Starting phenix.real_space_refine on Mon Mar 11 02:59:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9e_18278/03_2024/8q9e_18278.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9e_18278/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9e_18278/03_2024/8q9e_18278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9e_18278/03_2024/8q9e_18278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9e_18278/03_2024/8q9e_18278.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9e_18278/03_2024/8q9e_18278.pdb" } 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 Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.16, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 4.43 Conformation dependent library (CDL) restraints added in 653.9 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: 0.55 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: 2.04 Time building geometry restraints manager: 4.66 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: 96.25 - 102.94: 23 102.94 - 109.64: 5484 109.64 - 116.34: 3478 116.34 - 123.03: 2862 123.03 - 129.73: 591 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 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.571 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.578 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.580 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.601 1.850 ... (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 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: 2.380 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: 0.100 Extract box with map and model: 11.820 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.910 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.670 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 0.579 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: 2.3372 time to fit residues: 415.0363 Evaluate side-chains 138 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 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 B 327 ASN B 351 GLN E 327 ASN F 351 GLN F 359 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3366 Z= 0.246 Angle : 0.778 7.497 4500 Z= 0.411 Chirality : 0.054 0.146 504 Planarity : 0.004 0.034 570 Dihedral : 7.543 23.427 444 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -1.51 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.014 0.002 PHE B 378 TYR 0.011 0.002 TYR A 310 ARG 0.005 0.001 ARG F 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 fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8988 (p) cc_final: 0.8783 (p) REVERT: A 317 LYS cc_start: 0.7567 (mttt) cc_final: 0.7133 (tttm) REVERT: A 342 GLU cc_start: 0.7211 (tt0) cc_final: 0.6918 (tt0) REVERT: A 375 LYS cc_start: 0.7896 (ptpt) cc_final: 0.7497 (ptmt) REVERT: D 317 LYS cc_start: 0.7570 (mttt) cc_final: 0.7039 (tttm) REVERT: D 342 GLU cc_start: 0.7373 (tt0) cc_final: 0.6906 (mp0) REVERT: D 349 ARG cc_start: 0.7219 (ttm170) cc_final: 0.5324 (tpt90) REVERT: D 375 LYS cc_start: 0.7893 (ptpt) cc_final: 0.7563 (ptmt) REVERT: C 317 LYS cc_start: 0.8180 (mttt) cc_final: 0.7452 (tttt) REVERT: C 318 VAL cc_start: 0.8917 (t) cc_final: 0.8712 (p) REVERT: C 321 LYS cc_start: 0.7732 (ptpt) cc_final: 0.7145 (pttt) REVERT: C 340 LYS cc_start: 0.7383 (mttt) cc_final: 0.7112 (mtpt) REVERT: C 342 GLU cc_start: 0.7560 (tt0) cc_final: 0.7163 (tt0) REVERT: B 311 LYS cc_start: 0.7667 (tttt) cc_final: 0.7363 (pttt) REVERT: B 317 LYS cc_start: 0.8245 (mttt) cc_final: 0.7476 (tttt) REVERT: B 321 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7102 (pttt) REVERT: B 342 GLU cc_start: 