Starting phenix.real_space_refine on Sat Dec 28 17:11:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_15393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_15393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_15393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_15393.map" model { file = "/net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_15393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afa_15393/12_2024/8afa_15393.cif" } resolution = 3.16 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= 0.012 sd= 0.064 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 5944 2.51 5 N 1454 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 9008 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2989 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 16, 'TRANS': 384} Chain breaks: 1 Chain: "B" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2996 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 16, 'TRANS': 385} Chain breaks: 1 Chain: "C" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2996 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 16, 'TRANS': 385} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 5.93, per 1000 atoms: 0.66 Number of scatterers: 9008 At special positions: 0 Unit cell: (102.828, 106.172, 80.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1562 8.00 N 1454 7.00 C 5944 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 16 through 35 Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 45 through 59 removed outlier: 3.543A pdb=" N GLY A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 74 removed outlier: 3.525A pdb=" N SER A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 110 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 152 through 171 removed outlier: 3.721A pdb=" N VAL A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 222 removed outlier: 3.515A pdb=" N ARG A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 248 removed outlier: 3.632A pdb=" N LYS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.538A pdb=" N LYS A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 267 through 278 removed outlier: 3.720A pdb=" N MET A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.752A pdb=" N THR A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.654A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.550A pdb=" N LEU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 removed outlier: 3.654A pdb=" N VAL A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 removed outlier: 4.071A pdb=" N ILE A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N MET A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 393 removed outlier: 3.821A pdb=" N ILE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 removed outlier: 4.214A pdb=" N GLY A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'B' and resid 17 through 35 Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 45 through 59 removed outlier: 3.543A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 74 removed outlier: 3.527A pdb=" N SER B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 110 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 143 through 151 Processing helix chain 'B' and resid 152 through 171 removed outlier: 3.722A pdb=" N VAL B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 222 removed outlier: 3.516A pdb=" N ARG B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 248 removed outlier: 3.631A pdb=" N LYS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 256 removed outlier: 3.539A pdb=" N LYS B 254 " --> pdb=" O PHE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 267 Processing helix chain 'B' and resid 267 through 278 removed outlier: 3.721A pdb=" N MET B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 removed outlier: 3.751A pdb=" N THR B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 313 removed outlier: 3.655A pdb=" N SER B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Proline residue: B 307 - end of helix Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.550A pdb=" N LEU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 355 removed outlier: 3.655A pdb=" N VAL B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 353 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 373 removed outlier: 4.071A pdb=" N ILE B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N MET B 368 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.822A pdb=" N ILE B 393 " --> pdb=" O