Starting phenix.real_space_refine on Sat Aug 23 06:52:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yo5_39436/08_2025/8yo5_39436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yo5_39436/08_2025/8yo5_39436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yo5_39436/08_2025/8yo5_39436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yo5_39436/08_2025/8yo5_39436.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yo5_39436/08_2025/8yo5_39436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yo5_39436/08_2025/8yo5_39436.map" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 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 36 5.16 5 C 6624 2.51 5 N 1752 2.21 5 O 1930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10342 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "B" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "C" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1608 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain: "D" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1608 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 7, 'TRANS': 192} Time building chain proxies: 2.74, per 1000 atoms: 0.26 Number of scatterers: 10342 At special positions: 0 Unit cell: (121.68, 100.88, 113.36, 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 36 16.00 O 1930 8.00 N 1752 7.00 C 6624 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: 0.90 Conformation dependent library (CDL) restraints added in 419.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 14 sheets defined 45.0% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 9 through 11 No H-bonds generated for 'chain 'A' and resid 9 through 11' Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.731A pdb=" N ALA A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.687A pdb=" N PHE A 42 " --> pdb=" O PRO A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.664A pdb=" N GLY A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 76 through 84 removed outlier: 4.259A pdb=" N ALA A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.987A pdb=" N TYR A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 128' Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.755A pdb=" N TYR A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.911A pdb=" N GLN A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 254 removed outlier: 5.035A pdb=" N ASP A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 319 through 366 removed outlier: 3.927A pdb=" N LEU A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 338 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 383 removed outlier: 4.490A pdb=" N GLU A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 removed outlier: 3.764A pdb=" N SER A 390 " --> pdb=" O MET A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 404 through 428 removed outlier: 3.881A pdb=" N LYS A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.578A pdb=" N ILE A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 11 Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.704A pdb=" N ALA B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 52 removed outlier: 3.730A pdb=" N PHE B 42 " --> pdb=" O PRO B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.788A pdb=" N GLY B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 4.249A pdb=" N ALA B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.985A pdb=" N TYR B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 128' Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.754A pdb=" N TYR B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.906A pdb=" N GLN B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 247 through 254 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.837A pdb=" N PHE B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 366 removed outlier: 3.918A pdb=" N LEU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 338 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 removed outlier: 3.978A pdb=" N GLU B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 removed outlier: 3.760A pdb=" N SER B 390 " --> pdb=" O MET B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.884A pdb=" N THR B 404 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 428 removed outlier: 3.813A pdb=" N LYS B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 441 removed outlier: 3.576A pdb=" N ILE B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 448 through 455 removed outlier: 4.073A pdb=" N ASN C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 466 Processing helix chain 'C' and resid 494 through 504 removed outlier: 4.054A pdb=" N SER C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 513 removed outlier: 3.687A pdb=" N PHE C 510 " --> pdb=" O TRP C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 544 