Starting phenix.real_space_refine on Mon Apr 28 02:13:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9e_18278/04_2025/8q9e_18278.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9e_18278/04_2025/8q9e_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_18278/04_2025/8q9e_18278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9e_18278/04_2025/8q9e_18278.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9e_18278/04_2025/8q9e_18278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9e_18278/04_2025/8q9e_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-5669/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: 5.10, 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: 1.79 Conformation dependent library (CDL) restraints added in 624.4 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: 0.76 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: 2.00 Time building geometry restraints manager: 2.20 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: 0.01 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: 7.580 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.150 Find NCS groups from input model: 0.180 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:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.580 ------------------------------------------------------------------------------- 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= 0.705 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 Details of bonding type rmsd hydrogen bonds : bond 0.11340 ( 60) hydrogen bonds : angle 7.94081 ( 180) covalent geometry : bond 0.01115 ( 3366) covalent geometry : angle 1.89263 ( 4500) *********************** 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 : 0.606 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: 2.3898 time to fit residues: 424.2237 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 : 0.540 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.177641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.166165 restraints weight = 12276.112| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.72 r_work: 0.3996 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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= 0.172 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 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 60) hydrogen bonds : angle 5.67842 ( 180) covalent geometry : bond 0.00423 ( 3366) covalent geometry : angle 0.74995 ( 4500) *********************** 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 : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 349 ARG cc_start: 0.7933 (ttm170) cc_final: 0.6480 (tpt90) REVERT: C 317 LYS cc_start: 0.8525 (mttt) cc_final: 0.8171 (tttt) REVERT: C 318 VAL cc_start: 0.9032 (t) cc_final: 0.8789 (p) REVERT: C 321 LYS cc_start: 0.8165 (ptpt) cc_final: 0.7691 (pttt) REVERT: C 336 GLN cc_start: 0.7504 (tt0) cc_final: 0.6965 (mt0) REVERT: C 342 GLU cc_start: 0.8037 (tt0) cc_final: 0.7785 (tt0) REVERT: C 351 GLN cc_start: 0.8367 (mt0) cc_final: 0.8154 (mt0) REVERT: C 358 ASP cc_start: 0.7899 (m-30) cc_final: 0.7661 (m-30) REVERT: B 317 LYS cc_start: 0.8618 (mttt) cc_final: 0.8177 (tttt) REVERT: B 321 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7822 (pttt) REVERT: B 336 GLN cc_start: 0.7864 (tt0) cc_final: 0.7063 (mp10) REVERT: B 379 ARG cc_start: 0.6913 (mtt180) cc_final: 0.6399 (mtm110) REVERT: E 314 ASP cc_start: 0.8764 (t0) cc_final: 0.8520 (t70) REVERT: E 321 LYS cc_start: 0.7844 (ptpt) cc_final: 0.6948 (pmtt) REVERT: E 349 ARG cc_start: 0.7692 (ttm170) cc_final: 0.6235 (pmt170) REVERT: E 351 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: F 342 GLU cc_start: 0.7904 (tt0) cc_final: 0.7693 (tt0) REVERT: F 370 LYS cc_start: 0.5696 (mmtp) cc_final: 0.4798 (pttt) outliers start: 13 outliers final: 3 residues processed: 142 average time/residue: 2.7028 time to fit residues: 392.9237 Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.3980 chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 F 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.175284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.163632 restraints weight = 12528.117| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 1.69 r_work: 0.3971 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3366 Z= 0.145 Angle : 0.661 6.595 4500 Z= 0.336 Chirality : 0.054 0.138 504 Planarity : 0.004 0.043 570 Dihedral : 6.447 19.208 444 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.65 % Allowed : 21.96 % Favored : 75.40 % 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: -1.61 (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 0.003 0.001 HIS B 330 PHE 0.011 0.002 PHE B 378 TYR 0.011 0.002 TYR A 310 ARG 0.004 0.001 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 60) hydrogen bonds : angle 5.17422 ( 180) covalent geometry : bond 0.00342 ( 3366) covalent geometry : angle 0.66113 ( 4500) *********************** 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 141 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7764 (mtm-85) REVERT: D 349 ARG cc_start: 0.7938 (ttm170) cc_final: 0.6435 (tpt90) REVERT: C 317 LYS cc_start: 0.8581 (mttt) cc_final: 0.8263 (tttt) REVERT: C 321 LYS cc_start: 0.8205 (ptpt) cc_final: 0.7885 (pttt) REVERT: C 342 GLU cc_start: 0.8000 (tt0) cc_final: 0.7773 (tt0) REVERT: C 349 ARG cc_start: 0.7974 (ttm170) cc_final: 0.6845 (mmp-170) REVERT: B 314 ASP cc_start: 0.8710 (t0) cc_final: 0.8442 (t70) REVERT: B 317 LYS cc_start: 0.8538 (mttt) cc_final: 0.8166 (tttt) REVERT: B 321 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7747 (pttt) REVERT: B 379 ARG cc_start: 0.6853 (mtt180) cc_final: 0.6330 (mtm110) REVERT: E 321 LYS cc_start: 0.7907 (ptpt) cc_final: 0.6986 (pmtt) REVERT: E 349 ARG cc_start: 0.7731 (ttm170) cc_final: 0.6327 (pmt-80) REVERT: F 370 LYS cc_start: 0.5682 (mmtp) cc_final: 0.4852 (pttt) outliers start: 10 outliers final: 3 residues processed: 136 average time/residue: 2.6979 time to fit residues: 375.7019 Evaluate side-chains 130 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 1 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.171254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159606 restraints weight = 12766.343| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.76 r_work: 0.3906 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3366 Z= 0.149 Angle : 0.635 6.101 4500 Z= 0.319 Chirality : 0.052 0.140 504 Planarity : 0.005 0.047 570 Dihedral : 5.992 16.992 444 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.65 % Allowed : 25.40 % Favored : 71.96 % 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 0.010 0.002 PHE B 378 TYR 0.010 0.002 TYR A 310 ARG 0.006 0.001 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.02850 ( 60) hydrogen bonds : angle 4.91667 ( 180) covalent geometry : bond 0.00350 ( 3366) covalent geometry : angle 0.63455 ( 4500) *********************** 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 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7714 (mmmt) REVERT: D 349 ARG cc_start: 0.7956 (ttm170) cc_final: 0.6373 (tpt90) REVERT: C 317 LYS cc_start: 0.8632 (mttt) cc_final: 0.8288 (tttt) REVERT: C 321 LYS cc_start: 0.8230 (ptpt) cc_final: 0.7879 (pttt) REVERT: C 349 ARG cc_start: 0.7942 (ttm170) cc_final: 0.6864 (mmp-170) REVERT: B 311 LYS cc_start: 0.8546 (pttt) cc_final: 0.7948 (mttt) REVERT: B 314 ASP cc_start: 0.8686 (t0) cc_final: 0.8350 (t0) REVERT: B 317 LYS cc_start: 0.8536 (mttt) cc_final: 0.8122 (tttt) REVERT: B 321 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7742 (pttt) REVERT: B 379 ARG cc_start: 0.6730 (mtt180) cc_final: 0.6234 (mtm110) REVERT: E 314 ASP cc_start: 0.8373 (t70) cc_final: 0.7928 (t0) REVERT: E 317 LYS cc_start: 0.8533 (tttt) cc_final: 0.8260 (tmtp) REVERT: E 321 LYS cc_start: 0.7941 (ptpt) cc_final: 0.6998 (pmtt) REVERT: E 349 ARG cc_start: 0.7733 (ttm170) cc_final: 0.6116 (pmt-80) REVERT: E 369 LYS cc_start: 0.8725 (ptpt) cc_final: 0.8015 (pptt) REVERT: F 370 LYS cc_start: 0.5743 (mmtp) cc_final: 0.4827 (pttt) outliers start: 10 outliers final: 4 residues processed: 129 average time/residue: 2.9010 time to fit residues: 383.2519 Evaluate side-chains 130 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 27 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 chunk 25 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.176157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.164459 restraints weight = 12509.042| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.76 r_work: 0.3990 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3366 Z= 0.093 Angle : 0.560 5.859 4500 Z= 0.276 Chirality : 0.052 0.127 504 Planarity : 0.004 0.049 570 Dihedral : 5.322 14.728 444 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.79 % Allowed : 26.19 % Favored : 73.02 % 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: -1.42 (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 0.008 0.002 PHE C 346 TYR 0.007 0.001 TYR A 310 ARG 0.007 0.001 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.02305 ( 60) hydrogen bonds : angle 4.40682 ( 180) covalent geometry : bond 0.00237 ( 3366) covalent geometry : angle 0.56004 ( 4500) *********************** 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 135 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7743 (mmmt) REVERT: D 349 ARG cc_start: 0.7795 (ttm170) cc_final: 0.6317 (tpt90) REVERT: C 317 LYS cc_start: 0.8627 (mttt) cc_final: 0.8394 (tttt) REVERT: C 321 LYS cc_start: 0.8161 (ptpt) cc_final: 0.7822 (pttt) REVERT: C 336 GLN cc_start: 0.7494 (tt0) cc_final: 0.6791 (mp10) REVERT: C 342 GLU cc_start: 0.7992 (tt0) cc_final: 0.7750 (tt0) REVERT: C 349 ARG cc_start: 0.7855 (ttm170) cc_final: 0.6985 (mmp-170) REVERT: C 379 ARG cc_start: 0.6820 (mtt180) cc_final: 0.6178 (mtm110) REVERT: B 311 LYS cc_start: 0.8534 (pttt) cc_final: 0.7990 (mttt) REVERT: B 317 LYS cc_start: 0.8577 (mttt) cc_final: 0.8214 (tttt) REVERT: B 318 VAL cc_start: 0.9148 (t) cc_final: 0.8888 (p) REVERT: B 379 ARG cc_start: 0.6590 (mtt180) cc_final: 0.6080 (mtm110) REVERT: E 314 ASP cc_start: 0.8261 (t70) cc_final: 0.7884 (t0) REVERT: E 317 LYS cc_start: 0.8522 (tttt) cc_final: 0.8284 (tmtp) REVERT: E 321 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7048 (pmtt) REVERT: E 349 ARG cc_start: 0.7738 (ttm170) cc_final: 0.6308 (pmt-80) REVERT: E 369 LYS cc_start: 0.8707 (ptpt) cc_final: 0.8048 (pptt) REVERT: F 348 ASP cc_start: 0.8013 (t0) cc_final: 0.7549 (p0) REVERT: F 370 LYS cc_start: 0.5637 (mmtp) cc_final: 0.4896 (pttt) outliers start: 3 outliers final: 1 residues processed: 132 average time/residue: 2.6943 time to fit residues: 364.5506 Evaluate side-chains 124 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 11 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.172511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.160849 restraints weight = 12502.923| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.73 r_work: 0.3918 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3366 Z= 0.132 Angle : 0.570 5.443 4500 Z= 0.283 Chirality : 0.052 0.137 504 Planarity : 0.004 0.055 570 Dihedral : 5.215 14.580 444 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.85 % Allowed : 26.72 % Favored : 71.43 % 