Starting phenix.real_space_refine on Fri Oct 11 17:25:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo5_39436/10_2024/8yo5_39436.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo5_39436/10_2024/8yo5_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo5_39436/10_2024/8yo5_39436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo5_39436/10_2024/8yo5_39436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo5_39436/10_2024/8yo5_39436.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yo5_39436/10_2024/8yo5_39436.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/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: 6.56, per 1000 atoms: 0.63 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: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.31 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: 3.04 Time building geometry restraints manager: 2.94 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: 0.00 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: 1.760 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.690 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.210 ------------------------------------------------------------------------------- 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= 0.189 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (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 TRP 0.029 0.002 TRP D 584 HIS 0.009 0.001 HIS B 288 PHE 0.027 0.002 PHE A 274 TYR 0.017 0.001 TYR B 388 ARG 0.007 0.001 ARG D 438 *********************** 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 fitting. rotamer outliers: 6 poor density : 178 time to evaluate : 1.318 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: 0.2219 time to fit residues: 56.6013 Evaluate side-chains 166 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0829 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= 0.190 Angle : 0.573 10.693 14240 Z= 0.297 Chirality : 0.042 0.165 1540 Planarity : 0.004 0.045 1822 Dihedral : 4.812 46.534 1401 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.87 % Allowed : 33.21 % Favored : 61.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1276 helix: 0.67 (0.24), residues: 504 sheet: -1.73 (0.50), residues: 128 loop : -1.68 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 445 HIS 0.009 0.001 HIS B 288 PHE 0.020 0.001 PHE B 274 TYR 0.011 0.001 TYR C 496 ARG 0.005 0.001 ARG D 438 *********************** 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 225 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 171 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.9153 (mtpp) cc_final: 0.8839 (mtpp) REVERT: A 388 TYR cc_start: 0.8179 (m-10) cc_final: 0.7800 (m-10) REVERT: B 387 MET cc_start: 0.8674 (pmm) cc_final: 0.7987 (pmm) REVERT: B 398 MET cc_start: 0.7612 (mmp) cc_final: 0.7323 (mmm) REVERT: C 422 TYR cc_start: 0.8242 (m-80) cc_final: 0.7375 (t80) REVERT: C 431 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8462 (mp) REVERT: C 531 GLN cc_start: 0.7139 (pm20) cc_final: 0.6871 (pm20) REVERT: D 496 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7862 (m-80) outliers start: 54 outliers final: 27 residues processed: 205 average time/residue: 0.2163 time to fit residues: 64.0090 Evaluate side-chains 184 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 205 ARG 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 328 VAL Chi-restraints excluded: chain A residue 381 GLU 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 208 VAL 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 64 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10564 Z= 0.166 Angle : 0.546 9.536 14240 Z= 0.279 Chirality : 0.041 0.139 1540 Planarity : 0.003 0.041 1822 Dihedral : 4.432 20.830 1396 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.96 % Allowed : 32.76 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1276 helix: 0.65 (0.24), residues: 514 sheet: -1.64 (0.50), residues: 124 loop : -1.68 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 445 HIS 0.009 0.001 HIS B 288 PHE 0.019 0.001 PHE C 588 TYR 0.010 0.001 TYR B 278 ARG 0.004 0.000 ARG A 226 *********************** 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 229 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 174 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8140 (t80) REVERT: A 254 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8524 (mmtm) REVERT: A 292 MET cc_start: 0.8413 (mmm) cc_final: 0.8194 (mmm) REVERT: A 388 TYR cc_start: 0.8283 (m-10) cc_final: 0.7852 (m-10) REVERT: B 21 MET cc_start: 0.8381 (mmp) cc_final: 0.8091 (mmp) REVERT: B 95 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8085 (t80) REVERT: B 229 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8432 (pmm) REVERT: B 387 MET cc_start: 0.8668 (pmm) cc_final: 0.8003 (pmm) REVERT: B 388 TYR cc_start: 0.7837 (m-10) cc_final: 0.7461 (m-10) REVERT: B 402 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.7952 (t-90) REVERT: C 422 TYR cc_start: 0.8126 (m-80) cc_final: 0.7353 (t80) REVERT: C 590 MET cc_start: 0.8039 (tmm) cc_final: 0.7665 (mmm) REVERT: D 438 ARG cc_start: 0.8503 (tmm160) cc_final: 0.8285 (ttp80) REVERT: D 496 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7861 (m-80) outliers start: 55 outliers final: 33 residues processed: 208 average time/residue: 0.2386 time to fit residues: 70.2552 Evaluate side-chains 196 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 157 VAL Chi-restraints excluded: chain A residue 181 VAL 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 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 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 217 ILE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 328 VAL 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 D residue 422 TYR 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 578 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 123 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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** A 402 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1361 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= 0.204 Angle : 0.554 9.798 14240 Z= 0.285 Chirality : 0.041 0.187 1540 Planarity : 0.003 0.038 1822 Dihedral : 4.431 21.921 1396 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.78 % Allowed : 32.49 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.24), residues: 1276 helix: 0.75 (0.24), residues: 506 sheet: -1.94 (0.49), residues: 128 loop : -1.70 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 445 HIS 0.009 0.001 HIS B 288 PHE 0.021 0.002 PHE D 534 TYR 0.014 0.001 TYR A 278 ARG 0.005 0.000 ARG B 240 *********************** 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 221 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 157 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8207 (t80) REVERT: A 292 MET cc_start: 0.8614 (mmm) cc_final: 0.8401 (mmm) REVERT: B 21 MET cc_start: 0.8395 (mmp) cc_final: 0.8127 (mmp) REVERT: B 95 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8158 (t80) REVERT: B 229 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8386 (pmm) REVERT: B 292 MET cc_start: 0.7331 (mtm) cc_final: 0.7125 (mtm) REVERT: B 388 TYR cc_start: 0.8106 (m-10) cc_final: 0.7766 (m-10) REVERT: B 402 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.8012 (t-90) REVERT: C 422 TYR cc_start: 0.8121 (m-80) cc_final: 0.7461 (t80) REVERT: D 438 ARG cc_start: 0.8566 (tmm160) cc_final: 0.8278 (ttp80) REVERT: D 496 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: D 510 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7776 (t80) outliers start: 64 outliers final: 39 residues processed: 199 average time/residue: 0.2243 time to fit residues: 64.0208 Evaluate side-chains 197 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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 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 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 229 MET Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 328 VAL 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 D residue 395 HIS Chi-restraints excluded: chain D residue 422 TYR 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 510 PHE 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 578 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 9.9990 chunk 70 optimal weight: 0.0370 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 0.0010 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10564 Z= 0.191 Angle : 0.550 10.504 14240 Z= 0.280 Chirality : 0.041 0.161 1540 Planarity : 0.003 0.037 1822 Dihedral : 4.417 22.810 1396 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.69 % Allowed : 31.68 % Favored : 62.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.24), residues: 1276 helix: 0.83 (0.24), residues: 504 sheet: -1.75 (0.50), residues: 124 loop : -1.72 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 584 HIS 0.008 0.001 HIS B 288 PHE 0.022 0.001 PHE C 588 TYR 0.009 0.001 TYR C 422 ARG 0.005 0.000 ARG A 240 *********************** 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 225 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 162 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8227 (t80) REVERT: A 292 MET cc_start: 0.8657 (mmm) cc_final: 0.8442 (mmm) REVERT: A 387 MET cc_start: 0.8808 (pmm) cc_final: 0.8213 (pmm) REVERT: B 21 MET cc_start: 0.8403 (mmp) cc_final: 0.8189 (mmp) REVERT: B 37 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8691 (mtmm) REVERT: B 60 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8808 (mtpp) REVERT: B 95 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8162 (t80) REVERT: B 229 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8421 (pmm) REVERT: B 387 MET cc_start: 0.8737 (pmm) cc_final: 0.8119 (pmm) REVERT: B 388 TYR cc_start: 0.8168 (m-10) cc_final: 0.7607 (m-10) REVERT: B 402 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.8097 (t-90) REVERT: C 422 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7455 (t80) REVERT: C 512 GLN cc_start: 0.8732 (mm110) cc_final: 0.8521 (mm110) REVERT: C 590 MET cc_start: 0.8094 (tmm) cc_final: 0.7668 (mmm) REVERT: D 438 ARG cc_start: 0.8544 (tmm160) cc_final: 0.8247 (ttp80) REVERT: D 496 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: D 510 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7484 (t80) outliers start: 63 outliers final: 40 residues processed: 200 average time/residue: 0.2222 time to fit residues: 64.6925 Evaluate side-chains 199 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 150 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 181 VAL 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 328 VAL Chi-restraints excluded: chain A residue 333 THR 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 19 TYR 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 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 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 391 TYR Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 438 LEU 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 518 VAL Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain D residue 422 TYR 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 510 PHE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 0.0020 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10564 Z= 0.207 Angle : 0.570 10.949 14240 Z= 0.287 Chirality : 0.041 0.153 1540 Planarity : 0.003 0.039 1822 Dihedral : 4.489 34.427 1396 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 6.41 % Allowed : 31.59 % Favored : 62.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1276 helix: 0.79 (0.24), residues: 506 sheet: -1.91 (0.49), residues: 128 loop : -1.71 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 584 HIS 0.008 0.001 HIS B 288 PHE 0.018 0.001 PHE C 502 TYR 0.012 0.001 TYR B 388 ARG 0.004 0.000 ARG A 240 *********************** 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 228 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 157 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6873 (pmm) REVERT: A 95 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8211 (t80) REVERT: A 229 MET cc_start: 0.9260 (pmm) cc_final: 0.8680 (pmm) REVERT: A 292 MET cc_start: 0.8688 (mmm) cc_final: 0.8461 (mmm) REVERT: A 327 PHE cc_start: 0.8735 (t80) cc_final: 0.8335 (t80) REVERT: A 387 MET cc_start: 0.8821 (pmm) cc_final: 0.8292 (pmm) REVERT: A 404 THR cc_start: 0.7656 (m) cc_final: 0.6951 (p) REVERT: B 95 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8222 (t80) REVERT: B 229 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8381 (pmm) REVERT: B 231 ILE cc_start: 0.8778 (mm) cc_final: 0.8462 (mt) REVERT: B 292 MET cc_start: 0.7601 (mtm) cc_final: 0.7235 (mtm) REVERT: B 387 MET cc_start: 0.8797 (pmm) cc_final: 0.8337 (pmm) REVERT: C 422 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7487 (t80) REVERT: C 512 GLN cc_start: 0.8747 (mm110) cc_final: 0.8542 (mm110) REVERT: D 438 ARG cc_start: 0.8579 (tmm160) cc_final: 0.8274 (ttp80) REVERT: D 496 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7974 (m-80) outliers start: 71 outliers final: 53 residues processed: 202 average time/residue: 0.2112 time to fit residues: 61.9499 Evaluate side-chains 205 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 146 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 328 VAL Chi-restraints excluded: chain A residue 333 THR 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 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 19 TYR 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 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 368 ILE 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 438 LEU 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 517 PHE Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain D residue 403 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10564 Z= 0.186 Angle : 0.566 10.029 14240 Z= 0.284 Chirality : 0.041 0.142 1540 Planarity : 0.003 0.038 1822 Dihedral : 4.450 32.496 1396 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.42 % Allowed : 32.85 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.24), residues: 1276 helix: 0.83 (0.24), residues: 506 sheet: -1.73 (0.50), residues: 124 loop : -1.72 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 584 HIS 0.008 0.001 HIS B 288 PHE 0.016 0.001 PHE D 517 TYR 0.010 0.001 TYR B 388 ARG 0.003 0.000 ARG A 240 *********************** 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 219 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 159 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8182 (t80) REVERT: A 229 MET cc_start: 0.9198 (pmm) cc_final: 0.8633 (pmm) REVERT: A 254 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8487 (mmtm) REVERT: A 292 MET cc_start: 0.8726 (mmm) cc_final: 0.8493 (mmm) REVERT: A 387 MET cc_start: 0.8831 (pmm) cc_final: 0.8312 (pmm) REVERT: B 37 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8678 (mtmm) REVERT: B 60 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8798 (mtpp) REVERT: B 95 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8205 (t80) REVERT: B 226 ARG cc_start: 0.8393 (mmp80) cc_final: 0.8157 (mmp80) REVERT: B 292 MET cc_start: 0.7444 (mtm) cc_final: 0.7066 (mtm) REVERT: B 387 MET cc_start: 0.8781 (pmm) cc_final: 0.8396 (pmm) REVERT: B 402 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.8015 (t-90) REVERT: C 422 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7438 (t80) REVERT: C 512 GLN cc_start: 0.8729 (mm110) cc_final: 0.8519 (mm110) REVERT: C 590 MET cc_start: 0.8073 (tmm) cc_final: 0.7626 (mmm) REVERT: D 438 ARG cc_start: 0.8570 (tmm160) cc_final: 0.8264 (ttp80) REVERT: D 496 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: D 534 PHE cc_start: 0.7515 (m-10) cc_final: 0.6962 (m-10) outliers start: 60 outliers final: 43 residues processed: 199 average time/residue: 0.2479 time to fit residues: 69.2048 Evaluate side-chains 196 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 145 time to evaluate : 1.875 ------------------------------------------------------------------------------- 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 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 328 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 PHE 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 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 247 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 368 ILE 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 422 TYR Chi-restraints excluded: chain C residue 426 VAL 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 422 TYR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.0870 chunk 73 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10564 Z= 0.175 Angle : 0.570 10.015 14240 Z= 0.286 Chirality : 0.041 0.138 1540 Planarity : 0.003 0.037 1822 Dihedral : 4.431 33.085 1396 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.42 % Allowed : 33.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1276 helix: 0.86 (0.24), residues: 506 sheet: -2.04 (0.49), residues: 132 loop : -1.63 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 584 HIS 0.007 0.001 HIS B 288 PHE 0.021 0.001 PHE C 502 TYR 0.011 0.001 TYR B 388 ARG 0.003 0.000 ARG A 240 *********************** 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 216 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 156 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8068 (t80) REVERT: A 229 MET cc_start: 0.9177 (pmm) cc_final: 0.8608 (pmm) REVERT: A 254 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8475 (mmtm) REVERT: A 292 MET cc_start: 0.8714 (mmm) cc_final: 0.8501 (mmm) REVERT: A 361 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8475 (ptpp) REVERT: A 387 MET cc_start: 0.8861 (pmm) cc_final: 0.8421 (pmm) REVERT: B 37 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8698 (mtmm) REVERT: B 95 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8116 (t80) REVERT: B 229 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8434 (pmm) REVERT: B 231 ILE cc_start: 0.8776 (mm) cc_final: 0.8456 (mm) REVERT: B 387 MET cc_start: 0.8783 (pmm) cc_final: 0.8504 (pmm) REVERT: B 402 HIS cc_start: 0.8478 (OUTLIER) cc_final: 0.8012 (t-90) REVERT: C 422 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7415 (t80) REVERT: C 512 GLN cc_start: 0.8720 (mm110) cc_final: 0.8513 (mm110) REVERT: C 590 MET cc_start: 0.8095 (tmm) cc_final: 0.7708 (mmm) REVERT: D 438 ARG cc_start: 0.8486 (tmm160) cc_final: 0.8215 (ttp80) REVERT: D 480 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8773 (t0) REVERT: D 496 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8051 (m-80) outliers start: 60 outliers final: 40 residues processed: 196 average time/residue: 0.2201 time to fit residues: 61.7849 Evaluate side-chains 201 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 151 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 361 LYS 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 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 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 422 TYR Chi-restraints excluded: chain C residue 426 VAL 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 517 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 0.0020 chunk 90 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10564 Z= 0.192 Angle : 0.589 10.112 14240 Z= 0.294 Chirality : 0.041 0.137 1540 Planarity : 0.003 0.036 1822 Dihedral : 4.436 32.199 1396 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.69 % Allowed : 33.94 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1276 helix: 0.83 (0.24), residues: 508 sheet: -1.85 (0.49), residues: 128 loop : -1.65 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 584 HIS 0.010 0.001 HIS B 288 PHE 0.018 0.001 PHE D 517 TYR 0.016 0.001 TYR A 334 ARG 0.002 0.000 ARG A 240 *********************** 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 205 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 153 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8102 (t80) REVERT: A 229 MET cc_start: 0.9178 (pmm) cc_final: 0.8597 (pmm) REVERT: A 292 MET cc_start: 0.8760 (mmm) cc_final: 0.8519 (mmm) REVERT: A 361 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8463 (ptpp) REVERT: A 387 MET cc_start: 0.8867 (pmm) cc_final: 0.8450 (pmm) REVERT: B 37 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8671 (mtmm) REVERT: B 95 