Starting phenix.real_space_refine on Sun Dec 29 01:02:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xwo_10633/12_2024/6xwo_10633.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xwo_10633/12_2024/6xwo_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_10633/12_2024/6xwo_10633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xwo_10633/12_2024/6xwo_10633.map" model { file = "/net/cci-nas-00/data/ceres_data/6xwo_10633/12_2024/6xwo_10633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xwo_10633/12_2024/6xwo_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.65, per 1000 atoms: 0.59 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 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: 0.83 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: 2.81 Time building geometry restraints manager: 2.92 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: 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.790 Find NCS groups from input model: 0.400 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- 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 : 1.021 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: 0.2513 time to fit residues: 40.7947 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 : 1.179 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 1.149 Fit side-chains revert: symmetry clash REVERT: C 90 TYR cc_start: 0.8092 (t80) cc_final: 0.7861 (t80) REVERT: C 138 ASN cc_start: 0.8535 (m-40) cc_final: 0.8205 (m-40) outliers start: 13 outliers final: 4 residues processed: 115 average time/residue: 0.1758 time to fit residues: 30.4651 Evaluate side-chains 91 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL 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 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 95 optimal weight: 10.0000 chunk 77 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9731 Z= 0.177 Angle : 0.557 7.982 13244 Z= 0.281 Chirality : 0.039 0.170 1650 Planarity : 0.005 0.054 1627 Dihedral : 4.289 23.256 1365 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.89 % Allowed : 15.72 % Favored : 82.39 % 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: -0.81 (0.24), residues: 1274 helix: 0.00 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -2.10 (0.36), residues: 290 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 0.016 0.001 PHE C 302 TYR 0.007 0.001 TYR C 37 ARG 0.011 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 120 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.088 Fit side-chains REVERT: C 90 TYR cc_start: 0.8102 (t80) cc_final: 0.7877 (t80) REVERT: C 134 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7241 (mm-40) REVERT: C 138 ASN cc_start: 0.8580 (m-40) cc_final: 0.8271 (m-40) outliers start: 19 outliers final: 10 residues processed: 115 average time/residue: 0.1894 time to fit residues: 32.7984 Evaluate side-chains 99 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE 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 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 113 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 overall best weight: 1.8006 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9731 Z= 0.260 Angle : 0.593 8.524 13244 Z= 0.297 Chirality : 0.041 0.172 1650 Planarity : 0.004 0.053 1627 Dihedral : 4.278 29.553 1365 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.99 % Allowed : 17.61 % Favored : 80.40 % 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: -0.35 (0.24), residues: 1274 helix: 0.31 (0.17), residues: 985 sheet: None (None), residues: 0 loop : -1.83 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 16 HIS 0.003 0.001 HIS B 34 PHE 0.016 0.001 PHE C 302 TYR 0.011 0.001 TYR A 90 ARG 0.005 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 113 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.042 Fit side-chains REVERT: C 90 TYR cc_start: 0.8169 (t80) cc_final: 0.7872 (t80) REVERT: C 134 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7431 (mm-40) outliers start: 20 outliers final: 12 residues processed: 110 average time/residue: 0.1682 time to fit residues: 28.4856 Evaluate side-chains 100 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 6 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 101 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN C 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9731 Z= 0.168 Angle : 0.555 9.787 13244 Z= 0.275 Chirality : 0.039 0.171 1650 Planarity : 0.004 0.054 1627 Dihedral : 4.114 22.226 1365 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.89 % Allowed : 18.41 % Favored : 79.70 % 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: 0.64 (0.17), residues: 986 sheet: None (None), residues: 0 loop : -1.61 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 16 HIS 0.002 0.000 HIS B 34 PHE 0.012 0.001 PHE C 302 TYR 0.007 0.001 TYR C 238 ARG 0.002 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 116 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.999 Fit side-chains REVERT: C 90 TYR cc_start: 0.8065 (t80) cc_final: 0.7842 (t80) outliers start: 19 outliers final: 15 residues processed: 111 average time/residue: 0.1661 time to fit residues: 28.5103 Evaluate side-chains 104 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 A residue 403 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN C 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9731 Z= 0.186 Angle : 0.569 10.162 13244 Z= 0.279 Chirality : 0.039 0.173 1650 Planarity : 0.004 0.054 1627 Dihedral : 4.076 22.898 1365 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.69 % Allowed : 18.81 % Favored : 78.51 % 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: 0.42 (0.24), residues: 1274 helix: 0.80 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -1.36 (0.39), residues: 285 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 0.021 0.001 PHE A 100 TYR 0.011 0.001 TYR A 90 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 124 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8124 (tp-100) REVERT: A 393 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8214 (tp) REVERT: C 342 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8568 (tt) outliers start: 27 outliers final: 13 residues processed: 121 average time/residue: 0.1753 time to fit residues: 31.9277 Evaluate side-chains 106 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain B residue 50 ASP 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 396 ILE Chi-restraints excluded: chain B residue 406 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.1980 chunk 69 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9731 Z= 0.174 Angle : 0.559 10.631 13244 Z= 0.276 Chirality : 0.039 0.200 1650 Planarity : 0.004 0.054 1627 Dihedral : 4.073 25.754 1365 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.69 % Allowed : 18.41 % Favored : 78.91 % 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: 0.61 (0.25), residues: 1274 helix: 0.93 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -1.27 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 16 HIS 0.001 0.000 HIS B 34 PHE 0.019 0.001 PHE A 100 TYR 0.010 0.001 TYR A 90 ARG 0.001 0.000 ARG C 401 *********************** 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 122 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.093 Fit side-chains REVERT: A 244 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8019 (tp-100) REVERT: C 90 TYR cc_start: 0.8083 (t80) cc_final: 0.7671 (t80) outliers start: 27 outliers final: 17 residues processed: 117 average time/residue: 0.1866 time to fit residues: 32.8374 Evaluate side-chains 106 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 350 LEU 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 314 MET Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 406 VAL 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 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 72 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 95 optimal weight: 0.1980 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9731 Z= 0.227 Angle : 0.580 10.677 13244 Z= 0.288 Chirality : 0.040 0.182 1650 Planarity : 0.004 0.054 1627 Dihedral : 4.074 24.774 1365 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: 0.69 (0.24), residues: 1274 helix: 0.99 (0.17), residues: 991 sheet: None (None), residues: 0 loop : -1.28 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 16 HIS 0.002 0.000 HIS B 34 PHE 0.030 0.001 PHE A 100 TYR 0.008 0.001 TYR A 90 ARG 0.001 0.000 ARG C 225 *********************** 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 115 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8024 (tp-100) REVERT: C 90 TYR cc_start: 0.8153 (t80) cc_final: 0.7691 (t80) outliers start: 27 outliers final: 22 residues processed: 110 average time/residue: 0.1775 time to fit residues: 30.1734 Evaluate side-chains 108 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 393 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 LEU 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 314 MET 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 C residue 6 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 337 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN B 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9731 Z= 0.180 Angle : 0.568 11.248 13244 Z= 0.280 Chirality : 0.039 0.199 1650 Planarity : 0.004 0.054 1627 Dihedral : 4.019 24.911 1365 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.49 % Allowed : 19.00 % Favored : 78.51 % 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: 0.84 (0.24), residues: 1274 helix: 1.07 (0.17), residues: 994 sheet: None (None), residues: 0 loop : -1.13 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 16 HIS 0.001 0.000 HIS B 34 PHE 0.011 0.001 PHE C 302 TYR 0.012 0.001 TYR A 90 ARG 0.001 0.000 ARG B 179 *********************** 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 118 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8044 (tp-100) REVERT: C 90 TYR cc_start: 0.8084 (t80) cc_final: 0.7650 (t80) outliers start: 25 outliers final: 21 residues processed: 112 average time/residue: 0.1756 time to fit residues: 30.2761 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 : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 59 LEU 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 314 MET 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 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 337 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN B 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3189 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= 0.169 Angle : 0.569 11.502 13244 Z= 0.280 Chirality : 0.039 0.194 1650 Planarity : 0.004 0.054 1627 Dihedral : 3.993 25.251 1365 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.09 % Allowed : 20.00 % Favored : 77.91 % 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: 0.91 (0.24), residues: 1274 helix: 1.12 (0.17), residues: 988 sheet: None (None), residues: 0 loop : -1.06 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 16 HIS 0.001 0.000 HIS B 34 PHE 0.025 0.001 PHE A 100 TYR 0.012 0.001 TYR A 90 ARG 0.001 0.000 ARG A 173 ********************** 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 112 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.8017 (tp-100) REVERT: C 90 TYR cc_start: 0.8048 (t80) cc_final: 0.7626 (t80) outliers start: 21 outliers final: 18 residues processed: 108 average time/residue: 0.1743 time to fit residues: 29.1811 Evaluate side-chains 106 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 59 LEU 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 314 MET 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 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 383 VAL Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.075051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.062183 restraints weight = 27816.595| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.05 r_work: 0.2876 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 9731 Z= 0.181 Angle : 0.867 59.197 13244 Z= 0.481 Chirality : 0.040 0.239 1650 Planarity : 0.004 0.054 1627 Dihedral : 3.990 25.308 1365 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.19 % Allowed : 19.40 % Favored : 78.41 % 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: 0.94 (0.24), residues: 1274 helix: 1.14 (0.17), residues: 988 sheet: None (None), residues: 0 loop : -1.04 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 16 HIS 0.001 0.000 HIS B 34 PHE 0.016 0.001 PHE C 100 TYR 0.016 0.001 TYR B 90 ARG 0.001 0.000 ARG B 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1852.27 seconds wall clock time: 34 minutes 45.76 seconds (2085.76 seconds total)