Processing helix chain 'C' and resid 557 through 561 Processing helix chain 'C' and resid 562 through 572 Processing helix chain 'C' and resid 585 through 590 Processing helix chain 'D' and resid 416 through 427 Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.783A pdb=" N ASN D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 466 Processing helix chain 'D' and resid 494 through 504 removed outlier: 3.918A pdb=" N SER D 498 " --> pdb=" O SER D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 536 through 544 Processing helix chain 'D' and resid 562 through 572 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 165 Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 210 Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 225 removed outlier: 6.408A pdb=" N THR A 220 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 222 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 271 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 308 Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AA9, first strand: chain 'B' and resid 223 through 225 removed outlier: 5.790A pdb=" N PHE B 223 " --> pdb=" O HIS B 230 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N HIS B 230 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 228 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 271 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 306 through 308 Processing sheet with id=AB2, first strand: chain 'C' and resid 410 through 414 removed outlier: 5.918A pdb=" N LEU C 411 " --> pdb=" O ALA C 482 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N MET C 484 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU C 413 " --> pdb=" O MET C 484 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 481 " --> pdb=" O ARG C 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 523 through 526 removed outlier: 4.149A pdb=" N SER C 551 " --> pdb=" O HIS C 526 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 435 through 437 removed outlier: 7.349A pdb=" N TYR D 435 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE D 412 " --> pdb=" O TYR D 435 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU D 437 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR D 414 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU D 411 " --> pdb=" O ALA D 482 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE D 481 " --> pdb=" O ARG D 516 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL D 518 " --> pdb=" O ILE D 481 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE D 483 " --> pdb=" O VAL D 518 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.538A pdb=" N SER D 551 " --> pdb=" O HIS D 526 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1122 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: 1.48 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3346 1.34 - 1.46: 2363 1.46 - 1.58: 4789 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 10564 Sorted by residual: bond pdb=" CB LYS A 142 " pdb=" CG LYS A 142 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" CB MET C 590 " pdb=" CG MET C 590 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" CB PRO D 581 " pdb=" CG PRO D 581 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.29e+00 bond pdb=" CA LEU B 3 " pdb=" CB LEU B 3 " ideal model delta sigma weight residual 1.525 1.540 -0.015 1.29e-02 6.01e+03 1.28e+00 bond pdb=" CB PRO D 436 " pdb=" CG PRO D 436 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.25e+00 ... (remaining 10559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 14147 2.98 - 5.96: 81 5.96 - 8.94: 10 8.94 - 11.93: 1 11.93 - 14.91: 1 Bond angle restraints: 14240 Sorted by residual: angle pdb=" CA LEU B 3 " pdb=" CB LEU B 3 " pdb=" CG LEU B 3 " ideal model delta sigma weight residual 116.30 131.21 -14.91 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CA MET C 452 " pdb=" CB MET C 452 " pdb=" CG MET C 452 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CA LYS A 142 " pdb=" CB LYS A 142 " pdb=" CG LYS A 142 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CB LYS A 142 " pdb=" CG LYS A 142 " pdb=" CD LYS A 142 " ideal model delta sigma weight residual 111.30 118.31 -7.01 2.30e+00 1.89e-01 9.29e+00 angle pdb=" CA MET C 590 " pdb=" CB MET C 590 " pdb=" CG MET C 590 " ideal model delta sigma weight residual 114.10 119.88 -5.78 2.00e+00 2.50e-01 8.37e+00 ... (remaining 14235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 5193 17.16 - 34.32: 866 34.32 - 51.48: 222 51.48 - 68.64: 61 68.64 - 85.80: 20 Dihedral angle restraints: 6362 sinusoidal: 2618 harmonic: 3744 Sorted by residual: dihedral pdb=" CA ASP C 451 " pdb=" C ASP C 451 " pdb=" N MET C 452 " pdb=" CA MET C 452 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ALA C 487 " pdb=" C ALA C 487 " pdb=" N ASP C 488 " pdb=" CA ASP C 488 