Starting phenix.real_space_refine on Fri Mar 14 02:42:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xwo_10633/03_2025/6xwo_10633.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xwo_10633/03_2025/6xwo_10633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xwo_10633/03_2025/6xwo_10633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xwo_10633/03_2025/6xwo_10633.map" model { file = "/net/cci-nas-00/data/ceres_data/6xwo_10633/03_2025/6xwo_10633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xwo_10633/03_2025/6xwo_10633.cif" } resolution = 3.39 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= 0.000 sd= 0.020 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 48 5.16 5 C 6301 2.51 5 N 1545 2.21 5 O 1661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9555 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3184 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain: "B" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3184 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain: "C" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3187 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 1 Time building chain proxies: 6.09, per 1000 atoms: 0.64 Number of scatterers: 9555 At special positions: 0 Unit cell: (79.948, 109.296, 120.428, 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 48 16.00 O 1661 8.00 N 1545 7.00 C 6301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 0 sheets defined 77.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 13 through 36 Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.698A pdb=" N TYR A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.736A pdb=" N GLY A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 75 Processing helix chain 'A' and resid 81 through 110 removed outlier: 3.996A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 153 through 171 Processing helix chain 'A' and resid 176 through 222 Proline residue: A 208 - end of helix removed outlier: 3.816A pdb=" N VAL A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 256 removed outlier: 4.846A pdb=" N PHE A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 278 removed outlier: 5.604A pdb=" N ASP A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.763A pdb=" N VAL A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 362 through 374 Processing helix chain 'A' and resid 381 through 420 removed outlier: 3.729A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N MET A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'B' and resid 6 through 12 Processing helix chain 'B' and resid 17 through 32 Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.884A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 76 Processing helix chain 'B' and resid 81 through 109 removed outlier: 3.740A pdb=" N VAL B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 95 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 152 through 172 removed outlier: 3.575A pdb=" N VAL B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 223 Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 227 through 255 removed outlier: 4.570A pdb=" N GLY B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR B 238 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 5.706A pdb=" N ASP B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 298 through 313 removed outlier: 3.551A pdb=" N PHE B 302 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Proline residue: B 307 - end of helix removed outlier: 4.478A pdb=" N THR B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 332 removed outlier: 3.911A pdb=" N LEU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 360 through 374 removed outlier: 3.707A pdb=" N ILE B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 removed outlier: 3.567A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B 393 " --> pdb=" O MET B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 411 removed outlier: 4.513A pdb=" N MET B 403 " --> pdb=" O MET B 399 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP B 409 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'C' and resid 14 through 34 removed outlier: 4.264A pdb=" N TRP C 20 " --> pdb=" O TRP C 16 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY C 21 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 59 removed outlier: 3.559A pdb=" N GLY C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.885A pdb=" N SER C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 109 removed outlier: 3.872A pdb=" N ARG C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 138 Processing helix chain 'C' and resid 143 through 149 Processing helix chain 'C' and resid 152 through 171 removed outlier: 3.881A pdb=" N VAL C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 222 removed outlier: 3.910A pdb=" N GLN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Proline residue: C 208 - end of helix removed outlier: 3.615A pdb=" N VAL C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 247 removed outlier: 3.621A pdb=" N TYR C 238 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR C 239 " --> pdb=" O GLY C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 259 through 275 removed outlier: 5.608A pdb=" N ASP C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA C 270 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 292 removed outlier: 3.514A pdb=" N VAL C 290 " --> pdb=" O VAL C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 313 removed outlier: 4.304A pdb=" N PHE C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Proline residue: C 307 - end of helix removed outlier: 4.574A pdb=" N THR C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 331 removed outlier: 3.747A pdb=" N VAL C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL C 325 " --> pdb=" O GLN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.733A pdb=" N VAL C 344 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.131A pdb=" N GLY C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 355' Processing helix chain 'C' and resid 361 through 371 removed outlier: 3.629A pdb=" N MET C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET C 368 " --> pdb=" O ILE C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 removed outlier: 3.599A pdb=" N GLY C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.624A pdb=" N LEU C 397 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 removed outlier: 3.789A pdb=" N ASP C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1944 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: 2.87 Time building geometry restraints manager: 2.83 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: 2967 1.34 - 1.46: 1444 1.46 - 1.57: 5224 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 9731 Sorted by residual: bond pdb=" C THR C 378 " pdb=" N PRO C 379 " ideal model delta sigma weight residual 1.330 1.356 -0.026 1.23e-02 6.61e+03 4.30e+00 bond pdb=" CB THR B 168 " pdb=" CG2 THR B 168 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" CB VAL B 115 " pdb=" CG2 VAL B 115 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CB VAL A 233 " pdb=" CG2 VAL A 233 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CB VAL B 404 " pdb=" CG2 VAL B 404 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 ... (remaining 9726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12867 1.75 - 3.51: 311 3.51 - 5.26: 57 5.26 - 7.01: 8 7.01 - 8.77: 1 Bond angle restraints: 13244 Sorted by residual: angle pdb=" N TYR C 387 " pdb=" CA TYR C 387 " pdb=" C TYR C 387 " ideal model delta sigma weight residual 114.56 109.64 4.92 1.27e+00 6.20e-01 1.50e+01 angle pdb=" N LEU C 385 " pdb=" CA LEU C 385 " pdb=" C LEU C 385 " ideal model delta sigma weight residual 112.68 108.44 4.24 1.33e+00 5.65e-01 1.01e+01 angle pdb=" N ALA A 207 " pdb=" CA ALA A 207 " pdb=" C ALA A 207 " ideal model delta sigma weight residual 109.81 116.37 -6.56 2.21e+00 2.05e-01 8.80e+00 angle pdb=" N ALA C 386 " pdb=" CA ALA C 386 " pdb=" C ALA C 386 " ideal model delta sigma weight residual 112.93 110.04 2.89 1.12e+00 7.97e-01 6.66e+00 angle pdb=" N ASP A 394 " pdb=" CA ASP A 394 " pdb=" C ASP A 394 " ideal model delta sigma weight residual 110.80 116.23 -5.43 2.13e+00 2.20e-01 6.51e+00 ... (remaining 13239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5204 17.74 - 35.49: 455 35.49 - 53.23: 65 53.23 - 70.97: 9 70.97 - 88.72: 4 Dihedral angle restraints: 5737 sinusoidal: 2126 harmonic: 3611 Sorted by residual: dihedral pdb=" CA TRP C 