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 (0.33), 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 0.003 0.001 HIS E 330 PHE 0.008 0.002 PHE C 346 TYR 0.012 0.002 TYR A 310 ARG 0.006 0.001 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.02359 ( 60) hydrogen bonds : angle 4.31861 ( 180) covalent geometry : bond 0.00319 ( 3366) covalent geometry : angle 0.56972 ( 4500) *********************** 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 133 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7746 (mmmt) REVERT: D 349 ARG cc_start: 0.7806 (ttm170) cc_final: 0.6283 (tpt90) REVERT: C 317 LYS cc_start: 0.8633 (mttt) cc_final: 0.8322 (tttt) REVERT: C 321 LYS cc_start: 0.8223 (ptpt) cc_final: 0.7862 (pttt) REVERT: C 342 GLU cc_start: 0.8002 (tt0) cc_final: 0.7715 (tt0) REVERT: C 349 ARG cc_start: 0.7945 (ttm170) cc_final: 0.6899 (mmp-170) REVERT: B 311 LYS cc_start: 0.8561 (pttt) cc_final: 0.7916 (mttt) REVERT: B 317 LYS cc_start: 0.8529 (mttt) cc_final: 0.8144 (tttt) REVERT: B 379 ARG cc_start: 0.6600 (mtt180) cc_final: 0.6015 (mtm110) REVERT: E 314 ASP cc_start: 0.8286 (t70) cc_final: 0.8073 (t0) REVERT: E 317 LYS cc_start: 0.8575 (tttt) cc_final: 0.8314 (tmtp) REVERT: E 321 LYS cc_start: 0.7886 (ptpt) cc_final: 0.6968 (pmtt) REVERT: E 369 LYS cc_start: 0.8702 (ptpt) cc_final: 0.7991 (pptt) REVERT: F 348 ASP cc_start: 0.8094 (t0) cc_final: 0.7556 (p0) REVERT: F 370 LYS cc_start: 0.5641 (mmtp) cc_final: 0.4778 (pttt) outliers start: 7 outliers final: 0 residues processed: 129 average time/residue: 2.9908 time to fit residues: 395.5866 Evaluate side-chains 122 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.171796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160154 restraints weight = 12557.242| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.74 r_work: 0.3895 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.6085 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= 0.122 Angle : 0.579 5.928 4500 Z= 0.284 Chirality : 0.052 0.138 504 Planarity : 0.006 0.090 570 Dihedral : 5.123 14.598 444 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.26 % Allowed : 28.31 % Favored : 71.43 % 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: -1.48 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.007 0.002 PHE C 346 TYR 0.011 0.002 TYR A 310 ARG 0.010 0.001 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.02235 ( 60) hydrogen bonds : angle 4.21662 ( 180) covalent geometry : bond 0.00289 ( 3366) covalent geometry : angle 0.57902 ( 4500) *********************** 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 122 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7812 (mmmt) REVERT: D 349 ARG cc_start: 0.7798 (ttm170) cc_final: 0.6295 (tpt90) REVERT: C 317 LYS cc_start: 0.8629 (mttt) cc_final: 0.8325 (tttt) REVERT: C 321 LYS cc_start: 0.8181 (ptpt) cc_final: 0.7807 (pttt) REVERT: C 342 GLU cc_start: 0.7988 (tt0) cc_final: 0.7703 (tt0) REVERT: C 349 ARG cc_start: 0.7902 (ttm170) cc_final: 0.6864 (mmp-170) REVERT: B 311 LYS cc_start: 0.8567 (pttt) cc_final: 0.7923 (mttt) REVERT: B 317 LYS cc_start: 0.8553 (mttt) cc_final: 0.8170 (tttt) REVERT: B 379 ARG cc_start: 0.6551 (mtt180) cc_final: 0.5931 (mtm110) REVERT: E 314 ASP cc_start: 0.8291 (t70) cc_final: 0.7821 (t0) REVERT: E 317 LYS cc_start: 0.8567 (tttt) cc_final: 0.8275 (tmtp) REVERT: E 321 LYS cc_start: 0.7904 (ptpt) cc_final: 0.6962 (pmtt) REVERT: E 369 LYS cc_start: 0.8719 (ptpt) cc_final: 0.8001 (pptt) REVERT: F 311 LYS cc_start: 0.8375 (mtmt) cc_final: 0.7991 (mttt) REVERT: F 348 ASP cc_start: 0.8139 (t0) cc_final: 0.7554 (p0) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 2.6583 time to fit residues: 332.2082 Evaluate side-chains 120 