MET B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 420 removed outlier: 4.215A pdb=" N GLY B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP B 409 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'C' and resid 17 through 35 Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 45 through 59 removed outlier: 3.659A pdb=" N GLY C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 74 removed outlier: 3.526A pdb=" N SER C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 110 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 152 through 171 removed outlier: 3.721A pdb=" N VAL C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 222 removed outlier: 3.515A pdb=" N ARG C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG C 208 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE C 212 " --> pdb=" O ARG C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 248 removed outlier: 3.631A pdb=" N LYS C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 256 removed outlier: 3.538A pdb=" N LYS C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 267 Processing helix chain 'C' and resid 267 through 278 removed outlier: 3.720A pdb=" N MET C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 removed outlier: 3.751A pdb=" N THR C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 313 removed outlier: 3.655A pdb=" N SER C 303 " --> pdb=" O LYS C 299 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Proline residue: C 307 - end of helix Processing helix chain 'C' and resid 314 through 332 removed outlier: 3.549A pdb=" N LEU C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 355 removed outlier: 3.655A pdb=" N VAL C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 353 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 373 removed outlier: 4.071A pdb=" N ILE C 364 " --> pdb=" O GLY C 360 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N MET C 368 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 369 " --> pdb=" O MET C 365 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 393 removed outlier: 3.961A pdb=" N ALA C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE C 393 " --> pdb=" O MET C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 420 removed outlier: 4.215A pdb=" N GLY C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 701 hydrogen bonds defined for protein. 2076 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: 2.82 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1406 1.31 - 1.43: 2211 1.43 - 1.56: 5454 1.56 - 1.68: 0 1.68 - 1.81: 96 Bond restraints: 9167 Sorted by residual: bond pdb=" C PRO B 47 " pdb=" O PRO B 47 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.32e-02 5.74e+03 1.51e+01 bond pdb=" C PRO A 47 " pdb=" O PRO A 47 " ideal model delta sigma weight residual 1.235 1.185 0.050 1.30e-02 5.92e+03 1.49e+01 bond pdb=" C PRO C 47 " pdb=" O PRO C 47 " ideal model delta sigma weight residual 1.235 1.188 0.048 1.30e-02 5.92e+03 1.34e+01 bond pdb=" N ILE C 45 " pdb=" CA ILE C 45 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N VAL C 383 " pdb=" CA VAL C 383 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.41e-02 5.03e+03 5.87e+00 ... (remaining 9162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 12198 1.42 - 2.84: 203 2.84 - 4.26: 44 4.26 - 5.68: 11 5.68 - 7.10: 8 Bond angle restraints: 12464 Sorted by residual: angle pdb=" N LEU C 385 " pdb=" CA LEU C 385 " pdb=" C LEU C 385 " ideal model delta sigma weight residual 113.55 106.45 7.10 1.26e+00 6.30e-01 3.17e+01 angle pdb=" N PHE B 48 " pdb=" CA PHE B 48 " pdb=" C PHE B 48 " ideal model delta sigma weight residual 112.90 106.74 6.16 1.31e+00 5.83e-01 2.21e+01 angle pdb=" C THR C 378 " pdb=" CA THR C 378 " pdb=" CB THR C 378 " ideal model delta sigma weight residual 108.76 114.96 -6.20 1.37e+00 5.33e-01 2.05e+01 angle pdb=" N PHE A 48 " pdb=" CA PHE A 48 " pdb=" C PHE A 48 " ideal model delta sigma weight residual 112.90 107.13 5.77 1.31e+00 5.83e-01 1.94e+01 angle pdb=" N PHE C 48 " pdb=" CA PHE C 48 " pdb=" C PHE C 48 " ideal model delta sigma weight residual 112.90 107.13 5.77 1.31e+00 5.83e-01 1.94e+01 ... (remaining 12459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.21: 4495 13.21 - 26.42: 622 26.42 - 39.64: 172 39.64 - 52.85: 89 52.85 - 66.06: 18 Dihedral angle restraints: 5396 sinusoidal: 1997 harmonic: 3399 Sorted by residual: dihedral pdb=" CG ARG A 289 " pdb=" CD ARG A 289 " pdb=" NE ARG A 289 " pdb=" CZ ARG A 289 " ideal model delta