Starting phenix.real_space_refine on Fri Dec 27 22:13:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9e_18278/12_2024/8q9e_18278.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9e_18278/12_2024/8q9e_18278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q9e_18278/12_2024/8q9e_18278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9e_18278/12_2024/8q9e_18278.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9e_18278/12_2024/8q9e_18278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9e_18278/12_2024/8q9e_18278.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2082 2.51 5 N 612 2.21 5 O 612 1.98 5 H 3456 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6768 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1128 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "D" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1128 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "C" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1128 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "B" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1128 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "E" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1128 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "F" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1128 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 5.05, per 1000 atoms: 0.75 Number of scatterers: 6768 At special positions: 0 Unit cell: (95.237, 109.05, 40.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 612 8.00 N 612 7.00 C 2082 6.00 H 3456 1.00 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: 1.69 Conformation dependent library (CDL) restraints added in 669.9 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 52.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 309 through 310 removed outlier: 6.687A pdb=" N VAL A 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.987A pdb=" N VAL A 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.338A pdb=" N LYS A 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N SER F 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR A 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N CYS F 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS A 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SER F 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLY A 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.465A pdb=" N ILE A 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 336 through 346 removed outlier: 6.448A pdb=" N VAL A 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LYS D 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLU D 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER A 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU D 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LYS A 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N PHE D 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A 344 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP F 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE A 346 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.548A pdb=" N GLN A 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE F 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS A 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 359 through 362 Processing sheet with id=AA8, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.716A pdb=" N LYS A 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLU F 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N HIS F 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THR A 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU F 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS A 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.580A pdb=" N VAL C 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.910A pdb=" N VAL C 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.444A pdb=" N LYS C 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N SER B 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR C 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N CYS B 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS C 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER B 324 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY C 323 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.494A pdb=" N ILE C 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 336 through 346 removed outlier: 6.784A pdb=" N LEU C 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASP B 345 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE C 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 344 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP E 345 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE B 346 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.554A pdb=" N GLN C 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE B 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS C 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN B 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE E 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS B 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.410A pdb=" N ILE C 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 368 through 377 removed outlier: 6.598A pdb=" N LYS C 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLU B 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE C 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N HIS B 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR C 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU B 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS C 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS B 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLU E 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N HIS E 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU E 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS B 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 60 hydrogen bonds defined for protein. 180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3450 1.12 - 1.29: 546 1.29 - 1.47: 1122 1.47 - 1.64: 1698 1.64 - 1.82: 6 Bond restraints: 6822 Sorted by residual: bond pdb=" CE1 TYR D 310 " pdb=" HE1 TYR D 310 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ASP D 358 " pdb=" H ASP D 358 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" ND2 ASN E 359 " pdb="HD21 ASN E 359 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N VAL C 309 " pdb=" H VAL C 309 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N ILE A 354 " pdb=" H ILE A 354 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 6817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 10451 2.55 - 5.10: 1530 5.10 - 7.65: 432 7.65 - 10.20: 18 10.20 - 12.75: 7 Bond angle restraints: 12438 Sorted by residual: angle pdb=" C ASP E 348 " pdb=" N ARG E 349 " pdb=" CA ARG E 349 " ideal model delta sigma weight residual 120.90 129.73 -8.83 1.41e+00 5.03e-01 3.92e+01 angle pdb=" C ASP D 348 " pdb=" N ARG D 349 " pdb=" CA ARG D 349 " ideal model delta sigma weight residual 121.05 129.38 -8.33 1.43e+00 4.89e-01 3.40e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 120.90 128.94 -8.04 1.41e+00 5.03e-01 3.25e+01 angle pdb=" C ASP A 348 " pdb=" N ARG A 349 " pdb=" CA ARG A 349 " ideal model delta sigma weight residual 120.90 128.56 -7.66 1.41e+00 5.03e-01 2.95e+01 angle pdb=" C ASP C 348 " pdb=" N ARG C 349 " pdb=" CA ARG C 349 " ideal model delta sigma weight residual 121.05 128.64 -7.59 1.43e+00 4.89e-01 2.82e+01 ... (remaining 12433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.53: 2655 13.53 - 27.07: 283 27.07 - 40.60: 84 40.60 - 54.13: 48 54.13 - 67.66: 68 Dihedral angle restraints: 3138 sinusoidal: 1794 harmonic: 1344 Sorted by residual: dihedral pdb=" C LYS F 370 " pdb=" N LYS F 370 " pdb=" CA LYS F 370 " pdb=" CB LYS F 370 " ideal model delta harmonic sigma weight residual -122.60 -137.46 14.86 0 2.50e+00 1.60e-01 3.53e+01 dihedral pdb=" N LYS F 370 " pdb=" C LYS F 370 " pdb=" CA LYS F 370 " pdb=" CB LYS F 370 " ideal model delta harmonic sigma weight residual 122.80 137.27 -14.47 0 2.50e+00 1.60e-01 3.35e+01 dihedral pdb=" CA THR F 377 " pdb=" C THR F 377 " pdb=" N PHE F 378 " pdb=" CA PHE F 378 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 3135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 406 0.124 - 0.249: 81 0.249 - 0.373: 13 0.373 - 0.497: 3 0.497 - 0.621: 1 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA LYS F 370 " pdb=" N LYS F 370 " pdb=" C LYS F 370 " pdb=" CB LYS F 370 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" CA LYS E 370 " pdb=" N LYS E 370 " pdb=" C LYS E 370 " pdb=" CB LYS E 370 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA PRO A 332 " pdb=" N PRO A 332 " pdb=" C PRO A 332 " pdb=" CB PRO A 332 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 501 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 378 " 0.107 2.00e-02 2.50e+03 4.21e-02 5.33e+01 pdb=" CG PHE B 378 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 378 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE B 378 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE B 378 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE B 378 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 378 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE B 378 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 PHE B 378 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 PHE B 378 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE B 378 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 378 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 327 " -0.038 2.00e-02 2.50e+03 5.20e-02 4.05e+01 pdb=" CG ASN A 327 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN A 327 " 0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 327 " -0.053 2.00e-02 2.50e+03 pdb="HD21 ASN A 327 " -0.045 2.00e-02 2.50e+03 pdb="HD22 ASN A 327 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 358 " -0.034 2.00e-02 2.50e+03 6.09e-02 3.71e+01 pdb=" N ASN B 359 " 0.105 2.00e-02 2.50e+03 pdb=" CA ASN B 359 " -0.030 2.00e-02 2.50e+03 pdb=" H ASN B 359 " -0.041 2.00e-02 2.50e+03 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 542 2.18 - 2.78: 