0.7518 (tt0) cc_final: 0.7100 (tt0) REVERT: B 349 ARG cc_start: 0.7028 (ttm170) cc_final: 0.6773 (mtp85) REVERT: B 373 THR cc_start: 0.8187 (m) cc_final: 0.7915 (p) REVERT: B 375 LYS cc_start: 0.8004 (ptpt) cc_final: 0.7734 (ptpt) REVERT: E 311 LYS cc_start: 0.7888 (tttt) cc_final: 0.7659 (ptpt) REVERT: E 317 LYS cc_start: 0.8468 (mttt) cc_final: 0.7951 (tttt) REVERT: E 321 LYS cc_start: 0.7481 (ptpt) cc_final: 0.6346 (pmtt) REVERT: E 342 GLU cc_start: 0.7726 (tt0) cc_final: 0.7420 (tt0) REVERT: E 349 ARG cc_start: 0.6852 (ttm170) cc_final: 0.5022 (pmt-80) REVERT: E 351 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: E 369 LYS cc_start: 0.8126 (pttm) cc_final: 0.7125 (pmtt) REVERT: E 370 LYS cc_start: 0.5938 (mmtp) cc_final: 0.5483 (ptmt) REVERT: F 317 LYS cc_start: 0.7971 (mttt) cc_final: 0.7682 (tttm) REVERT: F 342 GLU cc_start: 0.7618 (tt0) cc_final: 0.7057 (mp0) REVERT: F 370 LYS cc_start: 0.4461 (mmtp) cc_final: 0.3344 (pttt) REVERT: F 375 LYS cc_start: 0.8140 (ptpt) cc_final: 0.7871 (ptmt) outliers start: 13 outliers final: 4 residues processed: 142 average time/residue: 2.6500 time to fit residues: 385.3379 Evaluate side-chains 141 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 316 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3366 Z= 0.184 Angle : 0.637 6.620 4500 Z= 0.326 Chirality : 0.052 0.133 504 Planarity : 0.005 0.046 570 Dihedral : 6.387 18.541 444 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.91 % Allowed : 16.40 % 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: -1.50 (0.34), 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 B 330 PHE 0.010 0.002 PHE B 378 TYR 0.010 0.002 TYR A 310 ARG 0.006 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 154 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 316 SER cc_start: 0.9053 (p) cc_final: 0.8800 (p) REVERT: A 317 LYS cc_start: 0.7594 (mttt) cc_final: 0.7206 (tttt) REVERT: A 342 GLU cc_start: 0.7254 (tt0) cc_final: 0.6595 (mp0) REVERT: A 375 LYS cc_start: 0.7882 (ptpt) cc_final: 0.7512 (ptmt) REVERT: D 317 LYS cc_start: 0.7581 (mttt) cc_final: 0.7039 (tttm) REVERT: D 342 GLU cc_start: 0.7482 (tt0) cc_final: 0.6981 (mp0) REVERT: D 349 ARG cc_start: 0.7204 (ttm170) cc_final: 0.5337 (tpt90) REVERT: D 375 LYS cc_start: 0.7911 (ptpt) cc_final: 0.7574 (ptmt) REVERT: C 317 LYS cc_start: 0.8238 (mttt) cc_final: 0.7535 (tttt) REVERT: C 318 VAL cc_start: 0.8941 (t) cc_final: 0.8704 (p) REVERT: C 321 LYS cc_start: 0.7784 (ptpt) cc_final: 0.7409 (pttt) REVERT: C 340 LYS cc_start: 0.7373 (mttt) cc_final: 0.7063 (mtpt) REVERT: C 342 GLU cc_start: 0.7545 (tt0) cc_final: 0.7134 (tt0) REVERT: B 311 LYS cc_start: 0.7671 (tttt) cc_final: 0.7350 (pttt) REVERT: B 317 LYS cc_start: 0.8231 (mttt) cc_final: 0.7459 (tttt) REVERT: B 321 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7060 (pttt) REVERT: B 342 GLU cc_start: 0.7534 (tt0) cc_final: 0.7159 (tt0) REVERT: B 349 ARG cc_start: 0.6967 (ttm170) cc_final: 0.6754 (mtp85) REVERT: B 373 THR cc_start: 0.8184 (m) cc_final: 0.7921 (p) REVERT: B 375 LYS cc_start: 0.7955 (ptpt) cc_final: 0.7720 (ptpt) REVERT: E 311 LYS cc_start: 0.7880 (tttt) cc_final: 0.7628 (ptpt) REVERT: E 317 LYS cc_start: 0.8474 (mttt) cc_final: 0.7960 (tttt) REVERT: E 321 LYS cc_start: 0.7547 (ptpt) cc_final: 0.6410 (pmtt) REVERT: E 342 GLU cc_start: 0.7760 (tt0) cc_final: 0.7428 (tt0) REVERT: E 349 ARG cc_start: 0.6818 (ttm170) cc_final: 0.4978 (pmt-80) REVERT: E 351 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: E 370 LYS cc_start: 0.5947 (mmtp) cc_final: 0.5553 (ptmt) REVERT: F 317 LYS cc_start: 0.7956 (mttt) cc_final: 0.7686 (tttm) REVERT: F 342 GLU cc_start: 0.7612 (tt0) cc_final: 0.6983 (mp0) REVERT: F 370 LYS cc_start: 0.4529 (mmtp) cc_final: 0.3433 (pttt) REVERT: F 375 LYS cc_start: 0.8105 (ptpt) cc_final: 0.7879 (ptmt) outliers start: 11 outliers final: 6 residues processed: 146 average time/residue: 2.4791 time to fit residues: 371.0595 Evaluate side-chains 143 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 316 SER 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: 1.