590 (t0) cc_final: 0.7205 (t0) REVERT: B 316 SER cc_start: 0.8355 (t) cc_final: 0.8008 (p) REVERT: B 317 CYS cc_start: 0.8003 (p) cc_final: 0.7756 (p) REVERT: N 108 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: N 113 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8493 (p) REVERT: R 181 ARG cc_start: 0.7013 (mmm-85) cc_final: 0.6673 (mmm-85) REVERT: R 309 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7824 (tp) REVERT: R 321 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7674 (tt) REVERT: R 342 VAL cc_start: 0.7873 (t) cc_final: 0.7557 (p) REVERT: R 360 LYS cc_start: 0.8322 (ttpp) cc_final: 0.7771 (ptpp) REVERT: R 368 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7896 (mp) REVERT: R 408 LYS cc_start: 0.8482 (tmtt) cc_final: 0.8234 (tptp) REVERT: R 429 TYR cc_start: 0.8214 (m-10) cc_final: 0.7962 (m-10) outliers start: 32 outliers final: 17 residues processed: 217 average time/residue: 0.2994 time to fit residues: 84.3380 Evaluate side-chains 206 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL 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 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 156 LEU 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 419 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 57 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** 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 = 0.3772 r_free = 0.3772 target = 0.140966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116036 restraints weight = 13146.822| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.81 r_work: 0.3298 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2716 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= 0.124 Angle : 0.743 32.342 13377 Z= 0.318 Chirality : 0.068 1.704 1471 Planarity : 0.004 0.036 1652 Dihedral : 12.073 176.799 1824 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.09 % Allowed : 18.06 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1147 helix: 2.45 (0.25), residues: 454 sheet: 0.72 (0.37), residues: 206 loop : -0.96 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.008 0.001 HIS R 420 PHE 0.021 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.006 0.000 ARG R 383 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 449) hydrogen bonds : angle 3.70705 ( 1284) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.66392 ( 8) covalent geometry : bond 0.00282 ( 9897) covalent geometry : angle 0.74327 (13369) Misc. bond : bond 0.01742 ( 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: 31 poor density : 189 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6660 (tmm) cc_final: 0.6330 (tmm) REVERT: A 25 LYS cc_start: 0.8354 (ttmm) cc_final: 0.7989 (ttmm) REVERT: A 309 GLU cc_start: 0.7773 (mp0) cc_final: 0.7398 (mp0) REVERT: A 314 GLU cc_start: 0.7513 (mp0) cc_final: 0.7130 (mp0) REVERT: A 344 GLU cc_start: 0.7808 (tp30) cc_final: 0.7251 (tp30) REVERT: B 78 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8098 (mtmm) REVERT: B 188 MET cc_start: 0.8075 (mmm) cc_final: 0.7843 (mmm) REVERT: B 217 MET cc_start: 0.7782 (ppp) cc_final: 0.7066 (ppp) REVERT: B 221 THR cc_start: 0.8002 (m) cc_final: 0.7639 (t) REVERT: B 275 SER cc_start: 0.7840 (t) cc_final: 0.7567 (t) REVERT: B 289 TYR cc_start: 0.8596 (m-80) cc_final: 0.8316 (m-80) REVERT: B 316 SER cc_start: 0.8359 (t) cc_final: 0.8012 (p) REVERT: B 317 CYS cc_start: 0.7943 (p) cc_final: 0.7638 (p) REVERT: N 108 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: N 113 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8483 (p) REVERT: R 181 ARG cc_start: 0.6996 (mmm-85) cc_final: 0.6632 (mmm-85) REVERT: R 195 TYR cc_start: 0.8136 (m-80) cc_final: 0.7899 (m-80) REVERT: R 321 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7688 (tt) REVERT: R 342 VAL cc_start: 0.7894 (t) cc_final: 0.7573 (p) REVERT: R 360 LYS cc_start: 0.8290 (ttpp) cc_final: 0.7939 (pttm) REVERT: R 429 TYR cc_start: 0.8223 (m-10) cc_final: 0.7912 (m-10) outliers start: 31 outliers final: 19 residues processed: 208 average time/residue: 0.3218 time to fit residues: 87.3883 Evaluate side-chains 206 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL 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 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR 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 419 