Starting phenix.real_space_refine on Fri Jul 19 17:40:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhb_36261/07_2024/8jhb_36261.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhb_36261/07_2024/8jhb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhb_36261/07_2024/8jhb_36261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhb_36261/07_2024/8jhb_36261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhb_36261/07_2024/8jhb_36261.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhb_36261/07_2024/8jhb_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 Residue "A ASP 22": "OD1" <-> "OD2" Residue "B ASP 267": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.59, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 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: 3.35 Conformation dependent library (CDL) restraints added in 1.8 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: 1.06 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: 2.48 Time building geometry restraints manager: 3.69 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: 94.18 - 102.16: 27 102.16 - 110.13: 1526 110.13 - 118.10: 5049 118.10 - 126.08: 5204 126.08 - 134.05: 151 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 2.440 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.196 2.440 nonbonded pdb=" OH TYR R 290 " pdb=" O PHE R 370 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR R 237 " pdb=" O VAL R 486 " model vdw 2.216 2.440 nonbonded pdb=" O ARG N 121 " pdb=" OH TYR N 138 " model vdw 2.233 2.440 ... (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 ========== 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: 1.150 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.910 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.280 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.919 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: 0.2573 time to fit residues: 63.0684 Evaluate side-chains 167 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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: 0.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 0.0060 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 295 ASN R 164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8835 Z= 0.191 Angle : 0.545 8.689 11957 Z= 0.284 Chirality : 0.042 0.144 1328 Planarity : 0.003 0.047 1521 Dihedral : 4.518 28.430 1194 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.50 % Allowed : 8.56 % Favored : 89.95 % 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: -0.22 (0.26), residues: 1077 helix: 1.28 (0.29), residues: 351 sheet: -0.18 (0.35), residues: 220 loop : -1.14 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.008 0.001 HIS B 91 PHE 0.022 0.001 PHE B 241 TYR 0.014 0.001 TYR N 138 ARG 0.003 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 194 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 299 GLU cc_start: 0.7684 (mp0) cc_final: 0.7343 (mt-10) REVERT: A 317 ARG cc_start: 0.7030 (ptp-110) cc_final: 0.6709 (ptp-110) REVERT: A 323 ASP cc_start: 0.7659 (t0) cc_final: 0.7371 (t0) REVERT: A 356 ARG cc_start: 0.7319 (mpt180) cc_final: 0.7105 (mpt180) REVERT: B 75 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7546 (mm110) REVERT: B 230 ASN cc_start: 0.8232 (m-40) cc_final: 0.8020 (m110) REVERT: B 289 TYR cc_start: 0.8589 (m-80) cc_final: 0.7980 (m-80) REVERT: B 303 ASP cc_start: 0.7096 (m-30) cc_final: 0.6868 (m-30) outliers start: 14 outliers final: 8 residues processed: 187 average time/residue: 0.2693 time to fit residues: 65.0356 Evaluate side-chains 179 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 170 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 75 GLN 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 53 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 32 optimal weight: 0.0060 chunk 77 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS R 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8835 Z= 0.182 Angle : 0.537 7.229 11957 Z= 0.277 Chirality : 0.041 0.165 1328 Planarity : 0.003 0.042 1521 Dihedral : 4.374 26.107 1194 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.60 % Allowed : 13.26 % Favored : 85.13 % 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: 1.52 (0.28), residues: 355 