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ALA D 487 " pdb=" C ALA D 487 " pdb=" N ASP D 488 " pdb=" CA ASP D 488 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 6359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1217 0.048 - 0.095: 257 0.095 - 0.143: 63 0.143 - 0.191: 2 0.191 - 0.238: 1 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CB VAL C 577 " pdb=" CA VAL C 577 " pdb=" CG1 VAL C 577 " pdb=" CG2 VAL C 577 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP B 34 " pdb=" N ASP B 34 " pdb=" C ASP B 34 " pdb=" CB ASP B 34 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CG LEU B 3 " pdb=" CB LEU B 3 " pdb=" CD1 LEU B 3 " pdb=" CD2 LEU B 3 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 1537 not shown) Planarity restraints: 1822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 506 " -0.037 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO C 507 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 507 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 507 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 506 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO D 507 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 507 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 507 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 244 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C VAL B 244 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL B 244 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 245 " -0.011 2.00e-02 2.50e+03 ... (remaining 1819 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 246 2.68 - 3.24: 10593 3.24 - 3.79: 16299 3.79 - 4.35: 20827 4.35 - 4.90: 33560 Nonbonded interactions: 81525 Sorted by model distance: nonbonded pdb=" O ASP B 34 " pdb=" OH TYR B 130 " model vdw 2.130 3.040 nonbonded pdb=" O ASP A 34 " pdb=" OH TYR A 130 " model vdw 2.141 3.040 nonbonded pdb=" O PHE C 502 " pdb=" ND2 ASN C 505 " model vdw 2.159 3.120 nonbonded pdb=" O HIS C 526 " pdb=" OG SER C 551 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASP A 239 " pdb=" OG1 THR A 242 " model vdw 2.195 3.040 ... (remaining 81520 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 1.700 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.190 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 0.057 10564 Z= 0.131 Angle : 0.634 14.908 14240 Z= 0.334 Chirality : 0.042 0.238 1540 Planarity : 0.004 0.057 1822 Dihedral : 18.803 85.805 3962 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.54 % Allowed : 38.54 % Favored : 60.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.24), residues: 1276 helix: 0.15 (0.24), residues: 504 sheet: -1.61 (0.48), residues: 136 loop : -1.68 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 438 TYR 0.017 0.001 TYR B 388 PHE 0.027 0.002 PHE A 274 TRP 0.029 0.002 TRP D 584 HIS 0.009 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00294 (10564) covalent geometry : angle 0.63359 (14240) hydrogen bonds : bond 0.16605 ( 396) hydrogen bonds : angle 6.69782 ( 1122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 TYR cc_start: 0.8083 (m-10) cc_final: 0.7733 (m-10) REVERT: B 398 MET cc_start: 0.7377 (mmp) cc_final: 0.7060 (mmm) REVERT: C 590 MET cc_start: 0.8197 (tmm) cc_final: 0.7938 (mmm) outliers start: 6 outliers final: 3 residues processed: 178 average time/residue: 0.0974 time to fit residues: 25.1188 Evaluate side-chains 166 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 TRP Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain D residue 537 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.0050 chunk 35 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN D 432 HIS D 480 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.127393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095676 restraints weight = 22299.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097281 restraints weight = 15172.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098389 restraints weight = 10987.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098704 restraints weight = 9794.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098955 restraints weight = 9387.424| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10564 Z= 0.130 Angle : 0.569 10.254 14240 Z= 0.295 Chirality : 0.041 0.161 1540 Planarity : 0.004 0.045 1822 Dihedral : 4.824 46.732 1401 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.23 % Allowed : 32.58 % Favored : 62.