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.0050 chunk 0 optimal weight: 6.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN B 351 GLN F 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3366 Z= 0.150 Angle : 0.576 5.725 4500 Z= 0.288 Chirality : 0.051 0.129 504 Planarity : 0.004 0.044 570 Dihedral : 5.600 15.205 444 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.12 % Allowed : 19.31 % Favored : 78.57 % 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: -1.47 (0.34), 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 0.002 0.001 HIS C 374 PHE 0.009 0.002 PHE B 378 TYR 0.008 0.001 TYR A 310 ARG 0.005 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 147 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 0.797 Fit side-chains 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: 0.7626 (mttt) cc_final: 0.7205 (tttm) REVERT: A 342 GLU cc_start: 0.7195 (tt0) cc_final: 0.6611 (mp0) REVERT: A 349 ARG cc_start: 0.7091 (mtm-85) cc_final: 0.6799 (mtm-85) REVERT: A 375 LYS cc_start: 0.7870 (ptpt) cc_final: 0.7482 (ptmt) REVERT: D 317 LYS cc_start: 0.7605 (mttt) cc_final: 0.7063 (tttm) REVERT: D 342 GLU cc_start: 0.7498 (tt0) cc_final: 0.7048 (mp0) REVERT: D 349 ARG cc_start: 0.7223 (ttm170) cc_final: 0.5183 (tpt90) REVERT: D 375 LYS cc_start: 0.7956 (ptpt) cc_final: 0.7625 (ptmt) REVERT: C 317 LYS cc_start: 0.8296 (mttt) cc_final: 0.7566 (tttt) REVERT: C 318 VAL cc_start: 0.8932 (t) cc_final: 0.8671 (p) REVERT: C 321 LYS cc_start: 0.7783 (ptpt) cc_final: 0.7408 (pttt) REVERT: C 336 GLN cc_start: 0.7197 (tt0) cc_final: 0.6213 (mp10) REVERT: C 340 LYS cc_start: 0.7361 (mttt) cc_final: 0.7049 (mtpt) REVERT: C 342 GLU cc_start: 0.7555 (tt0) cc_final: 0.7126 (tt0) REVERT: B 311 LYS cc_start: 0.7665 (tttt) cc_final: 0.7349 (pttt) REVERT: B 317 LYS cc_start: 0.8248 (mttt) cc_final: 0.7444 (tttt) REVERT: B 321 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7076 (pttt) REVERT: B 342 GLU cc_start: 0.7549 (tt0) cc_final: 0.7179 (tt0) REVERT: B 373 THR cc_start: 0.8189 (m) cc_final: 0.7915 (p) REVERT: B 375 LYS cc_start: 0.7921 (ptpt) cc_final: 0.7652 (ptpt) REVERT: E 311 LYS cc_start: 0.7890 (tttt) cc_final: 0.7605 (ptpt) REVERT: E 317 LYS cc_start: 0.8453 (mttt) cc_final: 0.7961 (tttt) REVERT: E 321 LYS cc_start: 0.7567 (ptpt) cc_final: 0.6453 (pmtt) REVERT: E 342 GLU cc_start: 0.7719 (tt0) cc_final: 0.7391 (tt0) REVERT: E 349 ARG cc_start: 0.6805 (ttm170) cc_final: 0.5013 (pmt-80) REVERT: E 351 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: E 370 LYS cc_start: 0.5906 (mmtp) cc_final: 0.5538 (ptmt) REVERT: F 317 LYS cc_start: 0.7964 (mttt) cc_final: 0.7679 (tttm) REVERT: F 342 GLU cc_start: 0.7520 (tt0) cc_final: 0.6951 (mp0) REVERT: F 370 LYS cc_start: 0.4472 (mmtp) cc_final: 0.3439 (pttt) REVERT: F 375 LYS cc_start: 0.8094 (ptpt) cc_final: 0.7878 (ptmt) outliers start: 8 outliers final: 4 residues processed: 141 average time/residue: 2.6063 time to fit residues: 376.8843 Evaluate side-chains 140 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 316 SER 