sheet: -0.20 (0.34), residues: 223 loop : -1.07 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS B 91 PHE 0.030 0.001 PHE A 212 TYR 0.013 0.001 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 191 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 1.018 Fit side-chains REVERT: A 227 GLN cc_start: 0.8629 (mp10) cc_final: 0.8208 (mp10) REVERT: A 299 GLU cc_start: 0.7763 (mp0) cc_final: 0.7557 (mp0) REVERT: A 317 ARG cc_start: 0.6984 (ptp-110) cc_final: 0.6629 (ptp-110) REVERT: A 323 ASP cc_start: 0.7663 (t0) cc_final: 0.7365 (t0) REVERT: B 230 ASN cc_start: 0.8245 (m-40) cc_final: 0.7941 (m110) REVERT: B 289 TYR cc_start: 0.8586 (m-80) cc_final: 0.8039 (m-80) REVERT: B 303 ASP cc_start: 0.7089 (m-30) cc_final: 0.6857 (m-30) outliers start: 15 outliers final: 10 residues processed: 183 average time/residue: 0.2507 time to fit residues: 60.0289 Evaluate side-chains 181 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR 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 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 425 LEU 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 95 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8835 Z= 0.172 Angle : 0.533 8.167 11957 Z= 0.273 Chirality : 0.041 0.150 1328 Planarity : 0.003 0.039 1521 Dihedral : 4.276 24.316 1194 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.67 % Allowed : 14.76 % 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: 0.08 (0.26), residues: 1077 helix: 1.74 (0.29), residues: 350 sheet: -0.25 (0.34), residues: 225 loop : -1.02 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS R 164 PHE 0.028 0.001 PHE B 241 TYR 0.014 0.001 TYR R 237 ARG 0.007 0.000 ARG B 52 *********************** 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 195 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 0.973 Fit side-chains REVERT: A 227 GLN cc_start: 0.8649 (mp10) cc_final: 0.8243 (mp10) REVERT: A 284 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 317 ARG cc_start: 0.6996 (ptp-110) cc_final: 0.6616 (ptp-110) REVERT: A 323 ASP cc_start: 0.7649 (t0) cc_final: 0.7375 (t0) REVERT: B 150 ARG cc_start: 0.7946 (mpt180) cc_final: 0.7594 (mpt180) REVERT: B 230 ASN cc_start: 0.8231 (m-40) cc_final: 0.7912 (m110) REVERT: B 289 TYR cc_start: 0.8600 (m-80) cc_final: 0.8029 (m-80) REVERT: B 303 ASP cc_start: 0.7114 (m-30) cc_final: 0.6876 (m-30) REVERT: R 287 MET cc_start: 0.6010 (tpp) cc_final: 0.5005 (mpp) REVERT: R 352 ASN cc_start: 0.6288 (OUTLIER) cc_final: 0.6072 (p0) REVERT: R 475 LEU cc_start: 0.4671 (tt) cc_final: 0.4382 (tt) REVERT: R 477 MET cc_start: 0.5760 (mmp) cc_final: 0.5551 (mmp) outliers start: 25 outliers final: 16 residues processed: 184 average time/residue: 0.2557 time to fit residues: 61.6866 Evaluate side-chains 180 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 347 ARG 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 136 SER 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 195 LEU Chi-restraints excluded: chain R residue 305 ILE Chi-restraints excluded: chain R residue 352 ASN Chi-restraints excluded: chain R residue 423 LEU Chi-restraints excluded: chain R residue 440 VAL 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 58 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 87 optimal weight: 0.4980 chunk 70 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 0.0010 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8835 Z= 0.138 Angle : 0.520 8.420 11957 Z= 0.266 Chirality : 0.041 0.164 1328 Planarity : 0.003 0.033 1521 Dihedral : 4.090 21.102 1194 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.57 % Allowed : 16.15 % Favored : 81.28 % 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: 0.19 (0.26), residues: 1077 helix: 1.85 (0.29), residues: 352 sheet: -0.27 (0.34), residues: 225 loop : -0.93 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS R 164 PHE 0.028 0.001 PHE B 241 TYR 0.015 0.001 TYR R 237 ARG 0.003 0.000 ARG B 52 *********************** 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 190 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.023 Fit side-chains REVERT: A 227 GLN cc_start: 0.8624 (mp10) cc_final: 0.8216 (mp10) REVERT: A 284 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8144 (p) REVERT: A 317 ARG