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.24), residues: 1276 helix: 0.61 (0.24), residues: 508 sheet: -1.72 (0.50), residues: 128 loop : -1.66 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 438 TYR 0.010 0.001 TYR C 422 PHE 0.020 0.001 PHE B 274 TRP 0.023 0.002 TRP C 445 HIS 0.009 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00300 (10564) covalent geometry : angle 0.56876 (14240) hydrogen bonds : bond 0.04418 ( 396) hydrogen bonds : angle 5.16879 ( 1122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.9145 (mtpp) cc_final: 0.8855 (mtpp) REVERT: A 95 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8126 (t80) REVERT: A 388 TYR cc_start: 0.8199 (m-10) cc_final: 0.7794 (m-10) REVERT: B 95 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8106 (t80) REVERT: B 387 MET cc_start: 0.8655 (pmm) cc_final: 0.8003 (pmm) REVERT: B 388 TYR cc_start: 0.7921 (m-10) cc_final: 0.7536 (m-10) REVERT: B 398 MET cc_start: 0.7604 (mmp) cc_final: 0.7329 (mmm) REVERT: C 422 TYR cc_start: 0.8262 (m-80) cc_final: 0.7377 (t80) REVERT: C 431 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8512 (mp) REVERT: C 531 GLN cc_start: 0.7189 (pm20) cc_final: 0.6924 (pm20) REVERT: D 496 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7930 (m-80) outliers start: 58 outliers final: 29 residues processed: 206 average time/residue: 0.0832 time to fit residues: 25.0651 Evaluate side-chains 190 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 496 TYR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 578 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 8.9990 chunk 124 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095700 restraints weight = 22464.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.095863 restraints weight = 17815.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096332 restraints weight = 18402.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098435 restraints weight = 13516.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098546 restraints weight = 10757.365| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10564 Z= 0.178 Angle : 0.583 9.828 14240 Z= 0.300 Chirality : 0.042 0.141 1540 Planarity : 0.004 0.042 1822 Dihedral : 4.594 21.478 1396 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 6.95 % Allowed : 30.87 % Favored : 62.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.24), residues: 1276 helix: 0.59 (0.23), residues: 518 sheet: -1.97 (0.44), residues: 144 loop : -1.77 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 226 TYR 0.011 0.001 TYR B 278 PHE 0.019 0.002 PHE C 588 TRP 0.022 0.002 TRP C 445 HIS 0.009 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00419 (10564) covalent geometry : angle 0.58292 (14240) hydrogen bonds : bond 0.04404 ( 396) hydrogen bonds : angle 5.03833 ( 1122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 158 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8330 (t80) REVERT: A 327 PHE cc_start: 0.8757 (t80) cc_final: 0.8448 (t80) REVERT: B 21 MET cc_start: 0.8333 (mmp) cc_final: 0.8076 (mmp) REVERT: B 95 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8216 (t80) REVERT: B 142 LYS cc_start: 0.8598 (tppt) cc_final: 0.8345 (tppt) REVERT: B 327 PHE cc_start: 0.8758 (t80) cc_final: 0.8396 (t80) REVERT: B 388 TYR cc_start: 0.8228 (m-10) cc_final: 0.7846 (m-10) REVERT: B 402 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.8067 (t-90) REVERT: D 438 ARG cc_start: 0.8535 (tmm160) cc_final: 0.8320 (ttp80) REVERT: D 496 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7958 (m-80) outliers start: 77 outliers final: 47 residues processed: 211 average time/residue: 0.0916 time to fit residues: 27.9180 Evaluate side-chains 201 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 496 TYR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 578 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 105 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.124370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.090721 restraints weight = 22522.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.093097 restraints weight = 15063.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094652 restraints weight = 11651.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095720 restraints weight = 9879.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096420 restraints weight = 8885.082| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10564 Z= 0.167 Angle : 0.572 9.854 14240 Z= 0.296 Chirality : 0.042 0.139 1540 Planarity : 0.004 0.039 1822 Dihedral : 4.593 21.523 1396 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 6.23 % Allowed : 31.41 % Favored : 62.