11409 2.78 - 3.39: 17221 3.39 - 3.99: 23083 3.99 - 4.60: 31947 Nonbonded interactions: 84202 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.571 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.578 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.601 2.450 ... (remaining 84197 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.730 Find NCS groups from input model: 0.170 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:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 : 0.011 0.035 3366 Z= 0.748 Angle : 1.893 8.827 4500 Z= 1.248 Chirality : 0.109 0.621 504 Planarity : 0.010 0.044 570 Dihedral : 11.771 57.284 1296 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.32 % Allowed : 1.85 % Favored : 96.83 % Cbeta Deviations : 0.53 % 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: -1.47 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS E 362 PHE 0.066 0.019 PHE B 378 TYR 0.034 0.009 TYR E 310 ARG 0.008 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 171 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8954 (p) cc_final: 0.8580 (p) REVERT: A 317 LYS cc_start: 0.7485 (mttt) cc_final: 0.7016 (tttt) REVERT: A 342 GLU cc_start: 0.7325 (tt0) cc_final: 0.6999 (tt0) REVERT: A 375 LYS cc_start: 0.7890 (ptpt) cc_final: 0.7533 (ptmt) REVERT: D 317 LYS cc_start: 0.7539 (mttt) cc_final: 0.6944 (tttt) REVERT: D 336 GLN cc_start: 0.6989 (tt0) cc_final: 0.6618 (mp10) REVERT: D 342 GLU cc_start: 0.7203 (tt0) cc_final: 0.6970 (tt0) REVERT: D 375 LYS cc_start: 0.7989 (ptpt) cc_final: 0.7647 (ptmt) REVERT: C 317 LYS cc_start: 0.8137 (mttt) cc_final: 0.7386 (tttt) REVERT: C 318 VAL cc_start: 0.8930 (t) cc_final: 0.8714 (p) REVERT: C 321 LYS cc_start: 0.7684 (ptpt) cc_final: 0.7225 (pttt) REVERT: C 336 GLN cc_start: 0.7296 (tt0) cc_final: 0.6224 (mp10) REVERT: C 340 LYS cc_start: 0.7393 (mttt) cc_final: 0.6863 (mmtm) REVERT: B 311 LYS cc_start: 0.7617 (tttt) cc_final: 0.7332 (ptpt) REVERT: B 317 LYS cc_start: 0.8208 (mttt) cc_final: 0.7446 (tttt) REVERT: B 342 GLU cc_start: 0.7555 (tt0) cc_final: 0.7202 (tt0) REVERT: B 349 ARG cc_start: 0.7162 (ttm170) cc_final: 0.6845 (mtm180) REVERT: B 373 THR cc_start: 0.8221 (m) cc_final: 0.7942 (p) REVERT: B 375 LYS cc_start: 0.8014 (ptpt) cc_final: 0.7737 (ptpt) REVERT: E 311 LYS cc_start: 0.7799 (tttt) cc_final: 0.7563 (ptpt) REVERT: E 317 LYS cc_start: 0.8525 (mttt) cc_final: 0.7966 (tttt) REVERT: E 321 LYS cc_start: 0.7417 (ptpt) cc_final: 0.6283 (pptt) REVERT: E 342 GLU cc_start: 0.7566 (tt0) cc_final: 0.7253 (tt0) REVERT: E 349 ARG cc_start: 0.6942 (ttm170) cc_final: 0.5361 (pmt-80) REVERT: E 368 ASN cc_start: 0.6046 (m110) cc_final: 0.5768 (m110) REVERT: E 369 LYS cc_start: 0.8195 (pttm) cc_final: 0.7975 (ptpt) REVERT: E 370 LYS cc_start: 0.5995 (mmtp) cc_final: 0.5375 (ptmt) REVERT: F 317 LYS cc_start: 0.7969 (mttt) cc_final: 0.7729 (tttt) REVERT: F 342 GLU cc_start: 0.7552 (tt0) cc_final: 0.7274 (tt0) REVERT: F 375 LYS cc_start: 0.8136 (ptpt) cc_final: 0.7824 (ptmt) outliers start: 5 outliers final: 0 residues processed: 173 average time/residue: 2.4369 time to fit residues: 432.7421 Evaluate side-chains 138 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 368 ASN D 351 GLN D 368 ASN C 351 GLN C 368 ASN B 327 ASN B 351 GLN E 327 ASN F 351 GLN F 359 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3366 Z= 0.276 Angle : 0.750 7.713 4500 Z= 0.389 Chirality : 0.054 0.143 504 Planarity : 0.004 0.035 570 Dihedral : 7.574 23.746 444 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.44 % Allowed : 13.49 % Favored : 83.07 % 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: -1.55 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.009 0.002 PHE B 378 TYR 0.010 0.001 TYR A 310 ARG 0.006 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.9024 (p) cc_final: 0.8808 (p) REVERT: A 317 LYS cc_start: 0.7616 (mttt) cc_final: 0.7198 (tttt) REVERT: A 342 GLU cc_start: 0.7199 (tt0) cc_final: 0.6876 (tt0) REVERT: A 349 ARG cc_start: 0.7192 (ttm170) cc_final: 0.6899 (mtm-85) REVERT: A 375 LYS cc_start: 0.7917 (ptpt) cc_final: 0.7526 (ptmt) REVERT: D 317 LYS cc_start: 0.7547 (mttt) cc_final: 0.7000 (tttm) REVERT: D 342 GLU cc_start: 0.7410 (tt0) cc_final: 0.6926 (mp0) REVERT: D 349 ARG cc_start: 0.7227 (ttm170) cc_final: 0.5328 (tpt90) REVERT: D 375 LYS cc_start: 0.7891 (ptpt) cc_final: 0.7568 (ptmt) REVERT: C 317 LYS cc_start: 0.8196 (mttt) cc_final: 0.7507 (tttt) REVERT: C 318 VAL cc_start: 0.8933 (t) cc_final: 0.8698 (p) REVERT: C 321 LYS cc_start: 0.7760 (ptpt) cc_final: 0.7173 (pttt) REVERT: C 336 GLN cc_start: 0.7215 (tt0) cc_final: 0.6464 (mt0) REVERT: C 340 LYS cc_start: 0.7375 (mttt) cc_final: 0.7088 (mtpt) REVERT: C 342 GLU cc_start: 0.7541 (tt0) cc_final: 0.7140 (tt0) REVERT: C 351 GLN cc_start: 0.7966 (mt0) cc_final: 0.7678 (mt0) REVERT: C 358 ASP cc_start: 0.7388 (m-30) cc_final: 0.7158 (m-30) REVERT: B 311 LYS cc_start: 0.7708 (tttt) cc_final: 0.7370 (pttt) REVERT: B 317 LYS cc_start: 0.8254 (mttt) cc_final: 0.7450 (tttt) REVERT: B 321 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7173 (pttt) REVERT: B 336 GLN cc_start: 0.7612 (tt0) cc_final: 0.6465 (mp10) REVERT: B 342 GLU cc_start: 0.7526 (tt0) cc_final: 0.7103 (tt0) REVERT: B 349 ARG cc_start: 0.7000 (ttm170) cc_final: 0.6683 (mtp85) REVERT: B 373 THR cc_start: 0.8172 (m) cc_final: 0.7936 (p) REVERT: B 375 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7721 (ptpt) REVERT: E 311 LYS cc_start: 0.7883 (tttt) cc_final: 0.7658 (ptpt) REVERT: E 314 ASP cc_start: 0.8419 (t0) cc_final: 0.8170 (t70) REVERT: E 317 LYS cc_start: 0.8429 (mttt) cc_final: 0.7923 (tttt) REVERT: E 321 LYS cc_start: 0.7491 (ptpt) cc_final: 0.6359 (pmtt) REVERT: E 342 GLU cc_start: 0.7736 (tt0) cc_final: 0.7379 (tt0) REVERT: E 349 ARG cc_start: 0.6899 (ttm170) cc_final: 0.5073 (pmt170) REVERT: E 351 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: E 369 LYS cc_start: 0.8096 (pttm) cc_final: 0.7893 (ptpt) REVERT: E 370 LYS cc_start: 0.5889 (mmtp) cc_final: 0.5499 (ptmt) REVERT: F 317 LYS cc_start: 0.7982 (mttt) cc_final: 0.7663 (tttm) REVERT: F 342 GLU cc_start: 0.7628 (tt0) cc_final: 0.7300 (tt0) REVERT: F 370 LYS cc_start: 0.4462 (mmtp) cc_final: 0.3346 (pttt) REVERT: F 375 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7910 (ptmt) outliers start: 13 outliers final: 3 residues processed: 142 average time/residue: 2.7487 time to fit residues: 399.6272 Evaluate side-chains 139 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain F residue 309 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3366 Z= 0.159 Angle : 0.622 6.551 4500 Z= 0.316 Chirality : 0.053 0.133 504 Planarity : 0.004 0.040 570 Dihedral : 6.352 18.989 444 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.12 % Allowed : 17.20 % Favored : 80.69 % 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: -1.53 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 374 PHE 0.010 0.002 PHE B 378 TYR 0.009 0.001 TYR A 310 ARG 0.005 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.9027 (p) cc_final: 0.8740 (p) REVERT: A 317 LYS cc_start: 0.7652 (mttt) cc_final: 0.7254 (tttt) REVERT: A 342 GLU cc_start: 0.7233 (tt0) cc_final: 0.6585 (mp0) REVERT: A 375 LYS cc_start: 0.7881 (ptpt) cc_final: 0.7515 (ptmt) REVERT: D 311 LYS cc_start: 0.7414 (mttt) cc_final: 0.7189 (mttt) REVERT: D 317 LYS cc_start: 0.7576 (mttt) cc_final: 0.7055 (tttm) REVERT: D 342 GLU cc_start: 0.7504 (tt0) cc_final: 0.7013 (mp0) REVERT: D 349 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6769 (mtt90) REVERT: D 375 LYS cc_start: 0.7960 (ptpt) cc_final: 0.7606 (ptmt) REVERT: C 317 LYS cc_start: 0.8294 (mttt) cc_final: 0.7560 (tttt) REVERT: C 318 VAL cc_start: 0.8940 (t) cc_final: 0.8691 (p) REVERT: C 321 LYS cc_start: 0.7747 (ptpt) cc_final: 0.7160 (pttt) REVERT: C 336 GLN cc_start: 0.7202 (tt0) cc_final: 0.6178 (mp10) REVERT: C 340 LYS cc_start: 0.7367 (mttt) cc_final: 0.7060 (mtpt) REVERT: C 342 GLU cc_start: 0.7529 (tt0) cc_final: 0.7118 (tt0) REVERT: C 349 ARG cc_start: 0.7141 (ttm170) cc_final: 0.5567 (mmp-170) REVERT: B 311 LYS cc_start: 0.7685 (tttt) cc_final: 0.7360 (pttt) REVERT: B 317 LYS cc_start: 0.8224 (mttt) cc_final: 0.7410 (tttt) REVERT: B 321 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7137 (pttt) REVERT: B 342 GLU cc_start: 0.7529 (tt0) cc_final: 0.7159 (tt0) REVERT: B 349 ARG cc_start: 0.7104 (ttm170) cc_final: 0.6718 (mtt90) REVERT: B 373 THR cc_start: 0.8112 (m) cc_final: 0.7864 (p) REVERT: B 375 LYS cc_start: 0.7951 (ptpt) cc_final: 0.7692 (ptpt) REVERT: E 311 LYS cc_start: 0.7882 (tttt) cc_final: 0.7598 (ptpt) REVERT: E 317 LYS cc_start: 0.8419 (mttt) cc_final: 0.7924 (tttt) REVERT: E 321 LYS cc_start: 0.7554 (ptpt) cc_final: 0.6399 (pmtt) REVERT: E 342 GLU cc_start: 0.7744 (tt0) cc_final: 0.7417 (tt0) REVERT: E 349 ARG cc_start: 0.6908 (ttm170) cc_final: 0.5023 (pmt-80) REVERT: E 369 LYS cc_start: 0.8097 (pttm) cc_final: 0.7894 (ptpt) REVERT: E 370 LYS cc_start: 0.5923 (mmtp) cc_final: 0.5545 (ptmt) REVERT: F 314 ASP cc_start: 0.7647 (t0) cc_final: 0.7227 (t0) REVERT: F 317 LYS cc_start: 0.7948 (mttt) cc_final: 0.7661 (tttm) REVERT: F 342 GLU cc_start: 0.7599 (tt0) cc_final: 0.6961 (mp0) REVERT: F 370 LYS cc_start: 0.4459 (mmtp) cc_final: 0.3423 (pttt) REVERT: F 375 LYS cc_start: 0.8114 (ptpt) cc_final: 0.7889 (ptmt) outliers start: 8 outliers final: 3 residues processed: 143 average time/residue: 2.7045 time to fit residues: 396.0980 Evaluate side-chains 139 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain F residue 309 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN D 327 ASN C 359 ASN B 351 GLN E 351 GLN E 359 ASN F 368 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3366 Z= 0.272 Angle : 0.633 5.871 4500 Z= 0.322 Chirality : 0.052 0.148 504 Planarity : 0.005 0.055 570 Dihedral : 6.029 17.306 444 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.70 % Allowed : 19.31 % Favored : 76.98 % 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: -1.68 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 330 PHE 0.011 0.002 PHE B 378 TYR 0.012 0.002 TYR A 310 ARG 0.004 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.9028 (p) cc_final: 0.8803 (p) REVERT: A 317 LYS cc_start: 0.7695 (mttt) cc_final: 0.7292 (tttt) REVERT: A 342 GLU cc_start: 0.7203 (tt0) cc_final: 