Starting phenix.real_space_refine on Fri Oct 10 14:53:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9e_18278/10_2025/8q9e_18278.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9e_18278/10_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_18278/10_2025/8q9e_18278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9e_18278/10_2025/8q9e_18278.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9e_18278/10_2025/8q9e_18278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9e_18278/10_2025/8q9e_18278.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.25, per 1000 atoms: 0.18 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: 0.46 Conformation dependent library (CDL) restraints added in 192.2 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 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: 0.14 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: 1.16 Time building geometry restraints manager: 0.66 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: 0.00 - 2.55: 10451 2.55 - 5.10: 1530 5.10 - 7.65: 432 7.65 - 10.20: 18 10.20 - 12.75: 7 Bond angle restraints: 12438 Sorted by residual: angle pdb=" C ASP E 348 " pdb=" N ARG E 349 " pdb=" CA ARG E 349 " ideal model delta sigma weight residual 120.90 129.73 -8.83 1.41e+00 5.03e-01 3.92e+01 angle pdb=" C ASP D 348 " pdb=" N ARG D 349 " pdb=" CA ARG D 349 " ideal model delta sigma weight residual 121.05 129.38 -8.33 1.43e+00 4.89e-01 3.40e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 120.90 128.94 -8.04 1.41e+00 5.03e-01 3.25e+01 angle pdb=" C ASP A 348 " pdb=" N ARG A 349 " pdb=" CA ARG A 349 " ideal model delta sigma weight residual 120.90 128.56 -7.66 1.41e+00 5.03e-01 2.95e+01 angle pdb=" C ASP C 348 " pdb=" N ARG C 349 " pdb=" CA ARG C 349 " ideal model delta sigma weight residual 121.05 128.64 -7.59 1.43e+00 4.89e-01 2.82e+01 ... (remaining 12433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.53: 2655 13.53 - 27.07: 283 27.07 - 40.60: 84 40.60 - 54.13: 48 54.13 - 67.66: 68 Dihedral angle restraints: 3138 sinusoidal: 1794 harmonic: 1344 Sorted by residual: dihedral pdb=" C LYS F 370 " pdb=" N LYS F 370 " pdb=" CA LYS F 370 " pdb=" CB LYS F 370 " ideal model delta harmonic sigma weight residual -122.60 -137.46 14.86 0 2.50e+00 1.60e-01 3.53e+01 dihedral pdb=" N LYS F 370 " pdb=" C LYS F 370 " pdb=" CA LYS F 370 " pdb=" CB LYS F 370 " ideal model delta harmonic sigma weight residual 122.80 137.27 -14.47 0 2.50e+00 1.60e-01 3.35e+01 dihedral pdb=" CA THR F 377 " pdb=" C THR F 377 " pdb=" N PHE F 378 " pdb=" CA PHE F 378 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 3135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 406 0.124 - 0.249: 81 0.249 - 0.373: 13 0.373 - 0.497: 3 0.497 - 0.621: 1 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA LYS F 370 " pdb=" N LYS F 370 " pdb=" C LYS F 370 " pdb=" CB LYS F 370 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" CA LYS E 370 " pdb=" N LYS E 370 " pdb=" C LYS E 370 " pdb=" CB LYS E 370 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA PRO A 332 " pdb=" N PRO A 332 " pdb=" C PRO A 332 " pdb=" CB PRO A 332 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 501 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 378 " 0.107 2.00e-02 2.50e+03 4.21e-02 5.33e+01 pdb=" CG PHE B 378 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 378 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE B 378 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE B 378 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE B 378 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 378 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE B 378 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 PHE B 378 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 PHE B 378 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE B 378 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 378 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 327 " -0.038 2.00e-02 2.50e+03 5.20e-02 4.05e+01 pdb=" CG ASN A 327 