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.24), residues: 1276 helix: 0.66 (0.23), residues: 518 sheet: -1.99 (0.48), residues: 128 loop : -1.80 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 226 TYR 0.010 0.001 TYR C 422 PHE 0.018 0.002 PHE D 534 TRP 0.015 0.002 TRP C 445 HIS 0.009 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00396 (10564) covalent geometry : angle 0.57227 (14240) hydrogen bonds : bond 0.04205 ( 396) hydrogen bonds : angle 4.92134 ( 1122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 155 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8278 (t80) REVERT: A 327 PHE cc_start: 0.8883 (t80) cc_final: 0.8540 (t80) REVERT: A 404 THR cc_start: 0.7837 (m) cc_final: 0.7222 (p) REVERT: B 95 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8247 (t80) REVERT: B 229 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8683 (pmm) REVERT: B 274 PHE cc_start: 0.7590 (m-80) cc_final: 0.7267 (m-80) REVERT: B 292 MET cc_start: 0.7544 (mtm) cc_final: 0.7323 (mtm) REVERT: B 327 PHE cc_start: 0.8910 (t80) cc_final: 0.8540 (t80) REVERT: B 402 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.8201 (t-90) REVERT: D 438 ARG cc_start: 0.8568 (tmm160) cc_final: 0.8277 (ttp80) REVERT: D 496 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: D 510 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7845 (t80) outliers start: 69 outliers final: 48 residues processed: 201 average time/residue: 0.0925 time to fit residues: 27.4276 Evaluate side-chains 198 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 496 TYR Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 578 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 124 optimal weight: 0.0030 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 402 HIS ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096271 restraints weight = 22357.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097108 restraints weight = 16114.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097412 restraints weight = 17003.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098926 restraints weight = 12649.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099096 restraints weight = 10220.472| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10564 Z= 0.123 Angle : 0.558 10.736 14240 Z= 0.283 Chirality : 0.041 0.139 1540 Planarity : 0.003 0.038 1822 Dihedral : 4.523 22.610 1396 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.14 % Allowed : 31.50 % Favored : 62.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.24), residues: 1276 helix: 0.72 (0.23), residues: 516 sheet: -1.91 (0.49), residues: 128 loop : -1.68 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 240 TYR 0.010 0.001 TYR A 278 PHE 0.020 0.001 PHE C 588 TRP 0.017 0.001 TRP D 584 HIS 0.009 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00289 (10564) covalent geometry : angle 0.55818 (14240) hydrogen bonds : bond 0.03896 ( 396) hydrogen bonds : angle 4.79940 ( 1122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 158 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8215 (t80) REVERT: A 292 MET cc_start: 0.8701 (mmm) cc_final: 0.8488 (mmm) REVERT: A 387 MET cc_start: 0.8792 (pmm) cc_final: 0.8249 (pmm) REVERT: A 404 THR cc_start: 0.7796 (m) cc_final: 0.7193 (p) REVERT: B 37 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8579 (mtmm) REVERT: B 95 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8187 (t80) REVERT: B 229 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8603 (pmm) REVERT: B 387 MET cc_start: 0.8678 (pmm) cc_final: 0.8214 (pmm) REVERT: B 402 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.8224 (t-90) REVERT: D 438 ARG cc_start: 0.8532 (tmm160) cc_final: 0.8255 (ttp80) REVERT: D 496 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8159 (m-80) REVERT: D 510 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7538 (t80) outliers start: 68 outliers final: 40 residues processed: 207 average time/residue: 0.0857 time to fit residues: 25.7518 Evaluate side-chains 188 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 496 TYR Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 583 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.091270 restraints weight = 22615.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.093748 restraints weight = 14975.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095301 restraints weight = 11453.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096425 restraints weight = 9698.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.097096 restraints weight = 8655.454| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10564 Z= 0.142 Angle : 0.573 9.977 14240 Z= 0.290 Chirality : 0.041 0.154 1540 Planarity : 0.003 0.040 1822 Dihedral : 4.554 33.235 1396 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.96 % Allowed : 31.77 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.24), residues: 1276 helix: 0.78 (0.24), residues: 504 sheet: -1.93 (0.49), residues: 128 loop : -1.74 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 226 TYR 0.015 0.001 TYR B 334 PHE 0.019 0.002 PHE D 502 TRP 0.018 0.002 TRP D 584 HIS 0.008 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00336 (10564) covalent geometry : angle 0.57268 (14240) hydrogen bonds : bond 0.03884 ( 396) hydrogen bonds : angle 4.77259 ( 