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 351 GLN Chi-restraints excluded: chain F residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN C 359 ASN B 351 GLN B 359 ASN E 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4717 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= 0.294 Angle : 0.624 5.688 4500 Z= 0.317 Chirality : 0.052 0.152 504 Planarity : 0.005 0.047 570 Dihedral : 5.663 15.234 444 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.44 % Allowed : 17.72 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 330 PHE 0.010 0.002 PHE B 378 TYR 0.014 0.002 TYR A 310 ARG 0.006 0.001 ARG E 349 *********************** 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 143 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7656 (mttt) cc_final: 0.7200 (tttm) REVERT: A 342 GLU cc_start: 0.7241 (tt0) cc_final: 0.6570 (mp0) REVERT: A 375 LYS cc_start: 0.7877 (ptpt) cc_final: 0.7494 (ptmt) REVERT: D 317 LYS cc_start: 0.7641 (mttt) cc_final: 0.7037 (tttm) REVERT: D 342 GLU cc_start: 0.7543 (tt0) cc_final: 0.7062 (mp0) REVERT: D 349 ARG cc_start: 0.7233 (ttm170) cc_final: 0.5344 (tpt90) REVERT: D 375 LYS cc_start: 0.7966 (ptpt) cc_final: 0.7647 (ptmt) REVERT: C 317 LYS cc_start: 0.8326 (mttt) cc_final: 0.7617 (tttt) REVERT: C 321 LYS cc_start: 0.7792 (ptpt) cc_final: 0.7373 (pttt) REVERT: C 340 LYS cc_start: 0.7393 (mttt) cc_final: 0.7063 (mtpt) REVERT: C 349 ARG cc_start: 0.7342 (ttm170) cc_final: 0.5637 (mmp-170) REVERT: B 311 LYS cc_start: 0.7724 (tttt) cc_final: 0.7412 (pttt) REVERT: B 317 LYS cc_start: 0.8317 (mttt) cc_final: 0.7504 (tttt) REVERT: B 321 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.6949 (pttt) REVERT: B 342 GLU cc_start: 0.7587 (tt0) cc_final: 0.7205 (tt0) REVERT: B 373 THR cc_start: 0.8230 (m) cc_final: 0.7924 (p) REVERT: B 375 LYS cc_start: 0.7940 (ptpt) cc_final: 0.7660 (ptpt) REVERT: E 311 LYS cc_start: 0.7889 (tttt) cc_final: 0.7620 (ptpt) REVERT: E 317 LYS cc_start: 0.8490 (mttt) cc_final: 0.7947 (tttt) REVERT: E 321 LYS cc_start: 0.7605 (ptpt) cc_final: 0.6446 (pmtt) REVERT: E 342 GLU cc_start: 0.7851 (tt0) cc_final: 0.7460 (tt0) REVERT: E 349 ARG cc_start: 0.6985 (ttm170) cc_final: 0.4962 (pmt-80) REVERT: E 369 LYS cc_start: 0.8372 (ptpt) cc_final: 0.7250 (pptt) REVERT: E 370 LYS cc_start: 0.5884 (mmtp) cc_final: 0.5463 (ptmt) REVERT: F 317 LYS cc_start: 0.7976 (mttt) cc_final: 0.7648 (tttm) REVERT: F 342 GLU cc_start: 0.7579 (tt0) cc_final: 0.6936 (mp0) REVERT: F 370 LYS cc_start: 0.4444 (mmtp) cc_final: 0.3292 (pttt) REVERT: F 375 LYS cc_start: 0.8170 (ptpt) cc_final: 0.7924 (ptmt) outliers start: 13 outliers final: 5 residues processed: 135 average time/residue: 2.6783 time to fit residues: 370.6686 Evaluate side-chains 134 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 316 SER 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 Chi-restraints excluded: chain F residue 316 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3366 Z= 0.198 Angle : 0.578 6.016 4500 Z= 0.287 Chirality : 0.051 0.135 504 Planarity : 0.005 0.059 570 Dihedral : 5.326 13.783 444 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.38 % Allowed : 19.58 % Favored : 78.04 % 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: -1.63 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.009 0.002 PHE B 378 TYR 0.009 0.002 TYR A 310 ARG 0.006 0.001 ARG D 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 141 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7656 (mttt) cc_final: 0.7220 (tttm) REVERT: A 342 GLU cc_start: 0.7271 (tt0) cc_final: 0.6729 (mp0) REVERT: A 375 