0.6517 (mp0) REVERT: A 375 LYS cc_start: 0.7867 (ptpt) cc_final: 0.7474 (ptmt) REVERT: D 317 LYS cc_start: 0.7629 (mttt) cc_final: 0.7072 (tttm) REVERT: D 342 GLU cc_start: 0.7520 (tt0) cc_final: 0.7005 (mp0) REVERT: D 349 ARG cc_start: 0.7217 (ttm170) cc_final: 0.5238 (tpt90) REVERT: D 375 LYS cc_start: 0.7992 (ptpt) cc_final: 0.7660 (ptmt) REVERT: C 317 LYS cc_start: 0.8356 (mttt) cc_final: 0.7645 (tttt) REVERT: C 321 LYS cc_start: 0.7797 (ptpt) cc_final: 0.7389 (pttt) REVERT: C 340 LYS cc_start: 0.7375 (mttt) cc_final: 0.7073 (mtpt) REVERT: C 349 ARG cc_start: 0.7151 (ttm170) cc_final: 0.5442 (mmp-170) REVERT: B 311 LYS cc_start: 0.7675 (tttt) cc_final: 0.7357 (pttt) REVERT: B 314 ASP cc_start: 0.7923 (t70) cc_final: 0.7366 (t0) REVERT: B 317 LYS cc_start: 0.8259 (mttt) cc_final: 0.7464 (tttt) REVERT: B 321 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7047 (pttt) REVERT: B 342 GLU cc_start: 0.7583 (tt0) cc_final: 0.7209 (tt0) REVERT: B 348 ASP cc_start: 0.8212 (t0) cc_final: 0.7989 (t0) REVERT: B 375 LYS cc_start: 0.7926 (ptpt) cc_final: 0.7666 (ptpt) REVERT: E 311 LYS cc_start: 0.7867 (tttt) cc_final: 0.7593 (ptpt) REVERT: E 314 ASP cc_start: 0.7992 (t70) cc_final: 0.7341 (t0) REVERT: E 317 LYS cc_start: 0.8480 (mttt) cc_final: 0.7954 (tttt) REVERT: E 321 LYS cc_start: 0.7592 (ptpt) cc_final: 0.6426 (pmtt) REVERT: E 342 GLU cc_start: 0.7777 (tt0) cc_final: 0.7403 (tt0) REVERT: E 349 ARG cc_start: 0.7080 (ttm170) cc_final: 0.5076 (pmt-80) REVERT: E 369 LYS cc_start: 0.8104 (pttm) cc_final: 0.7157 (pmtt) REVERT: E 370 LYS cc_start: 0.5848 (mmtp) cc_final: 0.5452 (ptmt) REVERT: F 317 LYS cc_start: 0.7980 (mttt) cc_final: 0.7653 (tttm) REVERT: F 342 GLU cc_start: 0.7564 (tt0) cc_final: 0.6936 (mp0) REVERT: F 370 LYS cc_start: 0.4428 (mmtp) cc_final: 0.3275 (pttt) REVERT: F 375 LYS cc_start: 0.8165 (ptpt) cc_final: 0.7930 (ptmt) outliers start: 14 outliers final: 5 residues processed: 134 average time/residue: 2.8163 time to fit residues: 386.3086 Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0040 chunk 16 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3366 Z= 0.142 Angle : 0.543 5.491 4500 Z= 0.268 Chirality : 0.052 0.126 504 Planarity : 0.004 0.050 570 Dihedral : 5.199 14.713 444 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.06 % Allowed : 21.43 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.010 0.002 PHE B 346 TYR 0.006 0.001 TYR F 310 ARG 0.008 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8981 (p) cc_final: 0.8746 (p) REVERT: A 317 LYS cc_start: 0.7729 (mttt) cc_final: 0.7301 (tttm) REVERT: A 342 GLU cc_start: 0.7207 (tt0) cc_final: 0.6712 (mp0) REVERT: A 349 ARG cc_start: 0.7126 (mtm-85) cc_final: 0.6875 (mtm-85) REVERT: A 375 LYS cc_start: 0.7775 (ptpt) cc_final: 0.7403 (ptmt) REVERT: D 311 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7290 (mtpt) REVERT: D 317 LYS cc_start: 0.7608 (mttt) cc_final: 0.7085 (tttm) REVERT: D 342 GLU cc_start: 0.7592 (tt0) cc_final: 0.7179 (mp0) REVERT: D 349 ARG cc_start: 0.7153 (ttm170) cc_final: 0.6795 (mtt90) REVERT: D 356 SER cc_start: 0.8917 (m) cc_final: 0.8276 (p) REVERT: D 370 LYS cc_start: 0.8311 (mtmt) cc_final: 0.8079 (ttpt) REVERT: D 375 LYS cc_start: 0.8007 (ptpt) cc_final: 0.7676 (ptmt) REVERT: C 317 LYS cc_start: 0.8380 (mttt) cc_final: 0.7650 (tttt) REVERT: C 321 LYS cc_start: 0.7789 (ptpt) cc_final: 0.7355 (pttt) REVERT: C 336 GLN cc_start: 0.7250 (tt0) cc_final: 0.6267 (mp10) REVERT: C 340 LYS cc_start: 0.7355 (mttt) cc_final: 0.7071 (mtpt) REVERT: C 342 GLU cc_start: 0.7556 (tt0) cc_final: 0.7092 (tt0) REVERT: C 349 ARG cc_start: 0.7187 (ttm170) cc_final: 0.5675 (mmm160) REVERT: B 314 ASP cc_start: 0.7894 (t70) cc_final: 0.7287 (t0) REVERT: B 317 LYS cc_start: 0.8288 (mttt) cc_final: 0.7424 (tttt) REVERT: B 318 VAL cc_start: 0.8849 (t) cc_final: 0.8518 (p) REVERT: B 342 GLU cc_start: 0.7536 (tt0) cc_final: 0.7231 (tt0) REVERT: B 349 ARG cc_start: 0.7086 (ttm170) cc_final: 0.6729 (mtt90) REVERT: B 373 THR cc_start: 0.8074 (m) cc_final: 0.7833 (p) REVERT: E 311 LYS cc_start: 0.7867 (tttt) cc_final: 0.7580 (ptpt) REVERT: E 314 ASP cc_start: 0.7875 (t70) cc_final: 0.7146 (t0) REVERT: E 317 LYS cc_start: 0.8465 (mttt) cc_final: 0.7981 (tttt) REVERT: E 321 LYS cc_start: 0.7569 (ptpt) cc_final: 0.6376 (pmtt) REVERT: E 342 GLU cc_start: 0.7732 (tt0) cc_final: 0.7399 (tt0) REVERT: E 349 ARG cc_start: 0.7033 (ttm170) cc_final: 0.5073 (pmt-80) REVERT: E 369 LYS cc_start: 0.8104 (pttm) cc_final: 0.7881 (ptpt) REVERT: E 370 LYS cc_start: 0.5879 (mmtp) cc_final: 0.5519 (ptmt) REVERT: F 317 LYS cc_start: 0.7930 (mttt) cc_final: 0.7619 (tttm) REVERT: F 340 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7742 (tptt) REVERT: F 342 GLU cc_start: 0.7461 (tt0) cc_final: 0.6852 (mp0) REVERT: F 348 ASP cc_start: 0.7648 (t0) cc_final: 0.6714 (p0) REVERT: F 370 LYS cc_start: 0.4482 (mmtp) cc_final: 0.3445 (pttt) REVERT: F 375 LYS cc_start: 0.8121 (ptpt) cc_final: 0.7911 (ptmt) outliers start: 4 outliers final: 1 residues processed: 137 average time/residue: 2.8061 time to fit residues: 393.4456 Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3366 Z= 0.264 