1122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 153 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8267 (t80) REVERT: A 229 MET cc_start: 0.9202 (pmm) cc_final: 0.8644 (pmm) REVERT: A 254 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8434 (mmtm) REVERT: A 292 MET cc_start: 0.8778 (mmm) cc_final: 0.8545 (mmm) REVERT: A 327 PHE cc_start: 0.8900 (t80) cc_final: 0.8571 (t80) REVERT: A 387 MET cc_start: 0.8738 (pmm) cc_final: 0.8232 (pmm) REVERT: A 404 THR cc_start: 0.7844 (m) cc_final: 0.7221 (p) REVERT: B 95 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8236 (t80) REVERT: B 229 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8564 (pmm) REVERT: B 231 ILE cc_start: 0.8830 (mm) cc_final: 0.8526 (mm) REVERT: B 292 MET cc_start: 0.7523 (mtm) cc_final: 0.7176 (mtm) REVERT: B 327 PHE cc_start: 0.8912 (t80) cc_final: 0.8582 (t80) REVERT: B 387 MET cc_start: 0.8644 (pmm) cc_final: 0.8242 (pmm) REVERT: B 398 MET cc_start: 0.7707 (mmp) cc_final: 0.7337 (mmm) REVERT: B 402 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.8190 (t-90) REVERT: C 422 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7403 (t80) REVERT: D 438 ARG cc_start: 0.8564 (tmm160) cc_final: 0.8251 (ttp80) REVERT: D 496 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8268 (m-80) outliers start: 66 outliers final: 52 residues processed: 204 average time/residue: 0.0837 time to fit residues: 25.0574 Evaluate side-chains 205 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 496 TYR Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 560 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 91 optimal weight: 0.0670 chunk 60 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.125223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096230 restraints weight = 22316.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096789 restraints weight = 16446.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097372 restraints weight = 15790.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098476 restraints weight = 12370.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098757 restraints weight = 10926.814| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10564 Z= 0.121 Angle : 0.568 9.962 14240 Z= 0.288 Chirality : 0.041 0.138 1540 Planarity : 0.003 0.039 1822 Dihedral : 4.544 32.693 1396 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 6.23 % Allowed : 32.13 % Favored : 61.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.24), residues: 1276 helix: 0.78 (0.24), residues: 506 sheet: -2.09 (0.44), residues: 148 loop : -1.66 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 226 TYR 0.012 0.001 TYR B 334 PHE 0.016 0.001 PHE D 517 TRP 0.020 0.001 TRP D 584 HIS 0.008 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00285 (10564) covalent geometry : angle 0.56790 (14240) hydrogen bonds : bond 0.03748 ( 396) hydrogen bonds : angle 4.77522 ( 1122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 162 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8131 (t80) REVERT: A 130 TYR cc_start: 0.8318 (m-80) cc_final: 0.7965 (m-80) REVERT: A 229 MET cc_start: 0.9150 (pmm) cc_final: 0.8660 (pmm) REVERT: A 292 MET cc_start: 0.8832 (mmm) cc_final: 0.8589 (mmm) REVERT: A 327 PHE cc_start: 0.8857 (t80) cc_final: 0.8589 (t80) REVERT: A 387 MET cc_start: 0.8828 (pmm) cc_final: 0.8384 (pmm) REVERT: A 398 MET cc_start: 0.7712 (mmp) cc_final: 0.7288 (mmm) REVERT: A 404 THR cc_start: 0.7837 (m) cc_final: 0.7287 (p) REVERT: B 37 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8594 (mtmm) REVERT: B 95 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8124 (t80) REVERT: B 142 LYS cc_start: 0.8631 (tppt) cc_final: 0.8393 (tppt) REVERT: B 229 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8619 (pmm) REVERT: B 274 PHE cc_start: 0.7671 (m-80) cc_final: 0.7066 (m-80) REVERT: B 292 MET cc_start: 0.7521 (mtm) cc_final: 0.7117 (mtm) REVERT: B 387 MET cc_start: 0.8689 (pmm) cc_final: 0.8322 (pmm) REVERT: B 398 MET cc_start: 0.7703 (mmp) cc_final: 0.7378 (mmm) REVERT: B 402 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8068 (t-90) REVERT: C 422 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7467 (t80) REVERT: D 438 ARG cc_start: 0.8569 (tmm160) cc_final: 0.8281 (ttp80) REVERT: D 496 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: D 534 PHE cc_start: 0.7600 (m-10) cc_final: 0.7113 (m-10) outliers start: 69 outliers final: 51 residues processed: 209 average time/residue: 0.0908 time to fit residues: 27.9207 Evaluate side-chains 206 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 148 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 496 TYR Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 560 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 125 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.126603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097231 restraints weight = 22388.