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.0030 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.174441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.162760 restraints weight = 12634.149| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 1.75 r_work: 0.3969 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.6226 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= 0.091 Angle : 0.545 5.869 4500 Z= 0.266 Chirality : 0.052 0.126 504 Planarity : 0.005 0.076 570 Dihedral : 4.773 14.600 444 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.26 % Allowed : 28.57 % Favored : 71.16 % 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 0.003 0.001 HIS D 374 PHE 0.007 0.001 PHE C 346 TYR 0.009 0.001 TYR A 310 ARG 0.014 0.002 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.01962 ( 60) hydrogen bonds : angle 3.93444 ( 180) covalent geometry : bond 0.00234 ( 3366) covalent geometry : angle 0.54474 ( 4500) *********************** 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 124 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7916 (mmmt) REVERT: D 349 ARG cc_start: 0.7718 (ttm170) cc_final: 0.6286 (tpt90) REVERT: C 317 LYS cc_start: 0.8632 (mttt) cc_final: 0.8424 (tttt) REVERT: C 321 LYS cc_start: 0.8151 (ptpt) cc_final: 0.7791 (pttt) REVERT: C 336 GLN cc_start: 0.7513 (tt0) cc_final: 0.6816 (mp10) REVERT: C 342 GLU cc_start: 0.8010 (tt0) cc_final: 0.7747 (tt0) REVERT: C 349 ARG cc_start: 0.7802 (ttm170) cc_final: 0.6993 (mmp-170) REVERT: B 311 LYS cc_start: 0.8550 (pttt) cc_final: 0.7966 (mttt) REVERT: B 317 LYS cc_start: 0.8547 (mttt) cc_final: 0.8239 (tttt) REVERT: B 379 ARG cc_start: 0.6544 (mtt180) cc_final: 0.5922 (mtm110) REVERT: E 314 ASP cc_start: 0.8269 (t70) cc_final: 0.7923 (t0) REVERT: E 317 LYS cc_start: 0.8514 (tttt) cc_final: 0.8284 (tmtp) REVERT: E 321 LYS cc_start: 0.7903 (ptpt) cc_final: 0.7068 (pmtt) REVERT: E 369 LYS cc_start: 0.8685 (ptpt) cc_final: 0.8037 (pptt) REVERT: F 311 LYS cc_start: 0.8277 (mtmt) cc_final: 0.7954 (mttt) REVERT: F 348 ASP cc_start: 0.8117 (t0) cc_final: 0.7637 (p0) REVERT: F 349 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7897 (mtp85) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 2.7637 time to fit residues: 351.9246 Evaluate side-chains 118 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.171035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159125 restraints weight = 12621.320| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.76 r_work: 0.3924 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3366 Z= 0.140 Angle : 0.578 6.189 4500 Z= 0.285 Chirality : 0.051 0.146 504 Planarity : 0.006 0.093 570 Dihedral : 4.973 14.643 444 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.79 % Allowed : 27.78 % Favored : 71.43 % 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: -1.42 (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 E 330 PHE 0.008 0.002 PHE B 378 TYR 0.011 0.002 TYR A 310 ARG 0.012 0.001 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.02289 ( 60) hydrogen bonds : angle 4.11049 ( 180) covalent geometry : bond 0.00323 ( 3366) covalent geometry : angle 0.57756 ( 4500) *********************** 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 122 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8422 (mtpt) cc_final: 0.7959 (mmmt) REVERT: D 349 ARG cc_start: 0.7806 (ttm170) cc_final: 0.6393 (tpt90) REVERT: C 321 LYS cc_start: 0.8214 (ptpt) cc_final: 0.7844 (pttt) REVERT: C 349 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7035 (mmp-170) REVERT: B 311 LYS cc_start: 0.8570 (pttt) cc_final: 0.8014 (mttt) REVERT: B 317 LYS cc_start: 0.8608 (mttt) cc_final: 0.8299 (tttt) REVERT: B 379 ARG cc_start: 0.6557 (mtt180) cc_final: 0.6008 (mtm110) REVERT: E 