Angle : 0.584 5.590 4500 Z= 0.294 Chirality : 0.052 0.145 504 Planarity : 0.005 0.059 570 Dihedral : 5.387 14.783 444 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.59 % Allowed : 21.96 % Favored : 76.46 % 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: -1.57 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.008 0.002 PHE B 378 TYR 0.013 0.002 TYR A 310 ARG 0.005 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.9021 (p) cc_final: 0.8790 (p) REVERT: A 317 LYS cc_start: 0.7680 (mttt) cc_final: 0.7248 (tttm) REVERT: A 342 GLU cc_start: 0.7217 (tt0) cc_final: 0.6638 (mp0) REVERT: A 349 ARG cc_start: 0.7077 (mtm-85) cc_final: 0.6616 (mtm-85) REVERT: A 375 LYS cc_start: 0.7859 (ptpt) cc_final: 0.7448 (ptmt) REVERT: D 317 LYS cc_start: 0.7624 (mttt) cc_final: 0.7047 (tttm) REVERT: D 342 GLU cc_start: 0.7539 (tt0) cc_final: 0.7120 (mp0) REVERT: D 349 ARG cc_start: 0.7233 (ttm170) cc_final: 0.5281 (tpt90) REVERT: D 375 LYS cc_start: 0.8010 (ptpt) cc_final: 0.7672 (ptmt) REVERT: C 317 LYS cc_start: 0.8384 (mttt) cc_final: 0.7672 (tttt) REVERT: C 321 LYS cc_start: 0.7755 (ptpt) cc_final: 0.7328 (pttt) REVERT: C 340 LYS cc_start: 0.7378 (mttt) cc_final: 0.7082 (mtpt) REVERT: C 342 GLU cc_start: 0.7561 (tt0) cc_final: 0.7096 (tt0) REVERT: C 349 ARG cc_start: 0.7169 (ttm170) cc_final: 0.5661 (mmp-170) REVERT: B 314 ASP cc_start: 0.7949 (t70) cc_final: 0.7492 (t0) REVERT: B 317 LYS cc_start: 0.8314 (mttt) cc_final: 0.7467 (tttt) REVERT: B 342 GLU cc_start: 0.7591 (tt0) cc_final: 0.7254 (tt0) REVERT: B 373 THR cc_start: 0.8134 (m) cc_final: 0.7858 (p) REVERT: E 311 LYS cc_start: 0.7842 (tttt) cc_final: 0.7589 (ptpt) REVERT: E 314 ASP cc_start: 0.7993 (t70) cc_final: 0.7307 (t0) REVERT: E 317 LYS cc_start: 0.8501 (mttt) cc_final: 0.7982 (tttt) REVERT: E 321 LYS cc_start: 0.7586 (ptpt) cc_final: 0.6371 (pmtt) REVERT: E 342 GLU cc_start: 0.7773 (tt0) cc_final: 0.7448 (tt0) REVERT: E 369 LYS cc_start: 0.8108 (pttm) cc_final: 0.7170 (pmtt) REVERT: E 370 LYS cc_start: 0.5822 (mmtp) cc_final: 0.5440 (ptmt) REVERT: F 317 LYS cc_start: 0.7969 (mttt) cc_final: 0.7673 (tttt) REVERT: F 324 SER cc_start: 0.8262 (p) cc_final: 0.7953 (p) REVERT: F 340 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7708 (tptt) REVERT: F 342 GLU cc_start: 0.7449 (tt0) cc_final: 0.6842 (mp0) REVERT: F 348 ASP cc_start: 0.7701 (t0) cc_final: 0.6756 (p0) REVERT: F 375 LYS cc_start: 0.8196 (ptpt) cc_final: 0.7965 (ptmt) outliers start: 6 outliers final: 1 residues processed: 132 average time/residue: 2.9000 time to fit residues: 391.4354 Evaluate side-chains 127 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3366 Z= 0.147 Angle : 0.543 6.067 4500 Z= 0.267 Chirality : 0.052 0.131 504 Planarity : 0.005 0.056 570 Dihedral : 5.015 14.623 444 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.26 % Allowed : 21.96 % Favored : 77.78 % 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: -1.50 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.008 0.002 PHE B 346 TYR 0.009 0.001 TYR A 310 ARG 0.010 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8961 (p) cc_final: 0.8720 (p) REVERT: A 317 LYS cc_start: 0.7746 (mttt) cc_final: 0.7275 (tttt) REVERT: A 342 GLU cc_start: 0.7242 (tt0) cc_final: 0.6729 (mp0) REVERT: A 349 ARG cc_start: 0.7040 (mtm-85) cc_final: 0.6740 (mtm-85) REVERT: A 375 LYS cc_start: 0.7827 (ptpt) cc_final: 0.7446 (ptmt) REVERT: D 317 LYS cc_start: 0.7619 (mttt) cc_final: 0.7035 (tttm) REVERT: D 342 GLU cc_start: 0.7541 (tt0) cc_final: 0.7127 (mp0) REVERT: D 349 ARG cc_start: 0.7204 (ttm170) cc_final: 0.5208 (tpt90) REVERT: D 356 SER cc_start: 0.8960 (m) cc_final: 0.8319 (p) REVERT: D 375 LYS cc_start: 0.7954 (ptpt) cc_final: 0.7637 (ptmt) REVERT: C 311 LYS cc_start: 0.7763 (mmtt) cc_final: 0.6607 (mmpt) REVERT: C 317 LYS cc_start: 0.8417 (mttt) cc_final: 0.7669 (tttt) REVERT: C 321 LYS cc_start: 0.7728 (ptpt) cc_final: 0.7298 (pttt) REVERT: C 336 GLN cc_start: 0.7313 (tt0) cc_final: 0.6270 (mp10) REVERT: C 340 LYS cc_start: 0.7359 (mttt) cc_final: 0.7077 (mtpt) REVERT: C 342 GLU cc_start: 0.7567 (tt0) cc_final: 0.7098 (tt0) REVERT: C 349 ARG cc_start: 0.7206 (ttm170) cc_final: 0.5649 (mmp-170) REVERT: C 373 THR cc_start: 0.8271 (m) cc_final: 0.7918 (p) REVERT: B 314 ASP cc_start: 0.7878 (t70) cc_final: 0.7359 (t0) REVERT: B 317 LYS cc_start: 0.8323 (mttt) cc_final: 0.7462 (tttt) REVERT: B 342 GLU cc_start: 0.7572 (tt0) cc_final: 0.7247 (tt0) REVERT: B 373 THR cc_start: 0.8093 (m) cc_final: 0.7846 (p) REVERT: E 311 LYS cc_start: 0.7859 (tttt) cc_final: 0.7599 (ptpt) REVERT: E 314 ASP cc_start: 0.7896 (t70) cc_final: 0.7245 (t0) REVERT: E 317 LYS cc_start: 0.8484 (mttt) cc_final: 0.7964 (tttt) REVERT: E 321 LYS cc_start: 0.7584 (ptpt) cc_final: 0.6368 (pmtt) REVERT: E 342 GLU cc_start: 0.7766 (tt0) cc_final: 0.7460 (tt0) REVERT: E 369 LYS cc_start: 0.8106 (pttm) cc_final: 0.7882 (ptpt) REVERT: E 370 LYS cc_start: 0.5817 (mmtp) cc_final: 0.5452 (ptmt) REVERT: F 311 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7209 (mttt) REVERT: F 317 LYS cc_start: 0.7936 (mttt) cc_final: 0.7666 (tttt) REVERT: F 324 SER cc_start: 0.8192 (p) cc_final: 0.7882 (p) REVERT: F 340 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7711 (tptt) REVERT: F 342 GLU cc_start: 0.7417 (tt0) cc_final: 0.6861 (mp0) REVERT: F 348 ASP cc_start: 0.7718 (t0) cc_final: 0.6761 (p0) REVERT: F 375 LYS cc_start: 0.8156 (ptpt) cc_final: 0.7950 (ptmt) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 2.7553 time to fit residues: 363.8331 Evaluate side-chains 127 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3366 Z= 0.174 Angle : 0.537 5.675 4500 Z= 0.266 Chirality : 0.051 0.133 504 Planarity : 0.006 0.079 570 Dihedral : 4.969 15.099 444 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.53 % Allowed : 22.22 % Favored : 77.25 % 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: -1.50 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.007 0.002 PHE C 346 TYR 0.012 0.002 TYR A 310 ARG 0.015 0.002 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8954 (p) cc_final: 0.8714 (p) REVERT: A 317 LYS cc_start: 0.7769 (mttt) cc_final: 0.7284 (tttt) REVERT: A 342 GLU cc_start: 0.7213 (tt0) cc_final: 0.6716 (mp0) REVERT: A 349 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.6778 (mtm-85) REVERT: A 375 LYS cc_start: 0.7798 (ptpt) cc_final: 0.7430 (ptmt) REVERT: D 317 LYS cc_start: 0.7619 (mttt) cc_final: 0.7031 (tttm) REVERT: D 342 GLU cc_start: 0.7535 (tt0) cc_final: 0.7279 (tt0) REVERT: D 349 ARG cc_start: 0.7190 (ttm170) cc_final: 0.5228 (tpt90) REVERT: D 356 SER cc_start: 0.8969 (m) cc_final: 0.8343 (p) REVERT: D 375 LYS cc_start: 0.7866 (ptpt) cc_final: 0.7566 (ptmt) REVERT: C 311 LYS cc_start: 0.7731 (mmtt) cc_final: 0.6683 (mmpt) REVERT: C 317 LYS cc_start: 0.8409 (mttt) cc_final: 0.7686 (tttt) REVERT: C 321 LYS cc_start: 0.7763 (ptpt) cc_final: 0.7325 (pttt) REVERT: C 336 GLN cc_start: 0.7316 (tt0) cc_final: 0.6273 (mp10) REVERT: C 340 LYS cc_start: 0.7343 (mttt) cc_final: 0.7048 (mtpt) REVERT: C 342 GLU cc_start: 0.7575 (tt0) cc_final: 0.7102 (tt0) REVERT: C 349 ARG cc_start: 0.7185 (ttm170) cc_final: 0.5606 (mmp-170) REVERT: C 373 THR cc_start: 0.8279 (m) cc_final: 0.7959 (p) REVERT: B 314 ASP cc_start: 0.7878 (t70) cc_final: 0.7288 (t0) REVERT: B 317 LYS cc_start: 0.8323 (mttt) cc_final: 0.7452 (tttt) REVERT: B 342 GLU cc_start: 0.7573 (tt0) cc_final: 0.7237 (tt0) REVERT: B 373 THR cc_start: 0.8091 (m) cc_final: 0.7831 (p) REVERT: B 375 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7616 (ptmt) REVERT: E 311 LYS cc_start: 0.7886 (tttt) cc_final: 0.7616 (ptpt) REVERT: E 314 ASP cc_start: 0.7933 (t70) cc_final: 0.7327 (t0) REVERT: E 317 LYS cc_start: 0.8469 (mttt) cc_final: 0.7931 (tmtp) REVERT: E 321 LYS cc_start: 0.7579 (ptpt) cc_final: 0.6367 (pmtt) REVERT: E 342 GLU cc_start: 0.7765 (tt0) cc_final: 0.7452 (tt0) REVERT: E 369 LYS cc_start: 0.8104 (pttm) cc_final: 0.7887 (ptpt) REVERT: E 370 LYS cc_start: 0.5816 (mmtp) cc_final: 0.5453 (ptmt) REVERT: F 311 LYS cc_start: 0.7730 (mtmt) cc_final: 0.7180 (mttt) REVERT: F 317 LYS cc_start: 0.7943 (mttt) cc_final: 0.7652 (tttt) REVERT: F 324 SER cc_start: 0.8239 (p) cc_final: 0.7933 (p) REVERT: F 340 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7677 (tptt) REVERT: F 342 GLU cc_start: 0.7420 (tt0) cc_final: 0.6819 (mp0) REVERT: F 349 ARG cc_start: 0.7192 (mtm-85) cc_final: 0.6577 (mtp85) REVERT: F 375 LYS cc_start: 0.8167 (ptpt) cc_final: 0.7956 (ptmt) outliers start: 2 outliers final: 2 residues processed: 128 average time/residue: 2.8143 time to fit residues: 369.0280 Evaluate side-chains 127 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3366 Z= 0.133 Angle : 0.525 5.811 4500 Z= 0.257 Chirality : 0.052 0.139 504 Planarity : 0.006 0.088 570 Dihedral : 4.634 14.644 444 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.26 % Allowed : 22.49 % Favored : 77.25 % 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 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.007 0.001 PHE C 346 TYR 0.006 0.001 TYR A 310 ARG 0.012 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8950 (p) cc_final: 0.8713 (p) REVERT: A 317 LYS cc_start: 0.7779 (mttt) cc_final: 0.7308 (tttt) REVERT: A 342 GLU cc_start: 0.7212 (tt0) cc_final: 0.6729 (mp0) REVERT: A 349 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.6755 (mtm-85) REVERT: A 375 LYS cc_start: 0.7737 (ptpt) cc_final: 0.7393 (ptmt) REVERT: D 317 LYS cc_start: 0.7581 (mttt) cc_final: 0.7001 (tttm) REVERT: D 342 GLU cc_start: 0.7545 (tt0) cc_final: 0.7255 (tt0) REVERT: D 349 ARG cc_start: 0.7115 (ttm170) cc_final: 0.5160 (tpt90) REVERT: D 356 SER cc_start: 0.8932 (m) cc_final: 0.8322 (p) REVERT: D 375 LYS cc_start: 0.7849 (ptpt) cc_final: 0.7547 (ptmt) REVERT: C 311 LYS cc_start: 0.7595 (mmtt) cc_final: 0.6544 (mmpt) REVERT: C 317 LYS cc_start: 0.8400 (mttt) cc_final: 0.7661 (tttt) REVERT: C 321 LYS cc_start: 0.7749 (ptpt) cc_final: 0.7307 (pttt) REVERT: C 336 GLN cc_start: 0.7287 (tt0) cc_final: 0.6288 (mp10) REVERT: C 340 LYS cc_start: 0.7329 (mttt) cc_final: 0.7034 (mtpt) REVERT: C 342 GLU cc_start: 0.7538 (tt0) cc_final: 0.7064 (tt0) REVERT: C 349 ARG cc_start: 0.7146 (ttm170) cc_final: 0.5727 (mmp-170) REVERT: C 351 GLN cc_start: 0.7927 (mt0) cc_final: 0.7685 (mt0) REVERT: C 373 THR