sinusoidal sigma weight residual -90.00 -39.67 -50.33 2 1.50e+01 4.44e-03 1.26e+01 dihedral pdb=" CG ARG B 289 " pdb=" CD ARG B 289 " pdb=" NE ARG B 289 " pdb=" CZ ARG B 289 " ideal model delta sinusoidal sigma weight residual -90.00 -39.68 -50.32 2 1.50e+01 4.44e-03 1.26e+01 dihedral pdb=" CG ARG C 289 " pdb=" CD ARG C 289 " pdb=" NE ARG C 289 " pdb=" CZ ARG C 289 " ideal model delta sinusoidal sigma weight residual -90.00 -39.70 -50.30 2 1.50e+01 4.44e-03 1.26e+01 ... (remaining 5393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1181 0.041 - 0.082: 318 0.082 - 0.122: 57 0.122 - 0.163: 3 0.163 - 0.204: 2 Chirality restraints: 1561 Sorted by residual: chirality pdb=" CA VAL C 383 " pdb=" N VAL C 383 " pdb=" C VAL C 383 " pdb=" CB VAL C 383 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL C 383 " pdb=" CA VAL C 383 " pdb=" CG1 VAL C 383 " pdb=" CG2 VAL C 383 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA PHE A 48 " pdb=" N PHE A 48 " pdb=" C PHE A 48 " pdb=" CB PHE A 48 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1558 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 44 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C TYR C 44 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR C 44 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE C 45 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 284 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO C 285 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 284 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO B 285 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 285 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 285 " -0.026 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1571 2.76 - 3.29: 9063 3.29 - 3.83: 15332 3.83 - 4.36: 18221 4.36 - 4.90: 31938 Nonbonded interactions: 76125 Sorted by model distance: nonbonded pdb=" OG SER C 280 " pdb=" OXT ASP C 501 " model vdw 2.223 3.040 nonbonded pdb=" OG SER B 280 " pdb=" OXT ASP B 501 " model vdw 2.223 3.040 nonbonded pdb=" OG SER A 280 " pdb=" OXT ASP A 501 " model vdw 2.223 3.040 nonbonded pdb=" O THR B 283 " pdb=" OG1 THR B 287 " model vdw 2.230 3.040 nonbonded pdb=" O THR C 283 " pdb=" OG1 THR C 287 " model vdw 2.230 3.040 ... (remaining 76120 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' selection = (chain 'B' and (resid 16 through 114 or resid 129 through 430 or resid 501)) selection = (chain 'C' and (resid 16 through 114 or resid 129 through 430 or resid 501)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.340 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: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9167 Z= 0.170 Angle : 0.484 7.098 12464 Z= 0.286 Chirality : 0.036 0.204 1561 Planarity : 0.004 0.047 1523 Dihedral : 14.988 66.061 3232 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.53 % Allowed : 16.16 % Favored : 83.32 % 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: 0.26 (0.23), residues: 1193 helix: 0.31 (0.16), residues: 996 sheet: None (None), residues: 0 loop : 0.20 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 16 HIS 0.001 0.000 HIS C 334 PHE 0.006 0.001 PHE B 302 TYR 0.006 0.001 TYR C 320 ARG 0.011 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.903 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 0.2300 time to fit residues: 34.4439 Evaluate side-chains 99 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 379 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 chunk 108 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9167 Z= 0.177 Angle : 0.497 5.762 12464 Z= 0.258 Chirality : 0.039 0.122 1561 Planarity : 0.004 0.048 1523 Dihedral : 3.775 58.435 1284 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.27 % Allowed : 14.36 % Favored : 84.37 % 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: 2.01 (0.25), residues: 1193 helix: 1.52 (0.16), residues: 1001 sheet: None (None), residues: 0 loop : 0.69 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 16 HIS 0.001 0.000 HIS A 34 PHE 0.014 0.001 PHE A 302 TYR 0.009 0.001 TYR B 387 ARG 0.002 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.022 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 105 average time/residue: 0.1643 time to fit residues: 26.7268 Evaluate side-chains 96 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 378 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 0.0270 chunk 30 optimal weight: 0.0570 chunk 109 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9167 