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN A 327 " 0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 327 " -0.053 2.00e-02 2.50e+03 pdb="HD21 ASN A 327 " -0.045 2.00e-02 2.50e+03 pdb="HD22 ASN A 327 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 358 " -0.034 2.00e-02 2.50e+03 6.09e-02 3.71e+01 pdb=" N ASN B 359 " 0.105 2.00e-02 2.50e+03 pdb=" CA ASN B 359 " -0.030 2.00e-02 2.50e+03 pdb=" H ASN B 359 " -0.041 2.00e-02 2.50e+03 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 542 2.18 - 2.78: 11409 2.78 - 3.39: 17221 3.39 - 3.99: 23083 3.99 - 4.60: 31947 Nonbonded interactions: 84202 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.571 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.578 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.601 2.450 ... (remaining 84197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 0.040 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (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 ARG 0.008 0.001 ARG E 349 TYR 0.034 0.009 TYR E 310 PHE 0.066 0.019 PHE B 378 HIS 0.009 0.003 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.01115 ( 3366) covalent geometry : angle 1.89263 ( 4500) hydrogen bonds : bond 0.11340 ( 60) hydrogen bonds : angle 7.94081 ( 180) *********************** 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 : 0.144 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: 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: 0.6998 (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: 0.6619 (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: 0.7646 (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: 0.6862 (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: 0.7201 (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: 0.5362 (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: 0.7273 (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: 1.1629 time to fit residues: 206.0957 Evaluate side-chains 137 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.176251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.164602 restraints weight = 12529.440| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 1.76 r_work: 0.3976 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3366 Z= 0.218 Angle : 0.762 7.578 4500 Z= 0.398 Chirality : 0.054 0.146 504 Planarity : 0.005 0.040 570 Dihedral : 7.533 23.717 444 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.44 % Allowed : 13.23 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 379 TYR 0.012 0.002 TYR A 310 PHE 0.010 0.002 PHE B 378 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 3366) covalent geometry : angle 0.76247 ( 4500) hydrogen bonds : bond 0.03440 ( 60) hydrogen bonds : angle 5.73797 ( 180) *********************** 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 145 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.8409 (mt0) cc_final: 0.8204 (mt0) REVERT: D 349 ARG cc_start: 0.7993 (ttm170) cc_final: 0.6492 (tpt90) REVERT: C 317 LYS cc_start: 0.8558 (mttt) cc_final: 0.8174 (tttt) REVERT: C 318 VAL cc_start: 0.9045 (t) cc_final: 0.8785 (p) REVERT: C 321 LYS cc_start: 0.8220 (ptpt) cc_final: 0.7729 (pttt) REVERT: C 342 GLU cc_start: 0.8048 (tt0) cc_final: 0.7822 (tt0) REVERT: C 351 GLN cc_start: 0.8375 (mt0) cc_final: 0.8162 (mt0) REVERT: B 317 LYS cc_start: 0.8646 (mttt) cc_final: 0.8198 (tttt) REVERT: B 321 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7806 (pttt) REVERT: B 379 ARG cc_start: 0.6913 (mtt180) cc_final: 0.6372 (mtm110) REVERT: E 314 ASP cc_start: 0.8766 (t0) cc_final: 0.8517 (t70) REVERT: E 321 LYS cc_start: 0.7866 (ptpt) cc_final: 0.6956 (pmtt) REVERT: E 349 ARG cc_start: 0.7767 (ttm170) cc_final: 0.6315 (pmt-80) REVERT: F 342 GLU cc_start: 0.7992 (tt0) cc_final: 0.7776 (mp0) REVERT: F 370 LYS cc_start: 0.5687 (mmtp) cc_final: 0.4756 (pttt) outliers start: 13 outliers final: 4 residues processed: 136 average time/residue: 1.3036 time to fit residues: 181.2546 Evaluate side-chains 126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 