LYS cc_start: 0.7844 (ptpt) cc_final: 0.7444 (ptmt) REVERT: D 311 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7287 (mtpt) REVERT: D 317 LYS cc_start: 0.7623 (mttt) cc_final: 0.6999 (tttm) REVERT: D 342 GLU cc_start: 0.7558 (tt0) cc_final: 0.7140 (tt0) REVERT: D 349 ARG cc_start: 0.7254 (ttm170) cc_final: 0.5282 (tpt90) REVERT: D 375 LYS cc_start: 0.7978 (ptpt) cc_final: 0.7637 (ptmt) REVERT: C 317 LYS cc_start: 0.8333 (mttt) cc_final: 0.7628 (tttt) REVERT: C 321 LYS cc_start: 0.7751 (ptpt) cc_final: 0.7307 (pttt) REVERT: C 340 LYS cc_start: 0.7375 (mttt) cc_final: 0.7091 (mtpt) REVERT: C 349 ARG cc_start: 0.7298 (ttm170) cc_final: 0.5682 (mmp-170) REVERT: B 311 LYS cc_start: 0.7726 (tttt) cc_final: 0.7415 (pttt) REVERT: B 317 LYS cc_start: 0.8315 (mttt) cc_final: 0.7468 (tttt) REVERT: B 342 GLU cc_start: 0.7578 (tt0) cc_final: 0.7209 (tt0) REVERT: B 373 THR cc_start: 0.8221 (m) cc_final: 0.7914 (p) REVERT: B 375 LYS cc_start: 0.7911 (ptpt) cc_final: 0.7588 (ptmt) REVERT: E 311 LYS cc_start: 0.7894 (tttt) cc_final: 0.7602 (ptpt) REVERT: E 317 LYS cc_start: 0.8493 (mttt) cc_final: 0.7939 (tttt) REVERT: E 321 LYS cc_start: 0.7623 (ptpt) cc_final: 0.6407 (pmtt) REVERT: E 342 GLU cc_start: 0.7797 (tt0) cc_final: 0.7417 (tt0) REVERT: E 370 LYS cc_start: 0.5863 (mmtp) cc_final: 0.5434 (ptmt) REVERT: F 317 LYS cc_start: 0.7965 (mttt) cc_final: 0.7640 (tttm) REVERT: F 324 SER cc_start: 0.8236 (p) cc_final: 0.7951 (p) REVERT: F 342 GLU cc_start: 0.7554 (tt0) cc_final: 0.6851 (mp0) REVERT: F 348 ASP cc_start: 0.7671 (t0) cc_final: 0.6667 (p0) REVERT: F 370 LYS cc_start: 0.4476 (mmtp) cc_final: 0.3355 (pttt) REVERT: F 375 LYS cc_start: 0.8168 (ptpt) cc_final: 0.7925 (ptmt) outliers start: 9 outliers final: 4 residues processed: 133 average time/residue: 2.6971 time to fit residues: 367.4220 Evaluate side-chains 135 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain F residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5120 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= 0.153 Angle : 0.536 5.762 4500 Z= 0.264 Chirality : 0.051 0.130 504 Planarity : 0.006 0.085 570 Dihedral : 5.001 13.314 444 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.59 % Allowed : 21.16 % 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: -1.58 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.008 0.002 PHE C 346 TYR 0.009 0.001 TYR A 310 ARG 0.011 0.001 ARG F 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 136 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7671 (mttt) cc_final: 0.7214 (tttm) REVERT: A 342 GLU cc_start: 0.7271 (tt0) cc_final: 0.6786 (mp0) REVERT: A 349 ARG cc_start: 0.6954 (mtm-85) cc_final: 0.6607 (mtm-85) REVERT: A 375 LYS cc_start: 0.7826 (ptpt) cc_final: 0.7442 (ptmt) REVERT: D 317 LYS cc_start: 0.7642 (mttt) cc_final: 0.7005 (tttm) REVERT: D 342 GLU cc_start: 0.7551 (tt0) cc_final: 0.7268 (tt0) REVERT: D 349 ARG cc_start: 0.7244 (ttm170) cc_final: 0.5288 (tpt90) REVERT: D 375 LYS cc_start: 0.7988 (ptpt) cc_final: 0.7667 (ptmt) REVERT: C 317 LYS cc_start: 0.8374 (mttt) cc_final: 0.7647 (tttt) REVERT: C 321 LYS cc_start: 0.7765 (ptpt) cc_final: 0.7308 (pttt) REVERT: C 336 GLN cc_start: 0.7263 (tt0) cc_final: 0.6276 (mp10) REVERT: C 340 LYS cc_start: 0.7376 (mttt) cc_final: 0.7075 (mtpt) REVERT: C 342 GLU cc_start: 0.7545 (tt0) cc_final: 0.7102 (tt0) REVERT: C 349 ARG cc_start: 0.7273 (ttm170) cc_final: 0.5615 (mmp-170) REVERT: B 317 LYS cc_start: 0.8301 (mttt) cc_final: 0.7458 (tttt) REVERT: B 342 GLU cc_start: 0.7563 (tt0) cc_final: 0.7250 (tt0) REVERT: B 373 THR cc_start: 