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS ** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113596 restraints weight = 13092.971| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.82 r_work: 0.3251 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9903 Z= 0.179 Angle : 0.768 32.247 13377 Z= 0.335 Chirality : 0.070 1.713 1471 Planarity : 0.004 0.034 1652 Dihedral : 12.037 176.208 1824 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.69 % Allowed : 18.66 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1147 helix: 2.31 (0.25), residues: 451 sheet: 0.58 (0.37), residues: 196 loop : -0.91 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.007 0.001 HIS R 420 PHE 0.023 0.002 PHE R 335 TYR 0.025 0.002 TYR R 191 ARG 0.006 0.001 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 449) hydrogen bonds : angle 3.82020 ( 1284) SS BOND : bond 0.00245 ( 4) SS BOND : angle 0.70356 ( 8) covalent geometry : bond 0.00425 ( 9897) covalent geometry : angle 0.76822 (13369) Misc. bond : bond 0.01737 ( 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 232 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6639 (tmm) cc_final: 0.6222 (tmm) REVERT: A 233 LYS cc_start: 0.8458 (mmtp) cc_final: 0.8220 (mmtt) REVERT: A 309 GLU cc_start: 0.7816 (mp0) cc_final: 0.7437 (mp0) REVERT: A 314 GLU cc_start: 0.7521 (mp0) cc_final: 0.7188 (mp0) REVERT: A 317 ARG cc_start: 0.8446 (ptp90) cc_final: 0.8213 (ptp90) REVERT: A 344 GLU cc_start: 0.7934 (tp30) cc_final: 0.7424 (tp30) REVERT: B 219 ARG cc_start: 0.8111 (mtp85) cc_final: 0.7655 (mtt-85) REVERT: B 221 THR cc_start: 0.8033 (m) cc_final: 0.7617 (t) REVERT: B 262 MET cc_start: 0.7589 (pmm) cc_final: 0.6993 (ptp) REVERT: B 275 SER cc_start: 0.7872 (t) cc_final: 0.7623 (t) REVERT: B 298 ASP cc_start: 0.7643 (t0) cc_final: 0.7273 (t0) REVERT: B 316 SER cc_start: 0.8336 (t) cc_final: 0.7936 (p) REVERT: B 317 CYS cc_start: 0.7868 (p) cc_final: 0.7594 (p) REVERT: N 13 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7966 (mp10) REVERT: N 108 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: N 113 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8523 (p) REVERT: R 181 ARG cc_start: 0.7079 (mmm-85) cc_final: 0.6703 (mmm-85) REVERT: R 195 TYR cc_start: 0.8151 (m-80) cc_final: 0.7801 (m-80) REVERT: R 321 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7645 (tt) REVERT: R 342 VAL cc_start: 0.8011 (t) cc_final: 0.7683 (p) REVERT: R 360 LYS cc_start: 0.8283 (ttpp) cc_final: 0.8031 (pttm) REVERT: R 368 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7855 (mp) REVERT: R 429 TYR cc_start: 0.8300 (m-10) cc_final: 0.7882 (m-10) outliers start: 37 outliers final: 22 residues processed: 219 average time/residue: 0.2712 time to fit residues: 78.1007 Evaluate side-chains 207 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain B residue 102 THR 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 327 VAL 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 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR 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 341 SER Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.138796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113526 restraints weight = 13109.293| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.82 r_work: 0.3247 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9903 Z= 0.166 Angle : 0.764 32.173 13377 Z= 0.331 Chirality : 0.070 1.719 1471 Planarity : 0.004 0.033 1652 Dihedral : 11.977 176.015 1824 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.59 % Allowed : 19.56 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1147 helix: 2.35 (0.25), residues: 451 sheet: 0.54 (0.37), residues: 196 loop : -0.95 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.013 0.001 HIS R 420 PHE 0.024 0.002 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.007 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 449) hydrogen bonds : angle 3.81177 ( 1284) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.64590 ( 8) covalent geometry : bond 0.00392 ( 9897) covalent geometry : angle 0.76372 (13369) Misc. bond : bond 0.01747 ( 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 219 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6643 (tmm) cc_final: 0.6259 (tmm) REVERT: A 309 GLU cc_start: 0.7824 (mp0) cc_final: 0.7457 (mp0) REVERT: A 314 GLU cc_start: 0.7561 (mp0) cc_final: 0.7234 (mp0) REVERT: A 317 ARG cc_start: 0.8447 (ptp90) cc_final: 0.8229 (ptp90) REVERT: A 344 GLU cc_start: 0.7925 (tp30) cc_final: 0.7466 (tp30) REVERT: B 217 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7507 (ppp) REVERT: B 219 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7732 (mtt-85) REVERT: B 262 MET cc_start: 0.7530 (pmm) cc_final: 0.7052 (ptp) REVERT: B 275 SER cc_start: 0.7900 (t) cc_final: 0.7652 (t) REVERT: B 289 TYR cc_start: 0.8665 (m-80) cc_final: 0.8453 (m-80) REVERT: B 316 SER cc_start: 0.8326 (t) cc_final: 0.7931 (p) REVERT: B 317 CYS cc_start: 0.7852 (p) cc_final: 0.7593 (p) REVERT: N 13 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: N 108 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: N 113 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8537 (p) REVERT: R 35 GLU cc_start: 0.7321 (mp0) cc_final: 0.6677 (mp0) REVERT: R 181 ARG cc_start: 0.7050 (mmm-85) cc_final: 0.6697 (mmm-85) REVERT: R 321 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7655 (tt) REVERT: R 342 VAL cc_start: 0.8040 (t) cc_final: 0.7721 (p) REVERT: R 360 LYS cc_start: 0.8284 (ttpp) cc_final: 0.8063 (pttm) REVERT: R 368 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7848 (mp) REVERT: R 429 TYR cc_start: 0.8285 (m-10) cc_final: 0.7825 (m-10) outliers start: 36 outliers final: 24 residues processed: 207 average time/residue: 0.2970 time to fit residues: 80.9317 Evaluate side-chains 211 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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 7 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 78 LYS 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 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL 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 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR 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 341 SER Chi-restraints excluded: chain R residue 368 LEU 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 13 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 32 optimal weight: 0.0030 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.0060 chunk 14 optimal weight: 0.6980 overall best weight: 0.4206 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.139973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114844 restraints weight = 13071.827| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.81 r_work: 0.3278 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9903 Z= 0.121 Angle : 0.740 32.151 13377 Z= 0.318 Chirality : 0.069 1.722 1471 Planarity : 0.003 0.041 1652 Dihedral : 11.869 176.375 1824 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.79 % Allowed : 19.86 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1147 helix: 2.49 (0.25), residues: 454 sheet: 0.53 (0.37), residues: 196 loop : -0.95 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.012 0.001 HIS R 420 PHE 0.019 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.009 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 449) hydrogen bonds : angle 3.67883 ( 1284) SS BOND : bond 0.00154 ( 4) SS BOND : angle 0.61574 ( 8) covalent geometry : bond 0.00270 ( 9897) covalent geometry : angle 0.73983 (13369) Misc. bond : bond 0.01731 ( 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 223 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6555 (tmm) cc_final: 0.6150 (tmm) REVERT: A 309 GLU cc_start: 0.7816 (mp0) cc_final: 0.7459 (mp0) REVERT: A 314 GLU cc_start: 0.7527 (mp0) cc_final: 0.7216 (mp0) REVERT: A 317 ARG cc_start: 0.8483 (ptp90) cc_final: 0.8257 (ptp90) REVERT: A 343 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: A 344 GLU cc_start: 0.7826 (tp30) cc_final: 0.7369 (tp30) REVERT: B 19 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7396 (ttp80) REVERT: B 78 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8061 (mtmm) REVERT: B 262 MET cc_start: 0.7335 (pmm) cc_final: 0.6961 (ptp) REVERT: B 275 SER cc_start: 0.7926 (t) cc_final: 0.7644 (t) REVERT: B 289 TYR cc_start: 0.8664 (m-80) cc_final: 0.8420 (m-80) REVERT: B 316 SER cc_start: 0.8334 (t) cc_final: 0.7943 (p) REVERT: B 317 CYS cc_start: 0.7868 (p) cc_final: 0.7580 (p) REVERT: G 21 MET cc_start: 0.8034 (mmm) cc_final: 0.7586 (mmm) REVERT: N 13 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8024 (mp10) REVERT: N 108 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: R 181 ARG cc_start: 0.6948 (mmm-85) cc_final: 0.6631 (mmm-85) REVERT: R 226 LEU cc_start: 0.8058 (tp) cc_final: 0.7764 (tp) REVERT: R 321 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7603 (tt) REVERT: R 342 VAL cc_start: 0.8003 (t) cc_final: 0.7675 (p) REVERT: R 408 LYS cc_start: 0.8561 (tptm) cc_final: 0.8353 (tptm) REVERT: R 429 TYR cc_start: 0.8297 (m-10) cc_final: 0.7838 (m-10) REVERT: R 444 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7453 (mm-30) outliers start: 38 outliers final: 23 residues processed: 211 average time/residue: 0.2676 time to fit residues: 74.3376 Evaluate side-chains 204 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 310 ASP Chi-restraints excluded: chain A residue 343 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 100 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL 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 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 317 GLU Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 341 SER 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 105 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 42 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.139649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114527 restraints weight = 13396.235| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.84 r_work: 0.3281 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3436 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= 0.125 Angle : 0.741 32.074 13377 Z= 0.318 Chirality : 0.069 1.729 1471 Planarity : 0.003 0.043 1652 Dihedral : 11.778 176.586 1824 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.29 % Allowed : 20.76 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1147 helix: 2.54 (0.25), residues: 454 sheet: 0.66 (0.36), residues: 202 loop : -0.92 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.013 0.001 HIS R 420 PHE 0.020 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.009 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 449) hydrogen bonds : angle 3.61012 ( 1284) SS BOND : bond 0.00164 ( 4) SS BOND : angle 0.57736 ( 8) covalent geometry : bond 0.00282 ( 9897) covalent geometry : angle 0.74148 (13369) Misc. bond : bond 0.01738 ( 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 210 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6553 (tmm) cc_final: 0.6194 (tmm) REVERT: A 25 LYS cc_start: 0.8386 (ttmm) cc_final: 0.8174 (ttmm) REVERT: A 295 ASP cc_start: 0.8024 (p0) cc_final: 0.7804 (p0) REVERT: A 309 GLU cc_start: 0.7828 (mp0) cc_final: 0.7506 (mp0) REVERT: A 314 GLU cc_start: 0.7535 (mp0) cc_final: 0.7225 (mp0) REVERT: A 317 ARG cc_start: 0.8510 (ptp90) cc_final: 0.8276 (ptp90) REVERT: A 319 THR cc_start: 0.8710 (t) cc_final: 0.8489 (p) REVERT: A 331 ASP cc_start: 0.7876 (t0) cc_final: 0.7676 (t0) REVERT: A 343 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: A 344 GLU cc_start: 0.7779 (tp30) cc_final: 0.7329 (tp30) REVERT: B 19 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7480 (ttp80) REVERT: B 63 TRP cc_start: 0.8605 (m100) cc_final: 0.8368 (m100) REVERT: B 78 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8048 (mtmm) REVERT: B 217 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7628 (ppp) REVERT: B 262 MET cc_start: 0.7430 (pmm) cc_final: 0.7045 (ptp) REVERT: B 275 SER cc_start: 0.7915 (t) cc_final: 0.7639 (t) REVERT: B 289 TYR cc_start: 0.8667 (m-80) cc_final: 0.8440 (m-80) REVERT: B 316 SER cc_start: 0.8336 (t) cc_final: 0.7926 (p) REVERT: B 317 CYS cc_start: 0.7862 (p) cc_final: 0.7564 (p) REVERT: G 21 MET cc_start: 0.8064 (mmm) cc_final: 0.7715 (mmm) REVERT: N 13 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8034 (mp10) REVERT: N 108 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: R 35 GLU cc_start: 0.7322 (mp0) cc_final: 0.6616 (mp0) REVERT: R 181 ARG cc_start: 0.6968 (mmm-85) cc_final: 0.6671 (mmm-85) REVERT: R 226 LEU cc_start: 0.8152 (tp) cc_final: 0.7858 (tp) REVERT: R 321 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7622 (tt) REVERT: R 342 VAL cc_start: 0.8050 (t) cc_final: 0.7717 (p) REVERT: R 408 LYS cc_start: 0.8564 (tptm) cc_final: 0.8357 (tptm) REVERT: R 444 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7573 (mm-30) outliers start: 33 outliers