314 ASP cc_start: 0.8295 (t70) cc_final: 0.7959 (t0) REVERT: E 317 LYS cc_start: 0.8534 (tttt) cc_final: 0.8250 (tmtp) REVERT: E 321 LYS cc_start: 0.7917 (ptpt) cc_final: 0.7087 (pmtt) REVERT: E 369 LYS cc_start: 0.8701 (ptpt) cc_final: 0.8088 (pptt) REVERT: F 311 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7996 (mttt) REVERT: F 349 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7881 (mtp85) outliers start: 3 outliers final: 1 residues processed: 121 average time/residue: 2.6324 time to fit residues: 326.2816 Evaluate side-chains 118 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.173252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.161238 restraints weight = 12642.528| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.74 r_work: 0.3957 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3366 Z= 0.093 Angle : 0.553 5.891 4500 Z= 0.271 Chirality : 0.052 0.145 504 Planarity : 0.006 0.092 570 Dihedral : 4.636 15.231 444 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.53 % Allowed : 28.57 % Favored : 70.90 % 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 0.008 0.001 PHE C 346 TYR 0.008 0.001 TYR A 310 ARG 0.012 0.001 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.01966 ( 60) hydrogen bonds : angle 3.87088 ( 180) covalent geometry : bond 0.00237 ( 3366) covalent geometry : angle 0.55334 ( 4500) ********************** 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 121 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8333 (mtpt) cc_final: 0.7843 (mmmt) REVERT: D 349 ARG cc_start: 0.7672 (ttm170) cc_final: 0.6192 (tpt90) REVERT: C 321 LYS cc_start: 0.8139 (ptpt) cc_final: 0.7755 (pttt) REVERT: C 336 GLN cc_start: 0.7551 (tt0) cc_final: 0.6818 (mp10) REVERT: C 342 GLU cc_start: 0.7994 (tt0) cc_final: 0.7695 (tt0) REVERT: C 349 ARG cc_start: 0.7819 (ttm170) cc_final: 0.6842 (mmp-170) REVERT: B 311 LYS cc_start: 0.8557 (pttt) cc_final: 0.7924 (mttt) REVERT: B 317 LYS cc_start: 0.8605 (mttt) cc_final: 0.8205 (tttt) REVERT: B 358 ASP cc_start: 0.8370 (m-30) cc_final: 0.8170 (m-30) REVERT: B 379 ARG cc_start: 0.6603 (mtt180) cc_final: 0.5947 (mtm110) REVERT: E 314 ASP cc_start: 0.8271 (t70) cc_final: 0.8038 (t0) REVERT: E 317 LYS cc_start: 0.8506 (tttt) cc_final: 0.8250 (tmtp) REVERT: E 321 LYS cc_start: 0.7906 (ptpt) cc_final: 0.7011 (pmtt) REVERT: E 369 LYS cc_start: 0.8698 (ptpt) cc_final: 0.8021 (pptt) REVERT: F 311 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7948 (mttt) outliers start: 2 outliers final: 0 residues processed: 121 average time/residue: 2.6580 time to fit residues: 329.9487 Evaluate side-chains 115 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN E 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.173549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.161679 restraints weight = 12691.445| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 1.71 r_work: 0.3963 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.6490 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= 0.107 Angle : 0.556 5.879 4500 Z= 0.272 Chirality : 0.051 0.131 504 Planarity : 0.006 0.094 570 Dihedral : 4.675 15.470 444 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.06 % Allowed : 28.31 % Favored : 70.63 % 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: -1.34 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 374 PHE 0.006 0.001 PHE B 378 TYR 0.009 0.002 TYR E 310 ARG 0.012 0.001 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.02067 ( 60) hydrogen bonds : angle 3.86473 ( 180) covalent geometry : bond 0.00260 ( 3366) covalent geometry : angle 0.55593 ( 4500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8802.27 seconds wall clock time: 154 minutes 21.68 seconds (9261.68 seconds total)