Starting phenix.real_space_refine on Thu Mar 13 04:38:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jhb_36261/03_2025/8jhb_36261.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhb_36261/03_2025/8jhb_36261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jhb_36261/03_2025/8jhb_36261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhb_36261/03_2025/8jhb_36261.map" model { file = "/net/cci-nas-00/data/ceres_data/8jhb_36261/03_2025/8jhb_36261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhb_36261/03_2025/8jhb_36261.cif" } resolution = 3.3 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= 0.026 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 64 5.16 5 C 5500 2.51 5 N 1499 2.21 5 O 1585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8648 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1984 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 2 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2675 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Time building chain proxies: 5.41, per 1000 atoms: 0.63 Number of scatterers: 8648 At special positions: 0 Unit cell: (79.04, 104.832, 152.256, 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 64 16.00 O 1585 8.00 N 1499 7.00 C 5500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 45 " - pdb=" SG CYS N 119 " distance=2.03 Simple disulfide: pdb=" SG CYS N 122 " - pdb=" SG CYS N 130 " distance=2.04 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 260 " distance=2.03 Simple disulfide: pdb=" SG CYS R 282 " - pdb=" SG CYS R 357 " distance=2.02 Simple disulfide: pdb=" SG CYS R 454 " - pdb=" SG CYS R 461 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2036 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 11 sheets defined 35.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 2 through 33 removed outlier: 3.841A pdb=" N MET A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.757A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.583A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.400A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 4.029A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.816A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'C' and resid 31 through 48 removed outlier: 3.977A pdb=" N ASN C 48 " --> pdb=" O LYS C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 68 removed outlier: 3.501A pdb=" N ALA C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 88 removed outlier: 3.631A pdb=" N LYS N 88 " --> pdb=" O GLY N 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 85 through 88' Processing helix chain 'R' and resid 193 through 214 removed outlier: 4.067A pdb=" N CYS R 211 " --> pdb=" O ILE R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 217 No H-bonds generated for 'chain 'R' and resid 215 through 217' Processing helix chain 'R' and resid 231 through 255 removed outlier: 4.220A pdb=" N ILE R 235 " --> pdb=" O GLU R 231 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR R 236 " --> pdb=" O ARG R 232 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY R 255 " --> pdb=" O GLY R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 312 removed outlier: 4.212A pdb=" N LEU R 285 " --> pdb=" O ALA R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 322 removed outlier: 3.897A pdb=" N GLN R 322 " --> pdb=" O ALA R 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 319 through 322' Processing helix chain 'R' and resid 323 through 332 removed outlier: 3.689A pdb=" N ALA R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL R 330 " --> pdb=" O TRP R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 339 removed outlier: 3.541A pdb=" N LEU R 338 " --> pdb=" O THR R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 345 Processing helix chain 'R' and resid 371 through 400 removed outlier: 3.732A pdb=" N LEU R 375 " --> pdb=" O VAL R 371 " (cutoff:3.500A) Processing helix chain 'R' and resid 408 through 423 removed outlier: 3.614A pdb=" N LYS R 412 " --> pdb=" O GLU R 408 " (cutoff:3.500A) Processing helix chain 'R' and resid 424 through 458 removed outlier: 4.245A pdb=" N ILE R 443 " --> pdb=" O GLN R 439 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR R 444 " --> pdb=" O VAL R 440 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE R 447 " --> pdb=" O ILE R 443 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ARG R 455 " --> pdb=" O SER R 451 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLN R 456 " --> pdb=" O ASP R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 