final: 25 residues processed: 199 average time/residue: 0.2874 time to fit residues: 75.5394 Evaluate side-chains 204 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 310 ASP Chi-restraints excluded: chain A residue 343 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 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL 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 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 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 341 SER 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 85 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 0.0980 chunk 97 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN N 31 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113659 restraints weight = 13217.461| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.84 r_work: 0.3267 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3598 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= 0.144 Angle : 0.748 32.085 13377 Z= 0.324 Chirality : 0.069 1.726 1471 Planarity : 0.003 0.042 1652 Dihedral : 11.756 176.662 1824 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.39 % Allowed : 21.16 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1147 helix: 2.51 (0.25), residues: 454 sheet: 0.53 (0.36), residues: 202 loop : -0.94 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.013 0.001 HIS R 420 PHE 0.024 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.010 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 449) hydrogen bonds : angle 3.65903 ( 1284) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.60567 ( 8) covalent geometry : bond 0.00334 ( 9897) covalent geometry : angle 0.74826 (13369) Misc. bond : bond 0.01735 ( 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 214 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6574 (tmm) cc_final: 0.6222 (tmm) REVERT: A 25 LYS cc_start: 0.8383 (ttmm) cc_final: 0.8164 (ttmm) REVERT: A 309 GLU cc_start: 0.7835 (mp0) cc_final: 0.7524 (mp0) REVERT: A 314 GLU cc_start: 0.7544 (mp0) cc_final: 0.7240 (mp0) REVERT: A 317 ARG cc_start: 0.8538 (ptp90) cc_final: 0.8304 (ptp90) REVERT: A 331 ASP cc_start: 0.7904 (t0) cc_final: 0.7700 (t0) REVERT: A 343 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: A 344 GLU cc_start: 0.7815 (tp30) cc_final: 0.7383 (tp30) REVERT: B 63 TRP cc_start: 0.8618 (m100) cc_final: 0.8374 (m100) REVERT: B 217 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7543 (ppp) REVERT: B 219 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7722 (mtt-85) REVERT: B 262 MET cc_start: 0.7465 (pmm) cc_final: 0.7100 (ptp) REVERT: B 275 SER cc_start: 0.7922 (t) cc_final: 0.7653 (t) REVERT: B 289 TYR cc_start: 0.8673 (m-80) cc_final: 0.8439 (m-80) REVERT: B 316 SER cc_start: 0.8357 (t) cc_final: 0.7928 (p) REVERT: B 317 CYS cc_start: 0.7868 (p) cc_final: 0.7560 (p) REVERT: G 21 MET cc_start: 0.8044 (mmm) cc_final: 0.7684 (mmm) REVERT: N 13 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: N 108 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: R 35 GLU cc_start: 0.7333 (mp0) cc_final: 0.6628 (mp0) REVERT: R 181 ARG cc_start: 0.7032 (mmm-85) cc_final: 0.6729 (mmm-85) REVERT: R 226 LEU cc_start: 0.8200 (tp) cc_final: 0.7886 (tp) REVERT: R 321 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7647 (tt) REVERT: R 342 VAL cc_start: 0.8109 (t) cc_final: 0.7780 (p) REVERT: R 444 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7591 (mm-30) outliers start: 34 outliers final: 24 residues processed: 202 average time/residue: 0.2835 time to fit residues: 75.1662 Evaluate side-chains 209 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 343 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 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL 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 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 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 341 SER 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 10 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 66 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 0.0020 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN N 31 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114426 restraints weight = 13248.984| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.78 r_work: 0.3284 