16 " pdb=" C TRP C 16 " pdb=" N LYS C 17 " pdb=" CA LYS C 17 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA PRO C 129 " pdb=" C PRO C 129 " pdb=" N PRO C 130 " pdb=" CA PRO C 130 " ideal model delta harmonic sigma weight residual -180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA TRP B 16 " pdb=" C TRP B 16 " pdb=" N LYS B 17 " pdb=" CA LYS B 17 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 900 0.032 - 0.063: 522 0.063 - 0.095: 153 0.095 - 0.126: 68 0.126 - 0.158: 7 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CG LEU C 241 " pdb=" CB LEU C 241 " pdb=" CD1 LEU C 241 " pdb=" CD2 LEU C 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA TRP C 16 " pdb=" N TRP C 16 " pdb=" C TRP C 16 " pdb=" CB TRP C 16 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 1647 not shown) Planarity restraints: 1627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 245 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ILE B 245 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE B 245 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 246 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 235 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C GLY B 235 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY B 235 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 236 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 207 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO C 208 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.028 5.00e-02 4.00e+02 ... (remaining 1624 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 403 2.71 - 3.26: 10374 3.26 - 3.81: 15713 3.81 - 4.35: 19709 4.35 - 4.90: 33672 Nonbonded interactions: 79871 Sorted by model distance: nonbonded pdb=" O THR B 378 " pdb=" OG SER B 381 " model vdw 2.167 3.040 nonbonded pdb=" O ASP C 269 " pdb=" OG1 THR C 273 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR B 238 " pdb=" O ILE B 396 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR B 305 " pdb=" OG1 THR B 413 " model vdw 2.243 3.040 nonbonded pdb=" O TYR B 9 " pdb=" NZ LYS B 17 " model vdw 2.247 3.120 ... (remaining 79866 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 430) selection = (chain 'B' and resid 5 through 430) selection = (chain 'C' and resid 5 through 430) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.270 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.006 0.053 9731 Z= 0.415 Angle : 0.692 8.766 13244 Z= 0.372 Chirality : 0.044 0.158 1650 Planarity : 0.005 0.050 1627 Dihedral : 13.226 88.717 3445 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % 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: -3.53 (0.20), residues: 1274 helix: -2.02 (0.14), residues: 979 sheet: None (None), residues: 0 loop : -2.77 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 16 HIS 0.006 0.001 HIS B 34 PHE 0.017 0.002 PHE C 302 TYR 0.013 0.001 TYR C 37 ARG 0.003 0.000 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.013 Fit side-chains REVERT: B 394 ASP cc_start: 0.7528 (t70) cc_final: 0.7258 (t70) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2589 time to fit residues: 43.2921 Evaluate side-chains 92 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.0870 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 114 optimal weight: 0.0980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN B 321 GLN B 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.058439 restraints weight = 27658.935| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.34 r_work: 0.2748 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9731 Z= 0.168 Angle : 0.575 8.909 13244 Z= 0.291 Chirality : 0.039 0.130 1650 Planarity : 0.005 0.054 1627 Dihedral : 4.555 33.268 1365 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.29 % Allowed : 13.33 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1274 helix: -0.56 (0.16), residues: 980 sheet: None (None), residues: 0 loop : -2.18 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 16 HIS 0.002 0.001 HIS B 34 PHE 0.019 0.001 PHE C 302 TYR 0.009 0.001 TYR C 238 ARG 0.002 0.000 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.8679 (mmm) cc_final: 0.8439 (mmm) REVERT: A 365 MET cc_start: 0.8581 (mtp) cc_final: 0.8376 (ttt) REVERT: B 222 