472 through 483 removed outlier: 3.626A pdb=" N PHE R 476 " --> pdb=" O GLU R 472 " (cutoff:3.500A) Processing helix chain 'R' and resid 484 through 486 No H-bonds generated for 'chain 'R' and resid 484 through 486' Processing helix chain 'R' and resid 488 through 494 removed outlier: 3.534A pdb=" N PHE R 492 " --> pdb=" O ILE R 488 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP R 493 " --> pdb=" O SER R 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.512A pdb=" N HIS A 36 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N PHE A 222 " --> pdb=" O HIS A 36 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 38 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL A 224 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU A 40 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ARG A 37 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE A 245 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 39 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL A 247 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 41 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ASP A 249 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.850A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.903A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.843A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.694A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.879A 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: 6.973A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.916A 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: 6.780A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.267A 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: 3.539A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 26 through 30 Processing sheet with id=AB1, first strand: chain 'N' and resid 81 through 83 removed outlier: 6.576A pdb=" N TRP N 59 " --> pdb=" O VAL N 71 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP N 73 " --> pdb=" O MET N 57 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET N 57 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 174 through 175 381 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2802 1.34 - 1.46: 2019 1.46 - 1.58: 3925 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 8835 Sorted by residual: bond pdb=" N MET R 482 " pdb=" CA MET R 482 " ideal model delta sigma weight residual 1.457 1.440 0.017 1.29e-02 6.01e+03 1.65e+00 bond pdb=" C ARG R 416 " pdb=" N ILE R 417 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.26e-02 6.30e+03 1.65e+00 bond pdb=" C VAL R 426 " pdb=" N PRO R 427 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.62e+00 bond pdb=" CB ASN N 100 " pdb=" CG ASN N 100 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" CG ARG R 397 " pdb=" CD ARG R 397 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.37e+00 ... (remaining 8830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 11886 3.70 - 7.41: 64 7.41 - 11.11: 6 11.11 - 14.82: 0 14.82 - 18.52: 1 Bond angle restraints: 11957 Sorted by residual: angle pdb=" CB MET R 482 " pdb=" CG MET R 482 " pdb=" SD MET R 482 " ideal model delta sigma weight residual 112.70 94.18 18.52 3.00e+00 1.11e-01 3.81e+01 angle pdb=" C MET R 482 " pdb=" CA MET R 482 " pdb=" CB MET R 482 " ideal model delta sigma weight residual 109.67 118.96 -9.29 2.01e+00 2.48e-01 2.14e+01 angle pdb=" C GLY R 355 " pdb=" N VAL R 356 " pdb=" CA VAL R 356 " ideal model delta sigma weight residual 121.96 127.79 -5.83 1.34e+00 5.57e-01 1.89e+01 angle pdb=" C LEU R 481 " pdb=" CA LEU R 481 " pdb=" CB LEU R 481 " ideal model delta sigma weight residual 110.85 103.58 7.27 1.70e+00 3.46e-01 1.83e+01 angle pdb=" N MET R 482 " pdb=" CA MET R 482 " pdb=" C MET R 482 " ideal model delta sigma weight residual 112.90 107.56 5.34 1.31e+00 5.83e-01 1.66e+01 ... (remaining 11952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4737 17.72 - 35.44: 423 35.44 - 53.17: 64 53.17 - 70.89: 17 70.89 - 88.61: 8 Dihedral angle restraints: 5249 sinusoidal: 2088 harmonic: 3161 Sorted by residual: dihedral pdb=" CB CYS N 122 " pdb=" SG CYS N 122 " pdb=" SG CYS N 130 " pdb=" CB CYS N 130 " ideal model delta sinusoidal sigma weight residual -86.00 2.61 -88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS R 161 " pdb=" SG CYS R 161 " pdb=" SG CYS R 181 " pdb=" CB CYS R 181 " ideal model delta sinusoidal sigma weight residual -86.00 -149.00 63.00 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CA LEU R 481 " pdb=" C LEU R 481 " pdb=" N MET R 482 " pdb=" CA MET R 482 " ideal model delta harmonic sigma weight residual 180.00 -154.33 -25.67 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 5246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1043 0.054 - 0.107: 238 0.107 - 0.161: 43 0.161 - 0.215: 2 0.215 - 0.268: 2 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CB ILE B 43 " pdb=" CA ILE B 43 " pdb=" CG1 ILE B 43 " pdb=" CG2 ILE B 43 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA VAL R 356 " pdb=" N VAL R 356 " pdb=" C VAL R 356 " pdb=" CB VAL R 356 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU A 291 " pdb=" CB LEU A 291 " pdb=" CD1 LEU A 291 " pdb=" CD2 LEU A 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 1325 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " -0.018 2.00e-02 2.50e+03 1.70e-02 7.24e+00 pdb=" CG TRP B 63 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 83 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO C 84 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER R 200 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C SER R 200 " 0.035 2.00e-02 2.50e+03 pdb=" O SER R 200 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE R 201 " -0.012 2.00e-02 2.50e+03 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 190 2.70 - 3.25: 8134 3.25 - 3.80: 13827 3.80 - 4.35: 17280 4.35 - 4.90: 28899 Nonbonded interactions: 68330 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR R 290 " pdb=" O PHE R 370 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR R 237 " pdb=" O VAL R 486 " model vdw 2.216 3.040 nonbonded pdb=" O ARG N 121 " pdb=" OH TYR N 138 " model vdw 2.233 3.040 ... (remaining 68325 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.110 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 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 0.056 8835 Z= 0.202 Angle : 0.749 18.519 11957 Z= 0.382 Chirality : 0.047 0.268 1328 Planarity : 0.005 0.053 1521 Dihedral : 14.029 86.188 3195 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.47 % 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: -0.77 (0.25), residues: 1077 helix: 0.44 (0.28), residues: 341 sheet: -0.39 (0.34), residues: 227 loop : -1.19 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 63 HIS 0.008 0.001 HIS A 220 PHE 0.022 0.002 PHE A 212 TYR 0.015 0.001 TYR R 237 ARG 0.012 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 299 GLU cc_start: 0.7363 (mp0) cc_final: 0.6928 (mp0) REVERT: A 317 ARG cc_start: 0.6977 (ptp-110) cc_final: 0.6689 (ptp-110) REVERT: A 374 ARG cc_start: 0.8290 (mtt180) cc_final: 0.8061 (mtt180) REVERT: B 150 ARG cc_start: 0.8142 (mmt-90) cc_final: 0.7770 (tpp-160) REVERT: B 217 MET cc_start: 0.6396 (ppp) cc_final: 0.6040 (ppp) REVERT: B 219 ARG cc_start: 0.7459 (tpp-160) cc_final: 0.6987 (tpp-160) REVERT: B 230 ASN cc_start: 0.8300 (m-40) cc_final: 0.8031 (m-40) REVERT: B 303 ASP cc_start: 0.7037 (m-30) cc_final: 0.6825 (m-30) REVERT: N 147 VAL cc_start: 0.7230 (p) cc_final: 0.7011 (m) REVERT: R 475 LEU cc_start: 0.4602 (tt) cc_final: 0.4369 (tt) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.2505 time to fit residues: 61.8290 Evaluate side-chains 167 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN N 105 GLN R 164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.174945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.146094 restraints weight = 12509.771| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.74 r_work: 0.3726 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8835 Z= 0.211 Angle : 0.575 8.198 11957 Z= 0.302 Chirality : 0.043 0.166 1328 Planarity : 0.004 0.048 1521 Dihedral : 4.622 24.514 1194 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.28 % Allowed : 8.24 % Favored : 90.48 % 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: -0.25 (0.26), residues: 1077 helix: 1.23 (0.29), residues: 350 sheet: -0.18 (0.34), residues: 220 loop : -1.16 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.008 0.001 HIS B 91 PHE 0.020 0.002 PHE B 241 TYR 0.018 0.001 TYR R 237 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8549 (mp10) cc_final: 0.8173 (mp10) REVERT: A 299 GLU cc_start: 0.7621 (mp0) cc_final: 0.7316 (mt-10) REVERT: A 317 ARG cc_start: 0.7484 (ptp-110) cc_final: 0.7109 (ptp-110) REVERT: A 323 ASP cc_start: 0.7871 (t0) cc_final: 0.7583 (t0) REVERT: A 331 ASP cc_start: 0.7601 (p0) cc_final: 0.7369 (p0) REVERT: A 356 ARG cc_start: 0.7686 (mpt180) cc_final: 0.7372 (mpt180) REVERT: B 126 LEU cc_start: 0.8183 (mm) cc_final: 0.7799 (mp) REVERT: B 289 TYR cc_start: 0.8456 (m-80) cc_final: 0.7942 (m-80) REVERT: B 303 ASP cc_start: 0.7263 (m-30) cc_final: 0.7026 (m-30) outliers start: 12 outliers final: 8 residues processed: 182 average time/residue: 0.2683 time to fit residues: 62.7657 Evaluate side-chains 174 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 166 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 287 MET Chi-restraints excluded: chain R residue 431 LEU Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 485 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.171823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142883 restraints weight = 12612.319| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.76 r_work: 0.3686 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8835 Z= 0.273 Angle : 0.598 6.972 11957 Z= 0.312 Chirality : 0.044 0.174 1328 Planarity : 0.004 0.047 1521 Dihedral : 4.673 28.019 1194 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.82 % Allowed : 12.51 % Favored : 85.67 % 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: -0.20 (0.26), residues: 1077 helix: 1.30 (0.28), residues: 353 sheet: -0.24 (0.34), residues: 225 loop : -1.12 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.012 0.002 HIS R 164 PHE 0.030 0.002 PHE B 241 TYR 0.018 0.002 TYR R 237 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.849 Fit side-chains REVERT: A 227 GLN cc_start: 0.8571 (mp10) cc_final: 0.8204 (mp10) REVERT: A 309 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6730 (mm-30) REVERT: A 317 ARG cc_start: 0.7457 (ptp-110) cc_final: 0.7055 (ptp-110) REVERT: A 323 ASP cc_start: 0.7880 (t0) cc_final: 0.7576 (t0) REVERT: B 126 LEU cc_start: 0.8182 (mm) cc_final: 0.7798 (mp) REVERT: B 289 TYR cc_start: 0.8468 (m-80) cc_final: 0.7958 (m-80) REVERT: B 303 ASP cc_start: 0.7382 (m-30) cc_final: 0.7073 (m-30) REVERT: R 428 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7084 (tt) outliers start: 17 outliers final: 11 residues processed: 183 average time/residue: 0.2562 time to fit residues: 61.2548 Evaluate side-chains 181 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain R residue 428 LEU Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 485 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 0.0000 chunk 91 optimal weight: 0.2980 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 26 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 overall best weight: 0.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146233 restraints weight = 12570.773| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.77 r_work: 0.3728 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8835 Z= 0.156 Angle : 0.549 8.381 11957 Z= 0.283 Chirality : 0.042 0.156 1328 Planarity : 0.003 0.041 1521 Dihedral : 4.330 22.496 1194 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.25 % Allowed : 15.19 % Favored : 82.57 % 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: -0.01 (0.26), residues: 1077 helix: 1.62 (0.29), residues: 345 sheet: -0.26 (0.34), residues: 226 loop : -1.03 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS R 164 PHE 0.033 0.001 PHE A 212 TYR 0.021 0.001 TYR R 237 ARG 0.004 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.910 Fit side-chains REVERT: A 227 GLN cc_start: 0.8489 (mp10) cc_final: 0.8119 (mp10) REVERT: A 323 ASP cc_start: 0.7833 (t0) cc_final: 0.7536 (t0) REVERT: A 356 ARG cc_start: 0.7798 (mpt180) cc_final: 0.7570 (mpt180) REVERT: B 126 LEU cc_start: 0.8162 (mm) cc_final: 0.7797 (mp) REVERT: B 230 ASN cc_start: 0.8273 (m-40) cc_final: 0.8004 (m110) REVERT: B 289 TYR cc_start: 0.8457 (m-80) cc_final: 0.7917 (m-80) REVERT: B 303 ASP cc_start: 0.7285 (m-30) cc_final: 0.7027 (m-30) REVERT: R 287 MET cc_start: 0.6331 (tpp) cc_final: 0.5405 (mpp) REVERT: R 380 PHE cc_start: 0.6669 (t80) cc_final: 0.6457 (t80) REVERT: R 411 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6566 (mmtt) REVERT: R 428 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6979 (tt) REVERT: R 477 MET cc_start: 0.5432 (mmp) cc_final: 0.5192 (mmp) outliers start: 21 outliers final: 11 residues processed: 187 average time/residue: 0.2451 time to fit residues: 60.0255 Evaluate side-chains 183 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 411 LYS Chi-restraints excluded: chain R residue 423 LEU Chi-restraints excluded: chain R residue 428 LEU Chi-restraints excluded: chain R residue 485 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 65 optimal weight: 0.0670 chunk 71 