cc_start: 0.6971 (ptp-110) cc_final: 0.6710 (ptp-110) REVERT: A 323 ASP cc_start: 0.7637 (t0) cc_final: 0.7369 (t0) REVERT: B 230 ASN cc_start: 0.8216 (m-40) cc_final: 0.7909 (m110) REVERT: B 289 TYR cc_start: 0.8595 (m-80) cc_final: 0.8011 (m-80) REVERT: B 291 ASP cc_start: 0.7564 (p0) cc_final: 0.6886 (p0) REVERT: B 303 ASP cc_start: 0.7069 (m-30) cc_final: 0.6837 (m-30) REVERT: R 287 MET cc_start: 0.5975 (tpp) cc_final: 0.4925 (mpp) REVERT: R 411 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7017 (mmtt) REVERT: R 477 MET cc_start: 0.5724 (mmp) cc_final: 0.5518 (mmp) outliers start: 24 outliers final: 10 residues processed: 180 average time/residue: 0.2567 time to fit residues: 60.2451 Evaluate side-chains 171 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 136 SER 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 411 LYS Chi-restraints excluded: chain R residue 423 LEU Chi-restraints excluded: chain R residue 440 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.0570 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8835 Z= 0.205 Angle : 0.548 8.538 11957 Z= 0.283 Chirality : 0.042 0.155 1328 Planarity : 0.003 0.035 1521 Dihedral : 4.268 21.352 1194 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.46 % Allowed : 16.90 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.26), residues: 1077 helix: 1.78 (0.28), residues: 353 sheet: -0.25 (0.34), residues: 221 loop : -1.03 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS R 164 PHE 0.029 0.001 PHE B 241 TYR 0.015 0.001 TYR R 237 ARG 0.004 0.000 ARG B 52 *********************** 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 199 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 0.953 Fit side-chains REVERT: A 227 GLN cc_start: 0.8665 (mp10) cc_final: 0.8270 (mp10) REVERT: A 317 ARG cc_start: 0.7047 (ptp-110) cc_final: 0.6658 (ptp-110) REVERT: A 323 ASP cc_start: 0.7633 (t0) cc_final: 0.7386 (t0) REVERT: B 126 LEU cc_start: 0.8118 (mm) cc_final: 0.7734 (mp) REVERT: B 230 ASN cc_start: 0.8232 (m-40) cc_final: 0.7935 (m110) REVERT: B 289 TYR cc_start: 0.8617 (m-80) cc_final: 0.8033 (m-80) REVERT: B 291 ASP cc_start: 0.7661 (p0) cc_final: 0.6952 (p0) REVERT: B 303 ASP cc_start: 0.7140 (m-30) cc_final: 0.6926 (m-30) REVERT: R 287 MET cc_start: 0.5999 (tpp) cc_final: 0.4888 (mpp) REVERT: R 397 ARG cc_start: 0.4470 (ttt180) cc_final: 0.3710 (ttt-90) REVERT: R 411 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6989 (mmtt) REVERT: R 475 LEU cc_start: 0.4347 (tt) cc_final: 0.3682 (tt) REVERT: R 476 PHE cc_start: 0.7213 (m-80) cc_final: 0.6995 (m-80) REVERT: R 477 MET cc_start: 0.5679 (mmp) cc_final: 0.5471 (mmp) outliers start: 23 outliers final: 15 residues processed: 189 average time/residue: 0.2442 time to fit residues: 60.5633 Evaluate side-chains 180 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 325 THR 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 136 SER 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 N residue 96 ASP Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 411 LYS Chi-restraints excluded: chain R residue 440 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8835 Z= 0.231 Angle : 0.576 10.695 11957 Z= 0.296 Chirality : 0.042 0.159 1328 Planarity : 0.003 0.034 1521 Dihedral : 4.334 22.096 1194 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.46 % Allowed : 17.43 % Favored : 80.11 % 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: 0.14 (0.26), residues: 1077 helix: 1.95 (0.28), residues: 344 sheet: -0.34 (0.34), residues: 225 loop : -1.01 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.010 0.001 HIS R 164 PHE 0.030 0.002 PHE B 241 TYR 0.014 0.001 TYR R 237 ARG 0.005 0.000 ARG B 52 *********************** 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 197 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 1.042 Fit side-chains REVERT: A 227 GLN cc_start: 0.8681 (mp10) cc_final: 0.8261 (mp10) REVERT: A 309 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6616 (mm-30) REVERT: A 317 ARG cc_start: 0.7061 (ptp-110) cc_final: 0.6672 (ptp-110) REVERT: A 323 ASP cc_start: 0.7640 (t0) cc_final: 0.7399 (t0) REVERT: B 126 LEU cc_start: 0.8123 (mm) cc_final: 0.7731 (mp) REVERT: B 230 ASN cc_start: 0.8226 (m-40) cc_final: 0.7959 (m110) REVERT: B 