0.8187 (m) cc_final: 0.7899 (p) REVERT: B 375 LYS cc_start: 0.7894 (ptpt) cc_final: 0.7574 (ptmt) REVERT: E 311 LYS cc_start: 0.7864 (tttt) cc_final: 0.7608 (ptpt) REVERT: E 317 LYS cc_start: 0.8480 (mttt) cc_final: 0.7924 (tttt) REVERT: E 321 LYS cc_start: 0.7612 (ptpt) cc_final: 0.6387 (pmtt) REVERT: E 342 GLU cc_start: 0.7780 (tt0) cc_final: 0.7461 (tt0) REVERT: E 369 LYS cc_start: 0.8354 (ptpt) cc_final: 0.7199 (pptt) REVERT: E 370 LYS cc_start: 0.5831 (mmtp) cc_final: 0.5453 (ptmt) REVERT: F 317 LYS cc_start: 0.7952 (mttt) cc_final: 0.7631 (tttm) REVERT: F 324 SER cc_start: 0.8209 (p) cc_final: 0.7911 (p) REVERT: F 340 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7701 (tptt) REVERT: F 342 GLU cc_start: 0.7430 (tt0) cc_final: 0.6848 (mp0) REVERT: F 348 ASP cc_start: 0.7677 (t0) cc_final: 0.6672 (p0) REVERT: F 370 LYS cc_start: 0.4573 (mmtp) cc_final: 0.3449 (pttt) REVERT: F 375 LYS cc_start: 0.8152 (ptpt) cc_final: 0.7938 (ptmt) outliers start: 6 outliers final: 4 residues processed: 131 average time/residue: 2.7288 time to fit residues: 366.0980 Evaluate side-chains 131 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain F residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3366 Z= 0.167 Angle : 0.541 5.958 4500 Z= 0.263 Chirality : 0.051 0.128 504 Planarity : 0.005 0.075 570 Dihedral : 4.812 13.139 444 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.85 % Allowed : 21.43 % 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: -1.54 (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 E 374 PHE 0.008 0.002 PHE B 378 TYR 0.009 0.002 TYR A 310 ARG 0.011 0.001 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 135 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7682 (mttt) cc_final: 0.7219 (tttm) REVERT: A 342 GLU cc_start: 0.7281 (tt0) cc_final: 0.6768 (mp0) REVERT: A 349 ARG cc_start: 0.6876 (mtm-85) cc_final: 0.6578 (mtm-85) REVERT: A 375 LYS cc_start: 0.7803 (ptpt) cc_final: 0.7434 (ptmt) REVERT: D 317 LYS cc_start: 0.7643 (mttt) cc_final: 0.7010 (tttm) REVERT: D 342 GLU cc_start: 0.7558 (tt0) cc_final: 0.7259 (tt0) REVERT: D 349 ARG cc_start: 0.7223 (ttm170) cc_final: 0.5203 (tpt90) REVERT: D 375 LYS cc_start: 0.7868 (ptpt) cc_final: 0.7566 (ptmt) REVERT: C 317 LYS cc_start: 0.8376 (mttt) cc_final: 0.7657 (tttt) REVERT: C 321 LYS cc_start: 0.7743 (ptpt) cc_final: 0.7300 (pttt) REVERT: C 336 GLN cc_start: 0.7308 (tt0) cc_final: 0.6314 (mp10) REVERT: C 340 LYS cc_start: 0.7346 (mttt) cc_final: 0.7059 (mtpt) REVERT: C 349 ARG cc_start: 0.7252 (ttm170) cc_final: 0.5631 (mmp-170) REVERT: B 317 LYS cc_start: 0.8318 (mttt) cc_final: 0.7462 (tttt) REVERT: B 342 GLU cc_start: 0.7559 (tt0) cc_final: 0.7254 (tt0) REVERT: B 373 THR cc_start: 0.8181 (m) cc_final: 0.7889 (p) REVERT: B 375 LYS cc_start: 0.7865 (ptpt) cc_final: 0.7604 (ptmt) REVERT: E 311 LYS cc_start: 0.7893 (tttt) cc_final: 0.7630 (ptpt) REVERT: E 317 LYS cc_start: 0.8487 (mttt) cc_final: 0.7927 (tttt) REVERT: E 321 LYS cc_start: 0.7583 (ptpt) cc_final: 0.6387 (pmtt) REVERT: E 342 GLU cc_start: 0.7760 (tt0) cc_final: 0.7450 (tt0) REVERT: E 370 LYS cc_start: 0.5862 (mmtp) cc_final: 0.5453 (ptmt) REVERT: F 311 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7191 (mttt) REVERT: F 317 LYS cc_start: 0.7974 (mttt) cc_final: 0.7681 (tttt) REVERT: F 324 SER cc_start: 0.8213 (p) cc_final: 0.7922 (p) REVERT: F 340 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7706 (tptt) REVERT: F 342 GLU cc_start: 0.7423 (tt0) cc_final: 0.6860 (mp0) REVERT: F 348 ASP cc_start: 0.7627 (t0) cc_final: 0.6672 (p0) REVERT: F 370 LYS