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.174456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.145529 restraints weight = 12607.893| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.73 r_work: 0.3721 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8835 Z= 0.184 Angle : 0.566 10.312 11957 Z= 0.291 Chirality : 0.042 0.168 1328 Planarity : 0.003 0.038 1521 Dihedral : 4.318 22.075 1194 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.25 % Allowed : 16.58 % Favored : 81.18 % 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: 0.05 (0.26), residues: 1077 helix: 1.67 (0.28), residues: 352 sheet: -0.31 (0.35), residues: 216 loop : -0.98 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.030 0.001 PHE B 241 TYR 0.019 0.001 TYR R 237 ARG 0.004 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.870 Fit side-chains REVERT: A 317 ARG cc_start: 0.7396 (ptp-110) cc_final: 0.6977 (ptp-110) REVERT: A 323 ASP cc_start: 0.7800 (t0) cc_final: 0.7515 (t0) REVERT: B 230 ASN cc_start: 0.8280 (m-40) cc_final: 0.7999 (m110) REVERT: B 289 TYR cc_start: 0.8464 (m-80) cc_final: 0.7916 (m-80) REVERT: B 291 ASP cc_start: 0.7615 (p0) cc_final: 0.6988 (p0) REVERT: B 303 ASP cc_start: 0.7322 (m-30) cc_final: 0.7060 (m-30) REVERT: N 54 ASN cc_start: 0.7896 (m110) cc_final: 0.7680 (m110) REVERT: R 237 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.7178 (t80) REVERT: R 287 MET cc_start: 0.6255 (tpp) cc_final: 0.5225 (mpp) REVERT: R 380 PHE cc_start: 0.6716 (t80) cc_final: 0.6500 (t80) REVERT: R 411 LYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6575 (mmtt) REVERT: R 477 MET cc_start: 0.5379 (mmp) cc_final: 0.5162 (mmp) outliers start: 21 outliers final: 11 residues processed: 186 average time/residue: 0.2500 time to fit residues: 61.2178 Evaluate side-chains 178 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 411 LYS Chi-restraints excluded: chain R residue 423 LEU Chi-restraints excluded: chain R residue 485 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN R 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.172591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.143788 restraints weight = 12529.199| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.75 r_work: 0.3700 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8835 Z= 0.230 Angle : 0.585 8.492 11957 Z= 0.303 Chirality : 0.043 0.167 1328 Planarity : 0.003 0.039 1521 Dihedral : 4.436 22.114 1194 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.14 % Allowed : 17.86 % Favored : 80.00 % 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: -0.04 (0.26), residues: 1077 helix: 1.69 (0.28), residues: 346 sheet: -0.42 (0.35), residues: 217 loop : -1.05 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.007 0.001 HIS A 220 PHE 0.031 0.002 PHE B 241 TYR 0.018 0.001 TYR R 237 ARG 0.004 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.890 Fit side-chains REVERT: A 227 GLN cc_start: 0.8546 (mp10) cc_final: 0.8183 (mp10) REVERT: A 317 ARG cc_start: 0.7500 (ptp-110) cc_final: 0.7071 (ptp-110) REVERT: A 323 ASP cc_start: 0.7776 (t0) cc_final: 0.7498 (t0) REVERT: B 126 LEU cc_start: 0.8141 (mm) cc_final: 0.7776 (mp) REVERT: B 230 ASN cc_start: 0.8285 (m-40) cc_final: 0.7998 (m110) REVERT: B 289 TYR cc_start: 0.8472 (m-80) cc_final: 0.7943 (m-80) REVERT: B 303 ASP cc_start: 0.7387 (m-30) cc_final: 0.7111 (m-30) REVERT: N 54 ASN cc_start: 0.7930 (m110) cc_final: 0.7711 (m110) REVERT: R 237 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.7152 (t80) REVERT: R 287 MET cc_start: 0.6178 (tpp) cc_final: 0.5119 (mpp) REVERT: R 380 PHE cc_start: 0.6720 (t80) cc_final: 0.6472 (t80) REVERT: R 385 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.5305 (tt) REVERT: R 411 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6558 (mmtt) REVERT: R 477 MET cc_start: 0.5427 (mmp) cc_final: 0.5191 (mmp) outliers start: 20 outliers final: 13 residues processed: 180 average time/residue: 0.2620 time to fit residues: 61.4244 Evaluate side-chains 182 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 411 LYS Chi-restraints excluded: chain R residue 485 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.173002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.144229 restraints weight = 12619.811| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.75 r_work: 0.3710 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8835 Z= 0.194 Angle : 0.566 8.570 11957 Z= 0.293 Chirality : 0.042 0.173 1328 Planarity : 0.003 0.040 1521 Dihedral : 4.351 21.711 1194 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.82 % Allowed : 19.04 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.26), residues: 1077 helix: 1.88 (0.28), residues: 345 sheet: -0.45 (0.35), residues: 217 loop : -1.04 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.008 0.001 HIS A 220 PHE 0.030 0.001 PHE B 241 TYR 0.019 0.001 TYR R 237 ARG 0.005 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.914 Fit side-chains REVERT: A 209 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6633 (mm-30) REVERT: A 309 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6700 (mm-30) REVERT: A 317 ARG cc_start: 0.7479 (ptp-110) cc_final: 0.7049 (ptp-110) REVERT: A 323 ASP cc_start: 0.7748 (t0) cc_final: 0.7474 (t0) REVERT: B 126 LEU cc_start: 0.8138 (mm) cc_final: 0.7694 (mp) REVERT: B 155 ASN cc_start: 0.8255 (t0) cc_final: 0.8046 (t0) REVERT: B 230 ASN cc_start: 0.8268 (m-40) cc_final: 0.7979 (m110) REVERT: B 289 TYR cc_start: 0.8462 (m-80) cc_final: 0.7929 (m-80) REVERT: B 303 ASP cc_start: 0.7375 (m-30) cc_final: 0.7095 (m-30) REVERT: N 54 ASN cc_start: 0.7873 (m110) cc_final: 0.7656 (m110) REVERT: R 237 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.7161 (t80) REVERT: R 287 MET cc_start: 0.6055 (tpp) cc_final: 0.5061 (mpp) REVERT: R 380 PHE cc_start: 0.6781 (t80) cc_final: 0.6481 (t80) REVERT: R 385 LEU cc_start: 0.5641 (tt) cc_final: 0.5327 (tt) REVERT: R 477 MET cc_start: 0.5369 (mmp) cc_final: 0.5167 (mmp) outliers start: 17 outliers final: 13 residues processed: 178 average time/residue: 0.2481 time to fit residues: 57.9125 Evaluate side-chains 178 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 485 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 67 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 69 optimal weight: 0.0060 chunk 11 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.173374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.144553 restraints weight = 12733.569| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.79 r_work: 0.3712 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8835 Z= 0.184 Angle : 0.576 9.119 11957 Z= 0.297 Chirality : 0.042 0.172 1328 Planarity : 0.003 0.043 1521 Dihedral : 4.316 20.652 1194 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.14 % Allowed : 19.57 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.08 (0.26), residues: 1077 helix: 1.95 (0.28), residues: 343 sheet: -0.46 (0.35), residues: 217 loop : -1.04 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.031 0.001 PHE B 241 TYR 0.018 0.001 TYR R 237 ARG 0.013 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.950 Fit side-chains REVERT: A 209 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6623 (mm-30) REVERT: A 309 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6687 (mm-30) REVERT: A 317 ARG cc_start: 0.7529 (ptp-110) cc_final: 0.7083 (ptp-110) REVERT: A 323 ASP cc_start: 0.7742 (t0) cc_final: 0.7459 (t0) REVERT: B 126 LEU cc_start: 0.8134 (mm) cc_final: 0.7697 (mp) REVERT: B 230 ASN cc_start: 0.8277 (m-40) cc_final: 0.7983 (m110) REVERT: B 289 TYR cc_start: 0.8471 (m-80) cc_final: 0.7941 (m-80) REVERT: B 303 ASP cc_start: 0.7373 (m-30) cc_final: 0.7079 (m-30) REVERT: C 62 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7203 (tmm) REVERT: R 237 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.7145 (t80) REVERT: R 287 MET cc_start: 0.6017 (tpp) cc_final: 0.5088 (mpp) REVERT: R 380 PHE cc_start: 0.6833 (t80) cc_final: 0.6507 (t80) REVERT: R 385 LEU cc_start: 0.5628 (tt) cc_final: 0.5346 (tt) REVERT: R 477 MET cc_start: 0.5443 (mmp) cc_final: 0.5235 (mmp) outliers start: 20 outliers final: 14 residues processed: 176 average time/residue: 0.2619 time to fit residues: 60.0535 Evaluate side-chains 179 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 485 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.172862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144091 restraints weight = 12544.409| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.77 r_work: 0.3696 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8835 Z= 0.221 Angle : 0.588 9.163 11957 Z= 0.305 Chirality : 0.043 0.177 1328 Planarity : 0.003 0.041 1521 Dihedral : 4.387 20.940 1194 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.03 % Allowed : 19.79 % Favored : 78.18 % 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: 0.03 (0.26), residues: 1077 helix: 1.84 (0.28), residues: 345 sheet: -0.43 (0.35), residues: 217 loop : -1.04 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.008 0.001 HIS A 220 PHE 0.030 