289 TYR cc_start: 0.8616 (m-80) cc_final: 0.8045 (m-80) REVERT: B 303 ASP cc_start: 0.7210 (m-30) cc_final: 0.6946 (m-30) REVERT: R 287 MET cc_start: 0.5941 (tpp) cc_final: 0.4865 (mpp) REVERT: R 397 ARG cc_start: 0.4495 (ttt180) cc_final: 0.3805 (ttt-90) REVERT: R 411 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6969 (mmtt) REVERT: R 475 LEU cc_start: 0.4586 (tt) cc_final: 0.3925 (tt) REVERT: R 477 MET cc_start: 0.5725 (mmp) cc_final: 0.5517 (mmp) outliers start: 23 outliers final: 20 residues processed: 186 average time/residue: 0.2660 time to fit residues: 64.3609 Evaluate side-chains 191 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR 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 136 SER 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 B residue 325 MET Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain R residue 279 ASN Chi-restraints excluded: chain R residue 305 ILE Chi-restraints excluded: chain R residue 356 VAL Chi-restraints excluded: chain R residue 411 LYS Chi-restraints excluded: chain R residue 440 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 92 optimal weight: 0.0970 chunk 97 optimal weight: 0.0570 chunk 89 optimal weight: 1.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN R 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8835 Z= 0.162 Angle : 0.544 8.243 11957 Z= 0.280 Chirality : 0.041 0.168 1328 Planarity : 0.003 0.031 1521 Dihedral : 4.199 20.940 1194 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.35 % Allowed : 17.86 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1077 helix: 2.06 (0.29), residues: 343 sheet: -0.38 (0.34), residues: 225 loop : -1.00 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS R 164 PHE 0.028 0.001 PHE B 241 TYR 0.016 0.001 TYR R 237 ARG 0.005 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 192 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.037 Fit side-chains REVERT: A 227 GLN cc_start: 0.8644 (mp10) cc_final: 0.8272 (mp10) REVERT: A 309 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6649 (mm-30) REVERT: A 317 ARG cc_start: 0.7051 (ptp-110) cc_final: 0.6654 (ptp-110) REVERT: A 323 ASP cc_start: 0.7620 (t0) cc_final: 0.7372 (t0) REVERT: B 126 LEU cc_start: 0.8112 (mm) cc_final: 0.7725 (mp) REVERT: B 230 ASN cc_start: 0.8230 (m-40) cc_final: 0.7940 (m110) REVERT: B 289 TYR cc_start: 0.8607 (m-80) cc_final: 0.8026 (m-80) REVERT: B 303 ASP cc_start: 0.7138 (m-30) cc_final: 0.6902 (m-30) REVERT: R 237 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.7027 (t80) REVERT: R 287 MET cc_start: 0.5876 (tpp) cc_final: 0.4842 (mpp) REVERT: R 397 ARG cc_start: 0.4505 (ttt180) cc_final: 0.3745 (ttt-90) REVERT: R 411 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6960 (mmtt) REVERT: R 475 LEU cc_start: 0.4443 (tt) cc_final: 0.3791 (tt) outliers start: 22 outliers final: 14 residues processed: 181 average time/residue: 0.2621 time to fit residues: 61.7210 Evaluate side-chains 182 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 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 246 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 411 LYS 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 95 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8835 Z= 0.222 Angle : 0.586 8.224 11957 Z= 0.300 Chirality : 0.043 0.180 1328 Planarity : 0.003 0.035 1521 Dihedral : 4.338 20.947 1194 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.35 % Allowed : 18.61 % Favored : 79.04 % 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: 0.11 (0.26), residues: 1077 helix: 1.94 (0.28), residues: 344 sheet: -0.38 (0.34), residues: 226 loop : -1.03 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.016 0.001 HIS R 164 PHE 0.028 0.001 PHE B 241 TYR 0.015 0.001 TYR R 237 ARG 0.006 0.000 ARG B 52 *********************** 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 192 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.026 Fit side-chains REVERT: A 227 GLN cc_start: 0.8712 (mp10) cc_final: 0.8301 (mp10) REVERT: A 317 ARG cc_start: 0.7069 (ptp-110) cc_final: 0.6683 (ptp-110) REVERT: A 323 ASP cc_start: 0.7618 (t0) cc_final: 0.7367 (t0) REVERT: B 49 ARG cc_start: 0.7801 (mpt180) cc_final: 0.7567 (mpt180) REVERT: B 126 LEU cc_start: 0.8121 (mm) cc_final: 0.7736 (mp) REVERT: B 230 ASN cc_start: 0.8252 (m-40) cc_final: 0.7967 (m110) REVERT: B 289 TYR cc_start: 0.8616 (m-80) cc_final: 0.8049 (m-80) REVERT: B 303 ASP cc_start: 0.7198 (m-30) cc_final: 0.6931 (m-30) REVERT: N 135 SER cc_start: 0.6742 (p) cc_final: 0.6495 (t) REVERT: R 397 ARG cc_start: 0.4609 (ttt180) cc_final: 0.3816 (ttt-90) REVERT: R 411 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6952 (mmtt) REVERT: R 475 LEU cc_start: 0.4398 (tt) cc_final: 0.3746 (tt) outliers start: 22 outliers final: 17 residues processed: 181 average time/residue: 0.2728 time to fit residues: 64.8080 Evaluate side-chains 187 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 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 246 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 279 ASN Chi-restraints excluded: chain R residue 411 LYS 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 61 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 97 optimal weight: 0.5980 chunk 84 optimal weight: 0.0570 chunk 8 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8835 Z= 0.154 Angle : 0.569 11.756 11957 Z= 0.291 Chirality : 0.042 0.181 1328 Planarity : 0.003 0.048 1521 Dihedral : 4.221 21.204 1194 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.82 % Allowed : 19.47 % Favored : 78.72 % 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: 0.22 (0.26), residues: 1077 helix: 2.11 (0.29), residues: 343 sheet: -0.39 (0.34), residues: 226 loop : -0.97 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.013 0.001 HIS R 164 PHE 0.027 0.001 PHE B 241 TYR 0.023 0.001 TYR R 237 ARG 0.010 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 190 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 0.930 Fit side-chains REVERT: A 227 GLN cc_start: 0.8627 (mp10) cc_final: 0.8274 (mp10) REVERT: A 317 ARG cc_start: 0.7058 (ptp-110) cc_final: 0.6663 (ptp-110) REVERT: A 323 ASP cc_start: 0.7605 (t0) cc_final: 0.7350 (t0) REVERT: B 126 LEU cc_start: 0.8111 (mm) cc_final: 0.7726 (mp) REVERT: B 230 ASN cc_start: 0.8253 (m-40) cc_final: 0.7951 (m110) REVERT: B 289 TYR cc_start: 0.8598 (m-80) cc_final: 0.8015 (m-80) REVERT: B 303 ASP cc_start: 0.7104 (m-30) cc_final: 0.6871 (m-30) REVERT: N 54 ASN cc_start: 0.7765 (m110) cc_final: 0.7540 (m110) REVERT: N 135 SER cc_start: 0.6668 (p) cc_final: 0.6403 (t) REVERT: R 397 ARG cc_start: 0.4534 (ttt180) cc_final: 0.3729 (ttt-90) REVERT: R 411 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6948 (mmtt) REVERT: R 475 LEU cc_start: 0.4360 (tt) cc_final: 0.3687 (tt) outliers start: 17 outliers final: 15 residues processed: 183 average time/residue: 0.2666 time to fit residues: 63.9032 Evaluate side-chains 188 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 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 246 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain R residue 279 ASN Chi-restraints excluded: chain R residue 411 LYS 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 25 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 0.0000 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 0.0170 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 73 optimal weight: 0.0570 chunk 4 optimal weight: 0.8980 overall best weight: 0.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** 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 = 0.4225 r_free = 0.4225 target = 0.175238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.146735 restraints weight = 12475.936| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.73 r_work: 0.3742 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2587 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= 0.146 Angle : 0.559 10.432 11957 Z= 0.285 Chirality : 0.041 0.173 1328 Planarity : 0.003 0.039 1521 Dihedral : 4.110 20.775 1194 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.82 % Allowed : 19.79 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1077 helix: 2.20 (0.29), residues: 343 sheet: -0.36 (0.34), residues: 226 loop : -0.96 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.007 0.001 HIS A 220 PHE 0.034 0.001 PHE B 241 TYR 0.022 0.001 TYR R 237 ARG 0.009 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2387.94 seconds wall clock time: 43 minutes 11.63 seconds (2591.63 seconds total)