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: B 244 GLN cc_start: 0.8983 (tt0) cc_final: 0.8671 (tp40) REVERT: B 288 MET cc_start: 0.8632 (mtp) cc_final: 0.8224 (mmt) REVERT: B 312 ILE cc_start: 0.9340 (pt) cc_final: 0.9100 (mp) REVERT: B 410 LEU cc_start: 0.9054 (pp) cc_final: 0.8815 (pp) REVERT: C 90 TYR cc_start: 0.8411 (t80) cc_final: 0.8002 (t80) REVERT: C 138 ASN cc_start: 0.9499 (m-40) cc_final: 0.8928 (m-40) REVERT: C 219 MET cc_start: 0.9051 (mmt) cc_final: 0.8832 (mmp) REVERT: C 225 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7329 (mpt180) REVERT: C 365 MET cc_start: 0.9104 (tpp) cc_final: 0.8714 (mmm) REVERT: C 389 MET cc_start: 0.8588 (mtm) cc_final: 0.8358 (mtp) outliers start: 13 outliers final: 4 residues processed: 115 average time/residue: 0.1787 time to fit residues: 31.1950 Evaluate side-chains 96 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 343 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 97 optimal weight: 0.0000 chunk 6 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN A 371 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.072750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059955 restraints weight = 28180.498| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.07 r_work: 0.2814 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9731 Z= 0.196 Angle : 0.549 7.809 13244 Z= 0.278 Chirality : 0.039 0.180 1650 Planarity : 0.005 0.057 1627 Dihedral : 4.246 22.344 1365 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.09 % Allowed : 16.32 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.75 (0.24), residues: 1274 helix: 0.05 (0.17), residues: 985 sheet: None (None), residues: 0 loop : -2.09 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 16 HIS 0.003 0.001 HIS B 34 PHE 0.015 0.001 PHE C 302 TYR 0.008 0.001 TYR C 238 ARG 0.012 0.000 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.412 Fit side-chains REVERT: A 97 MET cc_start: 0.9100 (mmm) cc_final: 0.8512 (mmm) REVERT: A 100 PHE cc_start: 0.8905 (t80) cc_final: 0.8501 (t80) REVERT: A 204 MET cc_start: 0.8985 (mmm) cc_final: 0.8707 (mmm) REVERT: B 204 MET cc_start: 0.9367 (mmm) cc_final: 0.9133 (mmm) REVERT: B 295 MET cc_start: 0.8617 (ttm) cc_final: 0.8393 (mtp) REVERT: B 410 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8952 (pp) REVERT: C 90 TYR cc_start: 0.8785 (t80) cc_final: 0.8326 (t80) REVERT: C 134 GLN cc_start: 0.8787 (mm-40) cc_final: 0.7999 (mm-40) REVERT: C 138 ASN cc_start: 0.9597 (m-40) cc_final: 0.9024 (m-40) REVERT: C 225 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7846 (mtp85) REVERT: C 321 GLN cc_start: 0.9210 (mt0) cc_final: 0.8894 (mt0) REVERT: C 365 MET cc_start: 0.9075 (tpp) cc_final: 0.8800 (mmm) REVERT: C 368 MET cc_start: 0.8950 (tmm) cc_final: 0.8696 (tmm) outliers start: 21 outliers final: 11 residues processed: 116 average time/residue: 0.2013 time to fit residues: 36.5409 Evaluate side-chains 103 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.0670 chunk 35 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.059122 restraints weight = 27996.249| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.41 r_work: 0.2771 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9731 Z= 0.149 Angle : 0.528 8.290 13244 Z= 0.266 Chirality : 0.039 0.169 1650 Planarity : 0.004 0.053 1627 Dihedral : 4.083 23.716 1365 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.89 % Allowed : 17.91 % Favored : 80.20 % 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 (0.24), residues: 1274 helix: 0.47 (0.17), residues: 971 sheet: None (None), residues: 0 loop : -1.74 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 16 HIS 0.002 0.000 HIS B 34 PHE 0.013 0.001 PHE C 302 TYR 0.012 0.001 TYR A 90 ARG 0.004 0.000 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.977 Fit side-chains REVERT: A 97 MET cc_start: 0.8800 (mmm) cc_final: 0.8224 (mmm) REVERT: A 100 PHE cc_start: 0.8694 (t80) cc_final: 0.8244 (t80) REVERT: A 204 MET cc_start: 0.8963 (mmm) cc_final: 0.8691 (mmm) REVERT: B 219 MET cc_start: 0.9161 (mmm) cc_final: 0.8763 (mmm) REVERT: B 288 MET cc_start: 0.8660 (mtp) cc_final: 0.8251 (mmt) REVERT: B 295 MET cc_start: 0.8799 (ttm) cc_final: 0.8529 (mtp) REVERT: B 312 ILE cc_start: 0.9314 (pt) cc_final: 0.9099 (mp) REVERT: B 410 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8794 (pp) REVERT: C 90 TYR cc_start: 0.8542 (t80) cc_final: 0.8054 (t80) REVERT: C 134 GLN cc_start: 0.8670 (mm-40) cc_final: 0.7916 (mm-40) REVERT: C 138 ASN cc_start: 0.9484 (m-40) cc_final: 0.8870 (m-40) REVERT: C 225 ARG cc_start: 0.8281 (mtp85) cc_final: 0.7907 (mtp85) REVERT: C 365 MET cc_start: 0.9117 (tpp) cc_final: 0.8806 (mmm) REVERT: C 368 MET cc_start: 0.8955 (tmm) cc_final: 0.8727 (tmm) outliers start: 19 outliers final: 12 residues processed: 122 average time/residue: 0.1811 time to fit residues: 33.1712 Evaluate side-chains 103 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.073290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.060340 restraints weight = 28210.002| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.13 r_work: 0.2834 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9731 Z= 0.189 Angle : 0.542 7.214 13244 Z= 0.271 Chirality : 0.039 0.186 1650 Planarity : 0.004 0.053 1627 Dihedral : 4.007 21.679 1365 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.39 % Allowed : 18.51 % Favored : 79.10 % 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: 0.21 (0.24), residues: 1274 helix: 0.70 (0.17), residues: 978 sheet: None (None), residues: 0 loop : -1.55 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 16 HIS 0.002 0.000 HIS B 34 PHE 0.013 0.001 PHE C 302 TYR 0.007 0.001 TYR C 238 ARG 0.003 0.000 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.993 Fit side-chains REVERT: A 59 LEU cc_start: 0.9157 (mt) cc_final: 0.8769 (mt) REVERT: A 100 PHE cc_start: 0.8897 (t80) cc_final: 0.8463 (t80) REVERT: A 194 GLU cc_start: 0.8708 (tp30) cc_final: 0.8446 (tp30) REVERT: A 196 MET cc_start: 0.9424 (mmt) cc_final: 0.9190 (mmp) REVERT: A 204 MET cc_start: 0.9032 (mmm) cc_final: 0.8747 (mmm) REVERT: B 288 MET cc_start: 0.8603 (mtp) cc_final: 0.8365 (mmt) REVERT: B 295 MET cc_start: 0.8642 (ttm) cc_final: 0.8375 (mtp) REVERT: B 410 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8966 (pp) REVERT: C 90 TYR cc_start: 0.8851 (t80) cc_final: 0.8417 (t80) REVERT: C 97 MET cc_start: 0.8628 (tpp) cc_final: 0.8339 (tpp) REVERT: C 134 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8141 (mm-40) REVERT: C 138 ASN cc_start: 0.9591 (m-40) cc_final: 0.9114 (m110) REVERT: C 225 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7961 (mtp85) REVERT: C 321 GLN cc_start: 0.8985 (mt0) cc_final: 0.8718 (mt0) REVERT: C 342 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8242 (tt) REVERT: C 368 MET cc_start: 0.8928 (tmm) cc_final: 0.8719 (tmm) outliers start: 24 outliers final: 18 residues processed: 123 average time/residue: 0.1598 time to fit residues: 30.4225 Evaluate side-chains 115 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059588 restraints weight = 28181.285| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.10 r_work: 0.2814 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9731 Z= 0.227 Angle : 0.563 7.668 13244 Z= 0.280 Chirality : 0.040 0.204 1650 Planarity : 0.004 0.053 1627 Dihedral : 4.040 21.920 1365 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.18 % Allowed : 18.01 % Favored : 78.81 % 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: 0.44 (0.24), residues: 1274 helix: 0.85 (0.17), residues: 978 sheet: None (None), residues: 0 loop : -1.42 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 16 HIS 0.002 0.000 HIS B 34 PHE 0.013 0.001 PHE C 302 TYR 0.007 0.001 TYR B 320 ARG 0.002 0.000 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.995 Fit side-chains REVERT: A 100 PHE cc_start: 0.8820 (t80) cc_final: 0.8380 (t80) REVERT: A 194 GLU cc_start: 0.8741 (tp30) cc_final: 0.8449 (tp30) REVERT: A 204 MET cc_start: 0.9074 (mmm) cc_final: 0.8800 (mmm) REVERT: B 288 MET cc_start: 0.8604 (mtp) cc_final: 0.8368 (mmt) REVERT: B 321 GLN cc_start: 0.8585 (mt0) cc_final: 0.8380 (mt0) REVERT: B 410 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9012 (pp) REVERT: C 90 TYR cc_start: 0.8861 (t80) cc_final: 0.8389 (t80) REVERT: C 97 MET cc_start: 0.8644 (tpp) cc_final: 0.8340 (tpp) REVERT: C 134 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8055 (mm-40) REVERT: C 138 ASN cc_start: 0.9589 (m-40) cc_final: 0.9102 (m110) REVERT: C 342 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8221 (tt) REVERT: C 368 MET cc_start: 0.8903 (tmm) cc_final: 0.8657 (tmm) outliers start: 32 outliers final: 19 residues processed: 124 average time/residue: 0.1670 time to fit residues: 31.7836 Evaluate side-chains 111 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN C 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.071469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058549 restraints weight = 28453.724| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.10 r_work: 0.2793 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9731 Z= 0.268 Angle : 0.586 7.098 13244 Z= 0.293 Chirality : 0.040 0.174 1650 Planarity : 0.004 0.054 1627 Dihedral : 4.106 24.938 1365 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.38 % Allowed : 17.81 % Favored : 78.81 % 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: 0.56 (0.24), residues: 1274 helix: 0.91 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -1.36 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 16 HIS 0.003 0.001 HIS B 34 PHE 0.013 0.001 PHE C 302 TYR 0.008 0.001 TYR B 320 ARG 0.001 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.867 Fit side-chains REVERT: A 100 PHE cc_start: 0.8835 (t80) cc_final: 0.8409 (t80) REVERT: A 194 GLU cc_start: 0.8758 (tp30) cc_final: 0.8517 (tp30) REVERT: A 204 MET cc_start: 0.9062 (mmm) cc_final: 0.8746 (mmm) REVERT: A 244 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.8919 (tp-100) REVERT: B 288 MET cc_start: 0.8665 (mtp) cc_final: 0.8429 (mmt) REVERT: B 410 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9002 (pp) REVERT: C 90 TYR cc_start: 0.8867 (t80) cc_final: 0.8391 (t80) REVERT: C 97 MET cc_start: 0.8670 (tpp) cc_final: 0.8360 (tpp) REVERT: C 134 GLN cc_start: 0.8816 (mm-40) cc_final: 0.7960 (mm-40) REVERT: C 138 ASN cc_start: 0.9607 (m-40) cc_final: 0.9015 (m110) REVERT: C 225 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7339 (tpm170) REVERT: C 321 GLN cc_start: 0.8944 (mt0) cc_final: 0.8637 (mt0) outliers start: 34 outliers final: 20 residues processed: 120 average time/residue: 0.1884 time to fit residues: 34.8260 Evaluate side-chains 109 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 371 GLN B 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.073698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060701 restraints weight = 28349.454| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.12 r_work: 0.2844 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9731 Z= 0.180 Angle : 0.558 8.819 13244 Z= 0.277 Chirality : 0.039 0.180 1650 Planarity : 0.004 0.055 1627 Dihedral : 4.047 25.059 1365 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.69 % Allowed : 18.71 % Favored : 78.61 % 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: 0.78 (0.24), residues: 1274 helix: 1.01 (0.17), residues: 995 sheet: None (None), residues: 0 loop : -1.07 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 16 HIS 0.001 0.000 HIS B 34 PHE 0.011 0.001 PHE C 302 TYR 0.006 0.001 TYR A 320 ARG 0.001 0.000 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.095 Fit side-chains REVERT: A 100 PHE cc_start: 0.8812 (t80) cc_final: 0.8375 (t80) REVERT: A 194 GLU cc_start: 0.8687 (tp30) cc_final: 0.8430 (tp30) REVERT: A 204 MET cc_start: 0.9110 (mmm) cc_final: 0.8788 (mmm) REVERT: B 365 MET cc_start: 0.8184 (ttm) cc_final: 0.7928 (ttm) REVERT: B 410 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8953 (pp) REVERT: C 90 TYR cc_start: 0.8841 (t80) cc_final: 0.8441 (t80) REVERT: C 134 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8051 (mm-40) REVERT: C 138 ASN cc_start: 0.9621 (m-40) cc_final: 0.9128 (m110) REVERT: C 225 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7368 (tpm170) outliers start: 27 outliers final: 21 residues processed: 116 average time/residue: 0.1669 time to fit residues: 29.9893 Evaluate side-chains 110 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 128 GLN C 321 GLN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.059092 restraints weight = 28524.343| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.12 r_work: 0.2809 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9731 Z= 0.266 Angle : 0.597 8.325 13244 Z= 0.297 Chirality : 0.041 0.173 1650 Planarity : 0.004 0.054 1627 Dihedral : 4.073 24.476 1365 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.69 % Allowed : 18.31 % Favored : 79.00 % 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: 0.78 (0.24), residues: 1274 helix: 1.06 (0.17), residues: 986 sheet: None (None), residues: 0 loop : -1.22 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 16 HIS 0.002 0.001 HIS B 34 PHE 0.013 0.001 PHE C 302 TYR 0.008 0.001 TYR A 197 ARG 0.001 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8842 (t80) cc_final: 0.8406 (t80) REVERT: A 194 GLU cc_start: 0.8719 (tp30) cc_final: 0.8465 (tp30) REVERT: A 244 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.8558 (tp40) REVERT: B 299 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8811 (tptp) REVERT: B 321 GLN cc_start: 0.8329 (mt0) cc_final: 0.7737 (mt0) REVERT: B 365 MET cc_start: 0.8277 (ttm) cc_final: 0.7966 (ttm) REVERT: B 410 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8976 (pp) REVERT: C 90 TYR cc_start: 0.8881 (t80) cc_final: 0.8443 (t80) REVERT: C 134 GLN cc_start: 0.8849 (mm-40) cc_final: 0.7957 (mm-40) REVERT: C 138 ASN cc_start: 0.9613 (m-40) cc_final: 0.9023 (m110) REVERT: C 219 MET cc_start: 0.8989 (mmt) cc_final: 0.8769 (mmp) outliers start: 27 outliers final: 19 residues processed: 111 average time/residue: 0.1795 time to fit residues: 30.4733 Evaluate side-chains 109 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 105 optimal weight: 0.0770 chunk 3 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.060945 restraints weight = 28289.906| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.14 r_work: 0.2848 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9731 Z= 0.178 Angle : 0.591 13.212 13244 Z= 0.289 Chirality : 0.040 0.173 1650 Planarity : 0.004 0.054 1627 Dihedral : 4.043 24.920 1365 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.09 % Allowed : 19.30 % Favored : 78.61 % 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: 0.96 (0.24), residues: 1274 helix: 1.16 (0.17), residues: 986 sheet: None (None), residues: 0 loop : -1.04 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 16 HIS 0.001 0.000 HIS B 34 PHE 0.011 0.001 PHE C 302 TYR 0.006 0.001 TYR B 90 ARG 0.002 0.000 ARG B 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.991 Fit side-chains REVERT: A 100 PHE cc_start: 0.8793 (t80) cc_final: 0.8364 (t80) REVERT: A 194 GLU cc_start: 0.8688 (tp30) cc_final: 0.8435 (tp30) REVERT: B 288 MET cc_start: 0.8595 (mmm) cc_final: 0.8332 (mtt) REVERT: B 321 GLN cc_start: 0.8319 (mt0) cc_final: 0.7808 (mt0) REVERT: B 365 MET cc_start: 0.8181 (ttm) cc_final: 0.7914 (ttm) REVERT: B 410 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8953 (pp) REVERT: C 90 TYR cc_start: 0.8830 (t80) cc_final: 0.8403 (t80) REVERT: C 134 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8052 (mm-40) REVERT: C 138 ASN cc_start: 0.9618 (m-40) cc_final: 0.9057 (m110) REVERT: C 225 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7393 (tpm170) REVERT: C 321 GLN cc_start: 0.8824 (mt0) cc_final: 0.8554 (mt0) outliers start: 21 outliers final: 19 residues processed: 110 average time/residue: 0.1672 time to fit residues: 28.3275 Evaluate side-chains 110 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 0.0870 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 105 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.061348 restraints weight = 28234.590| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.16 r_work: 0.2857 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9731 Z= 0.158 Angle : 0.585 12.511 13244 Z= 0.286 Chirality : 0.039 0.174 1650 Planarity : 0.004 0.054 1627 Dihedral : 4.031 24.995 1365 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.09 % Allowed : 19.20 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1274 helix: 1.19 (0.17), residues: 987 sheet: None (None), residues: 0 loop : -0.95 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 16 HIS 0.001 0.000 HIS C 334 PHE 0.011 0.001 PHE C 302 TYR 0.014 0.001 TYR A 197 ARG 0.001 0.000 ARG B 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3808.53 seconds wall clock time: 67 minutes 35.90 seconds (4055.90 seconds total)