324 SER 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 F residue 309 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.178110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.166348 restraints weight = 12452.866| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.73 r_work: 0.4001 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3366 Z= 0.109 Angle : 0.638 6.485 4500 Z= 0.323 Chirality : 0.054 0.134 504 Planarity : 0.004 0.046 570 Dihedral : 6.281 18.450 444 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 379 TYR 0.009 0.002 TYR A 310 PHE 0.012 0.002 PHE B 346 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3366) covalent geometry : angle 0.63776 ( 4500) hydrogen bonds : bond 0.02883 ( 60) hydrogen bonds : angle 5.05718 ( 180) *********************** 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 145 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7736 (mtm-85) REVERT: D 349 ARG cc_start: 0.7885 (ttm170) cc_final: 0.7651 (mtt90) REVERT: C 317 LYS cc_start: 0.8592 (mttt) cc_final: 0.8296 (tttt) REVERT: C 321 LYS cc_start: 0.8168 (ptpt) cc_final: 0.7875 (pttt) REVERT: C 342 GLU cc_start: 0.7989 (tt0) cc_final: 0.7777 (tt0) REVERT: C 349 ARG cc_start: 0.7804 (ttm170) cc_final: 0.6875 (mmp-170) REVERT: B 314 ASP cc_start: 0.8676 (t0) cc_final: 0.8439 (t70) REVERT: B 317 LYS cc_start: 0.8570 (mttt) cc_final: 0.8196 (tttt) REVERT: B 321 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7824 (pttt) REVERT: B 379 ARG cc_start: 0.6862 (mtt180) cc_final: 0.6432 (mtm110) REVERT: E 321 LYS cc_start: 0.7919 (ptpt) cc_final: 0.7034 (pmtt) REVERT: E 349 ARG cc_start: 0.7672 (ttm170) cc_final: 0.6288 (pmt-80) REVERT: F 370 LYS cc_start: 0.5697 (mmtp) cc_final: 0.4935 (pttt) outliers start: 7 outliers final: 4 residues processed: 140 average time/residue: 1.2946 time to fit residues: 185.4874 Evaluate side-chains 132 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 309 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 0.0980 chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.171660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.159893 restraints weight = 12776.898| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.76 r_work: 0.3942 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3366 Z= 0.151 Angle : 0.626 5.678 4500 Z= 0.315 Chirality : 0.052 0.139 504 Planarity : 0.005 0.045 570 Dihedral : 5.890 16.595 444 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.65 % Allowed : 25.13 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (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 ARG 0.006 0.001 ARG B 349 TYR 0.011 0.002 TYR A 310 PHE 0.010 0.002 PHE B 378 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3366) covalent geometry : angle 0.62558 ( 4500) hydrogen bonds : bond 0.02830 ( 60) hydrogen bonds : angle 4.82458 ( 180) *********************** 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 136 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7840 (mmmt) REVERT: D 349 ARG cc_start: 0.7940 (ttm170) cc_final: 0.6607 (tpt90) REVERT: C 317 LYS cc_start: 0.8636 (mttt) cc_final: 0.8367 (tttt) REVERT: C 321 LYS cc_start: 0.8240 (ptpt) cc_final: 0.7905 (pttt) REVERT: C 349 ARG cc_start: 0.7965 (ttm170) cc_final: 0.6951 (mmp-170) REVERT: B 311 LYS cc_start: 0.8538 (pttt) cc_final: 0.8005 (mttt) REVERT: B 314 ASP cc_start: 0.8681 (t0) cc_final: 0.8356 (t0) REVERT: B 317 LYS cc_start: 0.8539 (mttt) cc_final: 0.8219 (tttt) REVERT: B 318 VAL cc_start: 0.9155 (t) cc_final: 0.8878 (p) REVERT: B 321 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7713 (pttt) REVERT: B 379 ARG cc_start: 0.6680 (mtt180) cc_final: 0.6271 (mtm110) REVERT: E 314 ASP cc_start: 0.8328 (t70) cc_final: 0.8045 (t0) REVERT: E 321 LYS cc_start: 0.7950 (ptpt) cc_final: 0.7050 (pmtt) REVERT: E 349 ARG cc_start: 0.7800 (ttm170) cc_final: 0.6224 (pmt-80) REVERT: E 369 LYS cc_start: 0.8730 (ptpt) cc_final: 0.8111 (pmtt) REVERT: F 348 ASP cc_start: 0.8108 (t0) cc_final: 0.7553 (p0) REVERT: F 370 LYS cc_start: 0.5764 (mmtp) cc_final: 0.4929 (pttt) outliers start: 10 outliers final: 5 residues processed: 129 average time/residue: 1.3510 time to fit residues: 178.2148 Evaluate side-chains 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.0270 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.172968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.161232 restraints weight = 12738.018| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.78 r_work: 0.3955 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3366 Z= 0.113 Angle : 0.581 5.762 4500 Z= 0.289 Chirality : 0.052 0.131 504 Planarity : 0.004 0.044 570 Dihedral : 5.453 14.441 444 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.85 % Allowed : 25.66 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 379 TYR 0.009 0.001 TYR A 310 PHE 0.008 0.002 PHE B 378 HIS 0.002 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3366) covalent geometry : angle 0.58080 ( 4500) hydrogen bonds : bond 0.02516 ( 60) hydrogen bonds : angle 4.54545 ( 180) *********************** 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 132 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8354 (mtpt) cc_final: 0.7831 (mmmt) REVERT: D 349 ARG cc_start: 0.7909 (ttm170) cc_final: 0.6571 (tpt90) REVERT: C 317 LYS cc_start: 0.8627 (mttt) cc_final: 0.8359 (tttt) REVERT: C 321 LYS cc_start: 0.8205 (ptpt) cc_final: 0.7851 (pttt) REVERT: C 349 ARG cc_start: 0.7940 (ttm170) cc_final: 0.6976 (mmp-170) REVERT: B 311 LYS cc_start: 0.8548 (pttt) cc_final: 0.7988 (mttt) REVERT: B 317 LYS cc_start: 0.8548 (mttt) cc_final: 0.8206 (tttt) REVERT: B 379 ARG cc_start: 0.6625 (mtt180) cc_final: 0.6152 (mtm110) REVERT: E 314 ASP cc_start: 0.8296 (t70) cc_final: 0.7967 (t0) REVERT: E 317 LYS cc_start: 0.8550 (tttt) cc_final: 0.8304 (tmtp) REVERT: E 321 LYS cc_start: 0.7936 (ptpt) cc_final: 0.7033 (pmtt) REVERT: E 349 ARG cc_start: 0.7831 (ttm170) cc_final: 0.6324 (pmt-80) REVERT: E 369 LYS cc_start: 0.8716 (ptpt) cc_final: 0.8058 (pptt) REVERT: F 348 ASP cc_start: 0.8091 (t0) cc_final: 0.7567 (p0) REVERT: F 370 LYS cc_start: 0.5667 (mmtp) cc_final: 0.4902 (pttt) outliers start: 7 outliers final: 2 residues processed: 125 average time/residue: 1.3868 time to fit residues: 177.1655 Evaluate side-chains 125 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.166490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.154114 restraints weight = 12617.900| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.85 r_work: 0.3864 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3366 Z= 0.136 Angle : 0.582 5.861 4500 Z= 0.288 Chirality : 0.052 0.139 504 Planarity : 0.004 0.030 570 Dihedral : 5.289 14.436 444 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.85 % Allowed : 25.40 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.33), 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 ARG 0.002 0.000 ARG E 349 TYR 0.009 0.002 TYR A 310 PHE 0.008 0.002 PHE B 378 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3366) covalent geometry : angle 0.58203 ( 4500) hydrogen bonds : bond 0.02406 ( 60) hydrogen bonds : angle 4.43247 ( 180) *********************** 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 129 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7730 (mmmt) REVERT: D 349 ARG cc_start: 0.7893 (ttm170) cc_final: 0.6454 (tpt90) REVERT: C 317 LYS cc_start: 0.8636 (mttt) cc_final: 0.8260 (tttt) REVERT: C 321 LYS cc_start: 0.8168 (ptpt) cc_final: 0.7786 (pttt) REVERT: C 349 ARG cc_start: 0.7963 (ttm170) cc_final: 0.6837 (mmp-170) REVERT: B 311 LYS cc_start: 0.8569 (pttt) cc_final: 0.7881 (mttt) REVERT: B 317 LYS cc_start: 0.8556 (mttt) cc_final: 0.8098 (tttt) REVERT: B 379 ARG cc_start: 0.6610 (mtt180) cc_final: 0.5946 (mtm110) REVERT: E 314 ASP cc_start: 0.8319 (t70) cc_final: 0.7869 (t0) REVERT: E 317 LYS cc_start: 0.8569 (tttt) cc_final: 0.8327 (tmtp) REVERT: E 321 LYS cc_start: 0.7906 (ptpt) cc_final: 0.6920 (pmtt) REVERT: E 369 LYS cc_start: 0.8731 (ptpt) cc_final: 0.7963 (pptt) REVERT: F 348 ASP cc_start: 0.8121 (t0) cc_final: 0.7534 (p0) REVERT: F 370 LYS cc_start: 0.5731 (mmtp) cc_final: 0.4804 (pttt) outliers start: 7 outliers final: 3 residues processed: 126 average time/residue: 1.4387 time to fit residues: 185.2223 Evaluate side-chains 123 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.170813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.159163 restraints weight = 12657.668| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.75 r_work: 0.3865 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.6027 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= 0.136 Angle : 0.587 6.028 4500 Z= 0.291 Chirality : 0.052 0.142 504 Planarity : 0.006 0.105 570 Dihedral : 5.245 15.127 444 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.32 % Allowed : 25.93 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 379 TYR 0.011 0.002 TYR A 310 PHE 0.008 0.002 PHE B 378 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3366) covalent geometry : angle 0.58695 ( 4500) hydrogen bonds : bond 0.02331 ( 60) hydrogen bonds : angle 4.35249 ( 180) *********************** 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 124 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7793 (mmmt) REVERT: D 349 ARG cc_start: 0.7910 (ttm170) cc_final: 0.6493 (tpt90) REVERT: C 317 LYS cc_start: 0.8641 (mttt) cc_final: 0.8330 (tttt) REVERT: C 321 LYS cc_start: 0.8159 (ptpt) cc_final: 0.7770 (pttt) REVERT: C 349 ARG cc_start: 0.7971 (ttm170) cc_final: 0.6874 (mmp-170) REVERT: B 311 LYS cc_start: 0.8579 (pttt) cc_final: 0.7929 (mttt) REVERT: B 317 LYS cc_start: 0.8560 (mttt) cc_final: 0.8147 (tttt) REVERT: B 379 ARG cc_start: 0.6581 (mtt180) cc_final: 0.5932 (mtm110) REVERT: E 314 ASP cc_start: 0.8324 (t70) cc_final: 0.7943 (t0) REVERT: E 317 LYS cc_start: 0.8556 (tttt) cc_final: 0.8311 (tmtp) REVERT: E 321 LYS cc_start: 0.7935 (ptpt) cc_final: 0.6954 (pmtt) REVERT: E 369 LYS cc_start: 0.8727 (ptpt) cc_final: 0.7997 (pptt) REVERT: F 348 ASP cc_start: 0.8147 (t0) cc_final: 0.7579 (p0) outliers start: 5 outliers final: 2 residues processed: 120 average time/residue: 1.4319 time to fit residues: 175.6135 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.0020 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 0.0170 overall best weight: 0.9428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.172412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160335 restraints weight = 12631.289| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.76 r_work: 0.3947 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.6232 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 6.021 4500 Z= 0.270 Chirality : 0.052 0.128 504 Planarity : 0.005 0.073 570 Dihedral : 4.843 15.271 444 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.26 % Allowed : 27.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 379 TYR 0.008 0.001 TYR A 310 PHE 0.009 0.002 PHE C 346 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 3366) covalent geometry : angle 0.55325 ( 4500) hydrogen bonds : bond 0.02045 ( 60) hydrogen bonds : angle 4.01849 ( 180) *********************** 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 125 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7874 (mmmt) REVERT: D 349 ARG cc_start: 0.7840 (ttm170) cc_final: 0.6356 (tpt90) REVERT: C 317 LYS cc_start: 0.8648 (mttt) cc_final: 0.8418 (tttt) REVERT: C 321 LYS cc_start: 0.8141 (ptpt) cc_final: 0.7761 (pttt) REVERT: C 336 GLN cc_start: 0.7519 (tt0) cc_final: 0.6797 (mp10) REVERT: C 342 GLU cc_start: 0.7996 (tt0) cc_final: 0.7757 (tt0) REVERT: C 349 ARG cc_start: 0.7897 (ttm170) cc_final: 0.6917 (mmp-170) REVERT: B 311 LYS cc_start: 0.8567 (pttt) cc_final: 0.7977 (mttt) REVERT: B 317 LYS cc_start: 0.8565 (mttt) cc_final: 0.8232 (tttt) REVERT: B 379 ARG cc_start: 0.6550 (mtt180) cc_final: 0.5917 (mtm110) REVERT: E 314 ASP cc_start: 0.8254 (t70) cc_final: 0.7898 (t0) REVERT: E 317 LYS cc_start: 0.8534 (tttt) cc_final: 0.8288 (tmtp) REVERT: E 321 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7025 (pmtt) REVERT: E 369 