cc_start: 0.4582 (mmtp) cc_final: 0.3415 (pttt) REVERT: F 375 LYS cc_start: 0.8157 (ptpt) cc_final: 0.7901 (ptmt) outliers start: 7 outliers final: 4 residues processed: 130 average time/residue: 2.5929 time to fit residues: 345.1975 Evaluate side-chains 130 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 316 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5423 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= 0.185 Angle : 0.548 6.007 4500 Z= 0.268 Chirality : 0.051 0.131 504 Planarity : 0.006 0.093 570 Dihedral : 4.857 13.692 444 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.85 % Allowed : 20.90 % 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: -1.56 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (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 0.011 0.002 TYR A 310 ARG 0.013 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 135 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7691 (mttt) cc_final: 0.7212 (tttm) REVERT: A 342 GLU cc_start: 0.7267 (tt0) cc_final: 0.6741 (mp0) REVERT: A 349 ARG cc_start: 0.6976 (mtm-85) cc_final: 0.6689 (mtm-85) REVERT: A 375 LYS cc_start: 0.7791 (ptpt) cc_final: 0.7420 (ptmt) REVERT: D 317 LYS cc_start: 0.7635 (mttt) cc_final: 0.6990 (tttm) REVERT: D 342 GLU cc_start: 0.7528 (tt0) cc_final: 0.7220 (tt0) REVERT: D 349 ARG cc_start: 0.7243 (ttm170) cc_final: 0.5216 (tpt90) REVERT: D 375 LYS cc_start: 0.7853 (ptpt) cc_final: 0.7542 (ptmt) REVERT: C 311 LYS cc_start: 0.7829 (mttt) cc_final: 0.6767 (mmpt) REVERT: C 317 LYS cc_start: 0.8374 (mttt) cc_final: 0.7664 (tttt) REVERT: C 321 LYS cc_start: 0.7745 (ptpt) cc_final: 0.7292 (pttt) REVERT: C 336 GLN cc_start: 0.7334 (tt0) cc_final: 0.6325 (mp10) REVERT: C 340 LYS cc_start: 0.7354 (mttt) cc_final: 0.7062 (mtpt) REVERT: C 342 GLU cc_start: 0.7539 (tt0) cc_final: 0.7071 (tt0) REVERT: C 349 ARG cc_start: 0.7281 (ttm170) cc_final: 0.5653 (mmp-170) REVERT: C 373 THR cc_start: 0.8225 (m) cc_final: 0.7836 (p) REVERT: B 317 LYS cc_start: 0.8326 (mttt) cc_final: 0.7476 (tttt) REVERT: B 342 GLU cc_start: 0.7561 (tt0) cc_final: 0.7227 (tt0) REVERT: B 373 THR cc_start: 0.8188 (m) cc_final: 0.7896 (p) REVERT: B 375 LYS cc_start: 0.7886 (ptpt) cc_final: 0.7622 (ptmt) REVERT: E 311 LYS cc_start: 0.7889 (tttt) cc_final: 0.7634 (ptpt) REVERT: E 317 LYS cc_start: 0.8502 (mttt) cc_final: 0.7940 (tttt) REVERT: E 321 LYS cc_start: 0.7594 (ptpt) cc_final: 0.6379 (pmtt) REVERT: E 342 GLU cc_start: 0.7769 (tt0) cc_final: 0.7447 (tt0) REVERT: E 370 LYS cc_start: 0.5837 (mmtp) cc_final: 0.5450 (ptmt) REVERT: F 311 LYS cc_start: 0.7754 (mtpt) cc_final: 0.7204 (mttt) REVERT: F 317 LYS cc_start: 0.8017 (mttt) cc_final: 0.7709 (tttt) REVERT: F 324 SER cc_start: 0.8234 (p) cc_final: 0.7949 (p) REVERT: F 340 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7652 (tptt) REVERT: F 342 GLU cc_start: 0.7427 (tt0) cc_final: 0.6822 (mp0) REVERT: F 348 ASP cc_start: 0.7639 (t0) cc_final: 0.6659 (p0) REVERT: F 370 LYS cc_start: 0.4565 (mmtp) cc_final: 0.3366 (pttt) REVERT: F 375 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7910 (ptmt) outliers start: 7 outliers final: 4 residues processed: 130 average time/residue: 2.6281 time to fit residues: 349.8295 Evaluate side-chains 129 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain F residue 316 SER 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: 0.