0.001 PHE B 241 TYR 0.017 0.001 TYR R 237 ARG 0.004 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.920 Fit side-chains REVERT: A 309 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6663 (mm-30) REVERT: A 317 ARG cc_start: 0.7527 (ptp-110) cc_final: 0.7082 (ptp-110) REVERT: A 323 ASP cc_start: 0.7739 (t0) cc_final: 0.7465 (t0) REVERT: B 126 LEU cc_start: 0.8121 (mm) cc_final: 0.7726 (mp) REVERT: B 230 ASN cc_start: 0.8280 (m-40) cc_final: 0.7983 (m110) REVERT: B 289 TYR cc_start: 0.8477 (m-80) cc_final: 0.7948 (m-80) REVERT: B 303 ASP cc_start: 0.7404 (m-30) cc_final: 0.7104 (m-30) REVERT: C 62 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7225 (tmm) REVERT: R 237 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.7130 (t80) REVERT: R 287 MET cc_start: 0.6019 (tpp) cc_final: 0.5052 (mpp) REVERT: R 380 PHE cc_start: 0.6878 (t80) cc_final: 0.6574 (t80) REVERT: R 385 LEU cc_start: 0.5683 (tt) cc_final: 0.5412 (tt) REVERT: R 477 MET cc_start: 0.5500 (mmp) cc_final: 0.4994 (mmp) outliers start: 19 outliers final: 16 residues processed: 177 average time/residue: 0.2546 time to fit residues: 59.5294 Evaluate side-chains 179 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 338 LEU Chi-restraints excluded: chain R residue 485 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 82 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 0.0020 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 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 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.173530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.144684 restraints weight = 12571.971| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.77 r_work: 0.3688 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8835 Z= 0.195 Angle : 0.590 9.031 11957 Z= 0.304 Chirality : 0.042 0.178 1328 Planarity : 0.003 0.038 1521 Dihedral : 4.360 20.563 1194 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.03 % Allowed : 20.21 % Favored : 77.75 % 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: 0.01 (0.26), residues: 1077 helix: 1.84 (0.28), residues: 347 sheet: -0.45 (0.35), residues: 217 loop : -1.07 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.032 0.001 PHE B 241 TYR 0.018 0.001 TYR R 237 ARG 0.009 0.000 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.854 Fit side-chains REVERT: A 309 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6627 (mm-30) REVERT: A 317 ARG cc_start: 0.7540 (ptp-110) cc_final: 0.7096 (ptp-110) REVERT: B 126 LEU cc_start: 0.8131 (mm) cc_final: 0.7741 (mp) REVERT: B 150 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.7644 (tpp-160) REVERT: B 230 ASN cc_start: 0.8271 (m-40) cc_final: 0.7988 (m110) REVERT: B 289 TYR cc_start: 0.8474 (m-80) cc_final: 0.7944 (m-80) REVERT: B 303 ASP cc_start: 0.7375 (m-30) cc_final: 0.7072 (m-30) REVERT: C 62 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7200 (tmm) REVERT: N 128 ARG cc_start: 0.7073 (ptt-90) cc_final: 0.6749 (ptt-90) REVERT: R 237 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.7128 (t80) REVERT: R 287 MET cc_start: 0.6022 (tpp) cc_final: 0.5074 (mpp) REVERT: R 380 PHE cc_start: 0.6936 (t80) cc_final: 0.6616 (t80) REVERT: R 385 LEU cc_start: 0.5622 (tt) cc_final: 0.5352 (tt) REVERT: R 477 MET cc_start: 0.5522 (mmp) cc_final: 0.5029 (mmp) outliers start: 19 outliers final: 17 residues processed: 179 average time/residue: 0.2473 time to fit residues: 59.2522 Evaluate side-chains 186 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 338 LEU Chi-restraints excluded: chain R residue 485 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.171533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142960 restraints weight = 12639.030| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.75 r_work: 0.3680 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8835 Z= 0.266 Angle : 0.629 13.091 11957 Z= 0.323 Chirality : 0.044 0.181 1328 Planarity : 0.004 0.049 1521 Dihedral : 4.572 22.790 1194 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.25 % Allowed : 20.64 % Favored : 77.11 % 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: -0.03 (0.26), residues: 1077 helix: 1.78 (0.28), residues: 343 sheet: -0.41 (0.35), residues: 217 loop : -1.09 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.009 0.001 HIS A 220 PHE 0.031 0.002 PHE B 241 TYR 0.017 0.002 TYR R 237 ARG 0.007 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4395.30 seconds wall clock time: 76 minutes 6.84 seconds (4566.84 seconds total)