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9903 Z= 0.132 Angle : 0.744 32.054 13377 Z= 0.320 Chirality : 0.069 1.731 1471 Planarity : 0.003 0.041 1652 Dihedral : 11.715 176.685 1824 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.19 % Allowed : 21.46 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1147 helix: 2.56 (0.25), residues: 453 sheet: 0.52 (0.35), residues: 208 loop : -0.96 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.012 0.001 HIS R 420 PHE 0.025 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.009 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 449) hydrogen bonds : angle 3.63938 ( 1284) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.53630 ( 8) covalent geometry : bond 0.00303 ( 9897) covalent geometry : angle 0.74390 (13369) Misc. bond : bond 0.01733 ( 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 210 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6540 (tmm) cc_final: 0.6238 (tmm) REVERT: A 25 LYS cc_start: 0.8375 (ttmm) cc_final: 0.8172 (ttmm) REVERT: A 309 GLU cc_start: 0.7843 (mp0) cc_final: 0.7538 (mp0) REVERT: A 314 GLU cc_start: 0.7520 (mp0) cc_final: 0.7219 (mp0) REVERT: A 317 ARG cc_start: 0.8535 (ptp90) cc_final: 0.8282 (ptp90) REVERT: A 343 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7280 (m-30) REVERT: A 344 GLU cc_start: 0.7767 (tp30) cc_final: 0.7340 (tp30) REVERT: A 350 THR cc_start: 0.8849 (p) cc_final: 0.8641 (p) REVERT: B 63 TRP cc_start: 0.8615 (m100) cc_final: 0.8369 (m100) REVERT: B 78 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8032 (mtmm) REVERT: B 217 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7522 (ppp) REVERT: B 219 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7718 (mtt-85) REVERT: B 262 MET cc_start: 0.7416 (pmm) cc_final: 0.7064 (pmm) REVERT: B 275 SER cc_start: 0.7900 (t) cc_final: 0.7634 (t) REVERT: B 289 TYR cc_start: 0.8660 (m-80) cc_final: 0.8441 (m-80) REVERT: B 316 SER cc_start: 0.8357 (t) cc_final: 0.7918 (p) REVERT: B 317 CYS cc_start: 0.7861 (p) cc_final: 0.7558 (p) REVERT: G 21 MET cc_start: 0.8027 (mmm) cc_final: 0.7660 (mmm) REVERT: N 13 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: N 108 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: R 181 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6684 (mmm-85) REVERT: R 226 LEU cc_start: 0.8191 (tp) cc_final: 0.7876 (tp) REVERT: R 321 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7650 (tt) REVERT: R 342 VAL cc_start: 0.8096 (t) cc_final: 0.7762 (p) outliers start: 32 outliers final: 24 residues processed: 198 average time/residue: 0.2974 time to fit residues: 77.3305 Evaluate side-chains 210 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 310 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 35 ASN 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 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL 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 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 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 341 SER 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 98 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.138231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113129 restraints weight = 13229.077| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.82 r_work: 0.3257 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3731 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= 0.169 Angle : 0.760 32.071 13377 Z= 0.331 Chirality : 0.070 1.727 1471 Planarity : 0.004 0.041 1652 Dihedral : 11.730 176.589 1824 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.99 % Allowed : 21.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1147 helix: 2.47 (0.25), residues: 453 sheet: 0.52 (0.36), residues: 200 loop : -0.97 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.012 0.001 HIS R 420 PHE 0.029 0.002 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.009 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 449) hydrogen bonds : angle 3.70084 ( 1284) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.62357 ( 8) covalent geometry : bond 0.00400 ( 9897) covalent geometry : angle 0.76054 (13369) Misc. bond : bond 0.01729 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5889.84 seconds wall clock time: 102 minutes 47.32 seconds (6167.32 seconds total)