Z= 0.160 Angle : 0.462 5.647 12464 Z= 0.239 Chirality : 0.038 0.118 1561 Planarity : 0.004 0.045 1523 Dihedral : 3.693 58.462 1281 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.43 % Allowed : 14.68 % Favored : 82.89 % 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: 2.36 (0.25), residues: 1193 helix: 1.79 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : 0.60 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.001 0.000 HIS C 334 PHE 0.013 0.001 PHE A 242 TYR 0.008 0.001 TYR B 387 ARG 0.001 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.023 Fit side-chains REVERT: A 97 MET cc_start: 0.7503 (tpp) cc_final: 0.7290 (tpp) outliers start: 23 outliers final: 10 residues processed: 118 average time/residue: 0.1605 time to fit residues: 29.2819 Evaluate side-chains 104 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 391 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 0.0670 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9167 Z= 0.178 Angle : 0.471 5.660 12464 Z= 0.242 Chirality : 0.038 0.128 1561 Planarity : 0.004 0.042 1523 Dihedral : 3.738 59.123 1281 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.11 % Allowed : 15.31 % Favored : 82.58 % 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: 2.50 (0.25), residues: 1193 helix: 1.90 (0.17), residues: 1005 sheet: None (None), residues: 0 loop : 0.51 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.001 0.000 HIS A 34 PHE 0.014 0.001 PHE A 242 TYR 0.006 0.001 TYR B 387 ARG 0.001 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.910 Fit side-chains REVERT: A 97 MET cc_start: 0.7518 (tpp) cc_final: 0.7258 (tpp) outliers start: 20 outliers final: 17 residues processed: 113 average time/residue: 0.1659 time to fit residues: 29.2521 Evaluate side-chains 111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 391 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9167 Z= 0.170 Angle : 0.459 5.718 12464 Z= 0.235 Chirality : 0.038 0.116 1561 Planarity : 0.004 0.037 1523 Dihedral : 3.728 58.715 1281 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.43 % Allowed : 15.21 % Favored : 82.37 % 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: 2.58 (0.25), residues: 1193 helix: 1.94 (0.17), residues: 1011 sheet: None (None), residues: 0 loop : 0.57 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.000 0.000 HIS B 334 PHE 0.013 0.001 PHE C 302 TYR 0.006 0.001 TYR C 320 ARG 0.001 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.820 Fit side-chains REVERT: A 97 MET cc_start: 0.7558 (tpp) cc_final: 0.7285 (tpp) REVERT: A 242 PHE cc_start: 0.7286 (t80) cc_final: 0.7022 (t80) outliers start: 23 outliers final: 18 residues processed: 117 average time/residue: 0.1579 time to fit residues: 28.6871 Evaluate side-chains 111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 391 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.9980 chunk 104 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9167 Z= 0.166 Angle : 0.453 5.605 12464 Z= 0.232 Chirality : 0.038 0.115 1561 Planarity : 0.004 0.035 1523 Dihedral : 3.727 58.900 1281 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.64 % Allowed : 14.89 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.25), residues: 1193 helix: 1.99 (0.17), residues: 1011 sheet: None (None), residues: 0 loop : 0.53 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.000 0.000 HIS C 34 PHE 0.013 0.001 PHE A 302 TYR 0.006 0.001 TYR A 320 ARG 0.001 0.000 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 1.070 Fit side-chains REVERT: A 97 MET cc_start: 0.7567 (tpp) cc_final: 0.7272 (tpp) REVERT: A 242 PHE cc_start: 0.7291 (t80) cc_final: 0.7029 (t80) REVERT: C 68 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8138 (mm) outliers start: 25 outliers final: 17 residues processed: 121 average time/residue: 0.1645 time to fit residues: 30.8255 Evaluate side-chains 111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 115 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9167 Z= 0.160 Angle : 0.453 5.600 12464 Z= 0.232 Chirality : 0.037 0.116 1561 Planarity : 0.004 0.035 1523 Dihedral : 3.704 58.941 1281 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.43 % Allowed : 15.73 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.25), residues: 1193 helix: 2.00 (0.17), residues: 1013 sheet: None (None), residues: 0 loop : 0.54 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 16 HIS 0.000 0.000 HIS B 334 PHE 0.012 0.001 PHE C 302 TYR 0.007 0.001 TYR B 387 