cc_start: 0.8258 (m) cc_final: 0.7967 (p) REVERT: B 314 ASP cc_start: 0.7812 (t70) cc_final: 0.7217 (t0) REVERT: B 317 LYS cc_start: 0.8330 (mttt) cc_final: 0.7464 (tttt) REVERT: B 342 GLU cc_start: 0.7536 (tt0) cc_final: 0.7223 (tt0) REVERT: B 373 THR cc_start: 0.8056 (m) cc_final: 0.7815 (p) REVERT: B 375 LYS cc_start: 0.8098 (ptpt) cc_final: 0.7609 (ptmt) REVERT: E 311 LYS cc_start: 0.7884 (tttt) cc_final: 0.7610 (ptpt) REVERT: E 314 ASP cc_start: 0.7872 (t70) cc_final: 0.6987 (t0) REVERT: E 317 LYS cc_start: 0.8447 (mttt) cc_final: 0.7942 (tmtp) REVERT: E 321 LYS cc_start: 0.7589 (ptpt) cc_final: 0.6382 (pmtt) REVERT: E 369 LYS cc_start: 0.8156 (pttm) cc_final: 0.7920 (ptpt) REVERT: E 370 LYS cc_start: 0.5831 (mmtp) cc_final: 0.5515 (ptmt) REVERT: F 311 LYS cc_start: 0.7758 (mtmt) cc_final: 0.7198 (mttt) REVERT: F 317 LYS cc_start: 0.7953 (mttt) cc_final: 0.7662 (tttt) REVERT: F 324 SER cc_start: 0.8149 (p) cc_final: 0.7814 (p) REVERT: F 340 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7723 (tptt) REVERT: F 342 GLU cc_start: 0.7381 (tt0) cc_final: 0.6777 (mp0) REVERT: F 375 LYS cc_start: 0.8140 (ptpt) cc_final: 0.7886 (ptmt) outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 2.7523 time to fit residues: 358.1022 Evaluate side-chains 125 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3366 Z= 0.134 Angle : 0.512 5.754 4500 Z= 0.250 Chirality : 0.051 0.124 504 Planarity : 0.006 0.092 570 Dihedral : 4.527 14.436 444 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.26 % Allowed : 23.02 % Favored : 76.72 % 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: -1.36 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.007 0.001 PHE B 346 TYR 0.008 0.001 TYR A 310 ARG 0.014 0.001 ARG F 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8911 (p) cc_final: 0.8664 (p) REVERT: A 317 LYS cc_start: 0.7794 (mttt) cc_final: 0.7313 (tttt) REVERT: A 342 GLU cc_start: 0.7200 (tt0) cc_final: 0.6685 (mp0) REVERT: A 375 LYS cc_start: 0.7734 (ptpt) cc_final: 0.7402 (ptmt) REVERT: D 317 LYS cc_start: 0.7585 (mttt) cc_final: 0.7029 (tttt) REVERT: D 342 GLU cc_start: 0.7524 (tt0) cc_final: 0.7257 (tt0) REVERT: D 344 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7998 (tt) REVERT: D 349 ARG cc_start: 0.7076 (ttm170) cc_final: 0.5138 (tpt90) REVERT: D 356 SER cc_start: 0.8921 (m) cc_final: 0.8336 (p) REVERT: D 375 LYS cc_start: 0.7810 (ptpt) cc_final: 0.7515 (ptmt) REVERT: C 311 LYS cc_start: 0.7524 (mmtt) cc_final: 0.6480 (mmpt) REVERT: C 317 LYS cc_start: 0.8403 (mttt) cc_final: 0.7666 (tttt) REVERT: C 321 LYS cc_start: 0.7768 (ptpt) cc_final: 0.7323 (pttt) REVERT: C 336 GLN cc_start: 0.7272 (tt0) cc_final: 0.6299 (mp10) REVERT: C 340 LYS cc_start: 0.7328 (mttt) cc_final: 0.7020 (mtpt) REVERT: C 342 GLU cc_start: 0.7544 (tt0) cc_final: 0.7069 (tt0) REVERT: C 349 ARG cc_start: 0.7135 (ttm170) cc_final: 0.5734 (mmp-170) REVERT: C 351 GLN cc_start: 0.7921 (mt0) cc_final: 0.7698 (mt0) REVERT: C 373 THR cc_start: 0.8251 (m) cc_final: 0.7981 (p) REVERT: B 314 ASP cc_start: 0.7763 (t70) cc_final: 0.7159 (t0) REVERT: B 317 LYS cc_start: 0.8366 (mttt) cc_final: 0.7493 (tttt) REVERT: B 342 GLU cc_start: 0.7549 (tt0) cc_final: 0.7220 (tt0) REVERT: B 373 THR cc_start: 0.8087 (m) cc_final: 0.7841 (p) REVERT: B 375 LYS cc_start: 0.8100 (ptpt) cc_final: 0.7836 (ptpt) REVERT: E 311 LYS cc_start: 0.7879 (tttt) cc_final: 0.7611 (ptpt) REVERT: E 314 ASP cc_start: 0.7943 (t70) cc_final: 0.7063 (t0) REVERT: E 317 LYS cc_start: 0.8406 (mttt) cc_final: 0.7902 (tmtp) REVERT: E 321 LYS cc_start: 0.7568 (ptpt) cc_final: 0.6356 (pmtt) REVERT: E 369 LYS cc_start: 0.8146 (pttm) cc_final: 0.7916 (ptpt) REVERT: E 370 LYS cc_start: 0.5818 (mmtp) cc_final: 0.5506 (ptmt) REVERT: F 311 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7181 (mttt) REVERT: F 317 LYS cc_start: 0.7944 (mttt) cc_final: 0.7674 (tttt) REVERT: F 324 SER cc_start: 0.8161 (p) cc_final: 0.7851 (p) REVERT: F 340 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7659 (tptt) REVERT: F 342 GLU cc_start: 0.7359 (tt0) cc_final: 0.6748 (mp0) REVERT: F 349 ARG cc_start: 0.7141 (mtm-85) cc_final: 0.6705 (mtp85) REVERT: F 375 LYS cc_start: 0.8134 (ptpt) cc_final: 0.7898 (ptmt) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 2.8231 time to fit residues: 367.3591 Evaluate side-chains 126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.178681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.166876 restraints weight = 12311.578| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 1.71 r_work: 0.3999 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3366 Z= 0.169 Angle : 0.527 5.280 4500 Z= 0.260 Chirality : 0.051 0.132 504 Planarity : 0.006 0.095 570 Dihedral : 4.568 14.624 444 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.53 % Allowed : 23.02 % Favored : 76.46 % 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: -1.38 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 374 PHE 0.007 0.001 PHE B 378 TYR 0.009 0.002 TYR A 310 ARG 0.010 0.001 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6151.68 seconds wall clock time: 109 minutes 17.82 seconds (6557.82 seconds total)