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098256 restraints weight = 16866.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099103 restraints weight = 14883.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099856 restraints weight = 11500.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100258 restraints weight = 10388.671| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10564 Z= 0.112 Angle : 0.579 10.032 14240 Z= 0.292 Chirality : 0.041 0.222 1540 Planarity : 0.003 0.037 1822 Dihedral : 4.509 34.837 1396 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.32 % Allowed : 32.85 % Favored : 61.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.24), residues: 1276 helix: 0.77 (0.24), residues: 506 sheet: -2.03 (0.44), residues: 148 loop : -1.64 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 226 TYR 0.017 0.001 TYR A 334 PHE 0.022 0.001 PHE D 510 TRP 0.022 0.001 TRP D 584 HIS 0.007 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00263 (10564) covalent geometry : angle 0.57855 (14240) hydrogen bonds : bond 0.03677 ( 396) hydrogen bonds : angle 4.74673 ( 1122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 229 MET cc_start: 0.9117 (pmm) cc_final: 0.8538 (pmm) REVERT: A 292 MET cc_start: 0.8748 (mmm) cc_final: 0.8543 (mmm) REVERT: A 387 MET cc_start: 0.8852 (pmm) cc_final: 0.8481 (pmm) REVERT: A 398 MET cc_start: 0.7798 (mmp) cc_final: 0.7449 (mmm) REVERT: A 404 THR cc_start: 0.7849 (m) cc_final: 0.7255 (p) REVERT: B 37 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8646 (mtmm) REVERT: B 95 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8074 (t80) REVERT: B 142 LYS cc_start: 0.8630 (tppt) cc_final: 0.8396 (tppt) REVERT: B 229 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8481 (pmm) REVERT: B 231 ILE cc_start: 0.8794 (mm) cc_final: 0.8477 (mm) REVERT: B 274 PHE cc_start: 0.7657 (m-80) cc_final: 0.7037 (m-80) REVERT: B 387 MET cc_start: 0.8696 (pmm) cc_final: 0.8406 (pmm) REVERT: B 402 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.8046 (t-90) REVERT: C 422 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7432 (t80) REVERT: C 590 MET cc_start: 0.8002 (tmm) cc_final: 0.7618 (mmm) REVERT: D 438 ARG cc_start: 0.8558 (tmm160) cc_final: 0.8268 (ttp80) REVERT: D 496 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.8213 (m-80) outliers start: 59 outliers final: 44 residues processed: 203 average time/residue: 0.0867 time to fit residues: 25.3916 Evaluate side-chains 200 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 496 TYR Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 21 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 HIS D 480 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.126185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096695 restraints weight = 22473.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097533 restraints weight = 16735.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098155 restraints weight = 16737.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099957 restraints weight = 12073.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100100 restraints weight = 9959.988| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10564 Z= 0.126 Angle : 0.585 10.030 14240 Z= 0.297 Chirality : 0.041 0.212 1540 Planarity : 0.003 0.037 1822 Dihedral : 4.511 35.330 1396 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.69 % Allowed : 32.76 % Favored : 61.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.24), residues: 1276 helix: 0.76 (0.24), residues: 508 sheet: -1.86 (0.45), residues: 144 loop : -1.66 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 226 TYR 0.013 0.001 TYR A 334 PHE 0.039 0.002 PHE D 510 TRP 0.022 0.002 TRP D 584 HIS 0.009 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00298 (10564) covalent geometry : angle 0.58533 (14240) hydrogen bonds : bond 0.03701 ( 396) hydrogen bonds : angle 4.74481 ( 1122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 150 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8179 (t80) REVERT: A 229 MET cc_start: 0.9112 (pmm) cc_final: 0.8568 (pmm) REVERT: A 292 MET cc_start: 0.8795 (mmm) cc_final: 0.8560 (mmm) REVERT: A 387 MET cc_start: 0.8901 (pmm) cc_final: 0.8579 (pmm) REVERT: A 398 MET cc_start: 0.7890 (mmp) cc_final: 0.7619 (mmm) REVERT: A 404 THR cc_start: 0.7847 (m) cc_final: 0.7243 (p) REVERT: B 37 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8657 (mtmm) REVERT: B 95 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8036 (t80) REVERT: B 229 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8517 (pmm) REVERT: B 231 ILE cc_start: 0.8800 (mm) cc_final: 0.8453 (mm) REVERT: B 292 MET cc_start: 0.7408 (mtm) cc_final: 0.7086 (mtm) REVERT: B 387 MET cc_start: 0.8762 (pmm) cc_final: 0.8530 (pmm) REVERT: C 422 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7432 (t80) REVERT: C 590 MET cc_start: 0.8075 (tmm) cc_final: 0.7674 (mmm) REVERT: D 438 ARG cc_start: 0.8557 (tmm160) cc_final: 0.8251 (ttp80) REVERT: D 480 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8873 (t0) REVERT: D 496 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8220 (m-80) outliers start: 63 outliers final: 44 residues processed: 192 average time/residue: 0.0917 time to fit residues: 25.4844 Evaluate side-chains 196 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 496 TYR Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.125900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096347 restraints weight = 22301.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097227 restraints weight = 16875.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097597 restraints weight = 17348.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099775 restraints weight = 12564.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099867 restraints weight = 9766.308| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10564 Z= 0.136 Angle : 0.599 10.074 14240 Z= 0.303 Chirality : 0.042 0.214 1540 Planarity : 0.003 0.036 1822 Dihedral : 4.522 34.298 1396 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.69 % Allowed : 33.39 % Favored : 61.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.24), residues: 1276 helix: 0.74 (0.24), residues: 508 sheet: -1.97 (0.44), residues: 148 loop : -1.65 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 226 TYR 0.014 0.001 TYR A 334 PHE 0.032 0.002 PHE D 510 TRP 0.022 0.002 TRP D 584 HIS 0.009 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00331 (10564) covalent geometry : angle 0.59939 (14240) hydrogen bonds : bond 0.03722 ( 396) hydrogen bonds : angle 4.75924 ( 1122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8181 (t80) REVERT: A 229 MET cc_start: 0.9098 (pmm) cc_final: 0.8563 (pmm) REVERT: A 292 MET cc_start: 0.8777 (mmm) cc_final: 0.8557 (mmm) REVERT: A 327 PHE cc_start: 0.8806 (t80) cc_final: 0.8452 (t80) REVERT: A 387 MET cc_start: 0.8852 (pmm) cc_final: 0.8571 (pmm) REVERT: A 404 THR cc_start: 0.7839 (m) cc_final: 0.7341 (p) REVERT: B 37 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8639 (mtmm) REVERT: B 95 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8068 (t80) REVERT: B 229 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8170 (pmm) REVERT: B 231 ILE cc_start: 0.8834 (mm) cc_final: 0.8488 (mm) REVERT: B 292 MET cc_start: 0.7423 (mtm) cc_final: 0.7086 (mtm) REVERT: C 422 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7444 (t80) REVERT: C 440 LYS cc_start: 0.8635 (tptp) cc_final: 0.8233 (tptp) REVERT: C 590 MET cc_start: 0.8067 (tmm) cc_final: 0.7673 (mmm) REVERT: D 438 ARG cc_start: 0.8557 (tmm160) cc_final: 0.8254 (ttp80) REVERT: D 496 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8221 (m-80) REVERT: D 592 MET cc_start: 0.5268 (pmm) cc_final: 0.4741 (pmm) outliers start: 52 outliers final: 42 residues processed: 185 average time/residue: 0.0905 time to fit residues: 24.3989 Evaluate side-chains 195 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 484 MET Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 496 TYR Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 0.0870 chunk 92 optimal weight: 0.0980 chunk 98 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.127192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097823 restraints weight = 22606.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098904 restraints weight = 17025.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099250 restraints weight = 18204.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099841 restraints weight = 12664.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.100384 restraints weight = 11368.555| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10564 Z= 0.117 Angle : 0.610 9.921 14240 Z= 0.305 Chirality : 0.042 0.219 1540 Planarity : 0.003 0.037 1822 Dihedral : 4.489 33.605 1396 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.78 % Allowed : 34.12 % Favored : 61.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.24), residues: 1276 helix: 0.77 (0.24), residues: 508 sheet: -1.81 (0.45), residues: 144 loop : -1.64 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 226 TYR 0.013 0.001 TYR A 334 PHE 0.029 0.001 PHE D 510 TRP 0.022 0.001 TRP D 584 HIS 0.009 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00281 (10564) covalent geometry : angle 0.60965 (14240) hydrogen bonds : bond 0.03603 ( 396) hydrogen bonds : angle 4.72784 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.94 seconds wall clock time: 28 minutes 24.14 seconds (1704.14 seconds total)