ARG 0.001 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.996 Fit side-chains REVERT: A 97 MET cc_start: 0.7560 (tpp) cc_final: 0.7268 (tpp) REVERT: A 242 PHE cc_start: 0.7276 (t80) cc_final: 0.7055 (t80) REVERT: C 68 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8123 (mm) outliers start: 23 outliers final: 18 residues processed: 114 average time/residue: 0.1645 time to fit residues: 29.2913 Evaluate side-chains 111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9167 Z= 0.205 Angle : 0.474 5.613 12464 Z= 0.243 Chirality : 0.038 0.116 1561 Planarity : 0.003 0.035 1523 Dihedral : 3.771 59.678 1281 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.32 % Allowed : 15.63 % Favored : 82.05 % 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: 2.58 (0.25), residues: 1193 helix: 1.95 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : 0.51 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 16 HIS 0.000 0.000 HIS C 34 PHE 0.016 0.001 PHE C 302 TYR 0.006 0.001 TYR A 238 ARG 0.001 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.906 Fit side-chains REVERT: A 97 MET cc_start: 0.7607 (tpp) cc_final: 0.7331 (tpp) REVERT: A 242 PHE cc_start: 0.7327 (t80) cc_final: 0.7027 (t80) REVERT: C 68 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8209 (mm) outliers start: 22 outliers final: 19 residues processed: 111 average time/residue: 0.1600 time to fit residues: 27.6918 Evaluate side-chains 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 33 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9167 Z= 0.179 Angle : 0.465 5.595 12464 Z= 0.238 Chirality : 0.038 0.118 1561 Planarity : 0.003 0.036 1523 Dihedral : 3.749 59.660 1281 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.11 % Allowed : 16.16 % Favored : 81.73 % 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: 2.62 (0.25), residues: 1193 helix: 1.96 (0.17), residues: 1013 sheet: None (None), residues: 0 loop : 0.60 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 16 HIS 0.000 0.000 HIS C 34 PHE 0.013 0.001 PHE C 302 TYR 0.006 0.001 TYR B 387 ARG 0.001 0.000 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.985 Fit side-chains REVERT: A 97 MET cc_start: 0.7591 (tpp) cc_final: 0.7316 (tpp) REVERT: A 242 PHE cc_start: 0.7294 (t80) cc_final: 0.7067 (t80) REVERT: C 68 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8161 (mm) outliers start: 20 outliers final: 19 residues processed: 109 average time/residue: 0.1680 time to fit residues: 28.3080 Evaluate side-chains 113 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9167 Z= 0.200 Angle : 0.478 6.771 12464 Z= 0.245 Chirality : 0.038 0.115 1561 Planarity : 0.003 0.036 1523 Dihedral : 3.767 58.842 1281 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.11 % Allowed : 16.16 % Favored : 81.73 % 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: 2.61 (0.25), residues: 1193 helix: 1.96 (0.17), residues: 1012 sheet: None (None), residues: 0 loop : 0.62 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 16 HIS 0.000 0.000 HIS C 34 PHE 0.015 0.001 PHE C 302 TYR 0.006 0.001 TYR A 238 ARG 0.001 0.000 ARG C 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.993 Fit side-chains REVERT: A 97 MET cc_start: 0.7581 (tpp) cc_final: 0.7315 (tpp) REVERT: A 242 PHE cc_start: 0.7311 (t80) cc_final: 0.6998 (t80) REVERT: C 68 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8193 (mm) outliers start: 20 outliers final: 19 residues processed: 110 average time/residue: 0.1811 time to fit residues: 30.7342 Evaluate side-chains 113 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.181598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.138354 restraints weight = 9067.126| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.87 r_work: 0.3239 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9167 Z= 0.171 Angle : 0.462 5.926 12464 Z= 0.237 Chirality : 0.038 0.114 1561 Planarity : 0.003 0.036 1523 Dihedral : 3.731 58.710 1281 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.11 % Allowed : 16.16 % Favored : 81.73 % 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: 2.69 (0.25), residues: 1193 helix: 2.01 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : 0.64 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 16 HIS 0.000 0.000 HIS B 334 PHE 0.012 0.001 PHE C 302 TYR 0.006 0.001 TYR B 387 ARG 0.001 0.000 ARG C 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.12 seconds wall clock time: 35 minutes 17.15 seconds (2117.15 seconds total)