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 0.0570 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3366 Z= 0.143 Angle : 0.536 5.989 4500 Z= 0.258 Chirality : 0.051 0.128 504 Planarity : 0.006 0.092 570 Dihedral : 4.651 13.820 444 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -1.50 (0.34), 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 0.003 0.001 HIS D 374 PHE 0.007 0.001 PHE C 346 TYR 0.008 0.001 TYR A 310 ARG 0.012 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 135 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7700 (mttt) cc_final: 0.7222 (tttm) REVERT: A 342 GLU cc_start: 0.7231 (tt0) cc_final: 0.6680 (mp0) REVERT: A 375 LYS cc_start: 0.7755 (ptpt) cc_final: 0.7410 (ptmt) REVERT: D 317 LYS cc_start: 0.7630 (mttt) cc_final: 0.6992 (tttm) REVERT: D 342 GLU cc_start: 0.7561 (tt0) cc_final: 0.7224 (tt0) REVERT: D 349 ARG cc_start: 0.7216 (ttm170) cc_final: 0.5206 (tpt90) REVERT: D 375 LYS cc_start: 0.7842 (ptpt) cc_final: 0.7531 (ptmt) REVERT: C 311 LYS cc_start: 0.7773 (mttt) cc_final: 0.6679 (mmpt) REVERT: C 317 LYS cc_start: 0.8390 (mttt) cc_final: 0.7669 (tttt) REVERT: C 321 LYS cc_start: 0.7751 (ptpt) cc_final: 0.7293 (pttt) REVERT: C 336 GLN cc_start: 0.7318 (tt0) cc_final: 0.6338 (mp10) REVERT: C 340 LYS cc_start: 0.7343 (mttt) cc_final: 0.7047 (mtpt) REVERT: C 342 GLU cc_start: 0.7533 (tt0) cc_final: 0.7060 (tt0) REVERT: C 349 ARG cc_start: 0.7279 (ttm170) cc_final: 0.5660 (mmp-170) REVERT: C 373 THR cc_start: 0.8221 (m) cc_final: 0.7861 (p) REVERT: B 317 LYS cc_start: 0.8314 (mttt) cc_final: 0.7473 (tttt) REVERT: B 342 GLU cc_start: 0.7547 (tt0) cc_final: 0.7213 (tt0) REVERT: B 373 THR cc_start: 0.8175 (m) cc_final: 0.7886 (p) REVERT: B 375 LYS cc_start: 0.7865 (ptpt) cc_final: 0.7603 (ptmt) REVERT: E 311 LYS cc_start: 0.7890 (tttt) cc_final: 0.7635 (ptpt) REVERT: E 317 LYS cc_start: 0.8484 (mttt) cc_final: 0.7933 (tttt) REVERT: E 321 LYS cc_start: 0.7586 (ptpt) cc_final: 0.6378 (pmtt) REVERT: E 342 GLU cc_start: 0.7758 (tt0) cc_final: 0.7446 (tt0) REVERT: E 369 LYS cc_start: 0.8386 (ptpt) cc_final: 0.7292 (pptt) REVERT: E 370 LYS cc_start: 0.5879 (mmtp) cc_final: 0.5500 (ptmt) REVERT: F 311 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7188 (mttt) REVERT: F 317 LYS cc_start: 0.8009 (mttt) cc_final: 0.7706 (tttt) REVERT: F 324 SER cc_start: 0.8222 (p) cc_final: 0.7935 (p) REVERT: F 340 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7692 (tptt) REVERT: F 342 GLU cc_start: 0.7375 (tt0) cc_final: 0.6803 (mp0) REVERT: F 349 ARG cc_start: 0.7121 (mtm-85) cc_final: 0.6649 (mtp85) REVERT: F 375 LYS cc_start: 0.8151 (ptpt) cc_final: 0.7890 (ptmt) outliers start: 4 outliers final: 3 residues processed: 132 average time/residue: 2.5235 time to fit residues: 341.3306 Evaluate side-chains 130 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain F residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.176542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.164376 restraints weight = 12373.422| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.77 r_work: 0.3973 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3894 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5595 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= 0.131 Angle : 0.515 5.740 4500 Z= 0.247 Chirality : 0.050 0.123 504 Planarity : 0.005 0.091 570 Dihedral : 4.385 13.991 444 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.79 % Allowed : 22.75 % 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: -1.41 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 374 PHE 0.007 0.001 PHE C 346 TYR 0.007 0.001 TYR A 310 ARG 0.013 0.001 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6126.62 seconds wall clock time: 107 minutes 0.45 seconds (6420.45 seconds total)