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8146 (t80) REVERT: B 226 ARG cc_start: 0.8397 (mmp80) cc_final: 0.8014 (mmp80) REVERT: B 292 MET cc_start: 0.7308 (mtm) cc_final: 0.7034 (mtm) REVERT: B 387 MET cc_start: 0.8833 (pmm) cc_final: 0.8591 (pmm) REVERT: B 402 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.7984 (t-90) REVERT: C 422 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7370 (t80) REVERT: C 512 GLN cc_start: 0.8704 (mm110) cc_final: 0.8497 (mm110) REVERT: C 590 MET cc_start: 0.8140 (tmm) cc_final: 0.7772 (mmm) REVERT: D 438 ARG cc_start: 0.8497 (tmm160) cc_final: 0.8209 (ttp80) REVERT: D 496 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8066 (m-80) outliers start: 52 outliers final: 38 residues processed: 190 average time/residue: 0.2249 time to fit residues: 61.2222 Evaluate side-chains 194 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 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 328 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 361 LYS 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 19 TYR 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 181 VAL Chi-restraints excluded: chain B residue 208 VAL 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 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 422 TYR Chi-restraints excluded: chain C residue 426 VAL 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 496 TYR 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 74 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10564 Z= 0.252 Angle : 0.615 10.321 14240 Z= 0.308 Chirality : 0.042 0.141 1540 Planarity : 0.003 0.036 1822 Dihedral : 4.555 31.439 1396 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.24 % Allowed : 34.39 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1276 helix: 0.79 (0.24), residues: 508 sheet: -2.15 (0.44), residues: 152 loop : -1.62 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 584 HIS 0.009 0.001 HIS B 288 PHE 0.020 0.002 PHE C 502 TYR 0.014 0.001 TYR A 334 ARG 0.003 0.000 ARG C 438 ********************** 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 201 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 154 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8312 (t80) REVERT: A 229 MET cc_start: 0.9188 (pmm) cc_final: 0.8614 (pmm) REVERT: A 292 MET cc_start: 0.8765 (mmm) cc_final: 0.8533 (mmm) REVERT: A 327 PHE cc_start: 0.8832 (t80) cc_final: 0.8478 (t80) REVERT: A 361 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8515 (ptpp) REVERT: A 387 MET cc_start: 0.8866 (pmm) cc_final: 0.8510 (pmm) REVERT: A 404 THR cc_start: 0.7747 (m) cc_final: 0.7237 (p) REVERT: B 37 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8593 (mtmm) REVERT: B 95 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8291 (t80) REVERT: B 292 MET cc_start: 0.7459 (mtm) cc_final: 0.7194 (mtm) REVERT: B 327 PHE cc_start: 0.8867 (t80) cc_final: 0.8476 (t80) REVERT: C 422 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7445 (t80) REVERT: C 512 GLN cc_start: 0.8713 (mm110) cc_final: 0.8486 (mm110) REVERT: D 438 ARG cc_start: 0.8511 (tmm160) cc_final: 0.8203 (ttp80) REVERT: D 496 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: D 510 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7730 (t80) REVERT: D 592 MET cc_start: 0.5372 (pmm) cc_final: 0.4918 (pmm) outliers start: 47 outliers final: 36 residues processed: 187 average time/residue: 0.2239 time to fit residues: 59.4894 Evaluate side-chains 191 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 361 LYS 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 181 VAL Chi-restraints excluded: chain B residue 208 VAL 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 379 THR 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 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 447 MET Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 496 TYR Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 0.0010 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.0040 chunk 42 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 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 = 0.3765 r_free = 0.3765 target = 0.127560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098546 restraints weight = 22089.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099096 restraints weight = 16502.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099515 restraints weight = 16716.241| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10564 Z= 0.176 Angle : 0.613 11.347 14240 Z= 0.306 Chirality : 0.041 0.165 1540 Planarity : 0.003 0.036 1822 Dihedral : 4.542 44.369 1396 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.16 % Allowed : 36.19 % Favored : 60.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1276 helix: 0.81 (0.24), residues: 508 sheet: -1.99 (0.45), residues: 148 loop : -1.57 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 259 HIS 0.009 0.001 HIS B 288 PHE 0.019 0.001 PHE D 517 TYR 0.014 0.001 TYR A 334 ARG 0.004 0.000 ARG B 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.53 seconds wall clock time: 42 minutes 6.40 seconds (2526.40 seconds total)