LYS cc_start: 0.8712 (ptpt) cc_final: 0.8036 (pptt) REVERT: F 311 LYS cc_start: 0.8291 (mtmt) cc_final: 0.7938 (mttt) REVERT: F 349 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7747 (mtp85) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 1.3123 time to fit residues: 166.6433 Evaluate side-chains 116 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 9.9990 chunk 10 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.171654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.159630 restraints weight = 12619.484| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.76 r_work: 0.3934 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.6249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3366 Z= 0.130 Angle : 0.571 6.035 4500 Z= 0.282 Chirality : 0.051 0.140 504 Planarity : 0.006 0.094 570 Dihedral : 4.976 15.497 444 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.37 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (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 ARG 0.012 0.001 ARG F 379 TYR 0.011 0.002 TYR A 310 PHE 0.007 0.001 PHE B 378 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3366) covalent geometry : angle 0.57088 ( 4500) hydrogen bonds : bond 0.02204 ( 60) hydrogen bonds : angle 4.11131 ( 180) *********************** 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 120 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7951 (mmmt) REVERT: D 349 ARG cc_start: 0.7868 (ttm170) cc_final: 0.6443 (tpt90) REVERT: C 321 LYS cc_start: 0.8201 (ptpt) cc_final: 0.7815 (pttt) REVERT: C 336 GLN cc_start: 0.7508 (tt0) cc_final: 0.6880 (mp10) REVERT: C 349 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7002 (mmp-170) REVERT: B 311 LYS cc_start: 0.8563 (pttt) cc_final: 0.8013 (mttt) REVERT: B 317 LYS cc_start: 0.8577 (mttt) cc_final: 0.8301 (tttt) REVERT: B 379 ARG cc_start: 0.6534 (mtt180) cc_final: 0.5983 (mtm110) REVERT: E 314 ASP cc_start: 0.8313 (t70) cc_final: 0.8021 (t0) REVERT: E 317 LYS cc_start: 0.8515 (tttt) cc_final: 0.8226 (tmtp) REVERT: E 321 LYS cc_start: 0.7954 (ptpt) cc_final: 0.7096 (pmtt) REVERT: E 369 LYS cc_start: 0.8691 (ptpt) cc_final: 0.8084 (pptt) REVERT: F 311 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7991 (mttt) REVERT: F 349 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7895 (mtp85) outliers start: 1 outliers final: 1 residues processed: 119 average time/residue: 1.3394 time to fit residues: 162.9912 Evaluate side-chains 117 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.173557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161842 restraints weight = 12590.845| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.71 r_work: 0.3966 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3366 Z= 0.096 Angle : 0.558 6.178 4500 Z= 0.271 Chirality : 0.052 0.144 504 Planarity : 0.006 0.092 570 Dihedral : 4.747 15.650 444 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.26 % Allowed : 29.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (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 ARG 0.012 0.001 ARG F 379 TYR 0.008 0.001 TYR A 310 PHE 0.007 0.001 PHE C 346 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 3366) covalent geometry : angle 0.55784 ( 4500) hydrogen bonds : bond 0.01946 ( 60) hydrogen bonds : angle 3.89299 ( 180) ********************** 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 119 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: D 340 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7858 (mmmt) REVERT: D 344 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8391 (tt) REVERT: D 349 ARG cc_start: 0.7727 (ttm170) cc_final: 0.6270 (tpt90) REVERT: C 321 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7780 (pttt) REVERT: C 336 GLN cc_start: 0.7567 (tt0) cc_final: 0.6836 (mp10) REVERT: C 349 ARG cc_start: 0.7862 (ttm170) cc_final: 0.6867 (mmp-170) REVERT: B 311 LYS cc_start: 0.8562 (pttt) cc_final: 0.7940 (mttt) REVERT: B 317 LYS cc_start: 0.8578 (mttt) cc_final: 0.8203 (tttt) REVERT: B 379 ARG cc_start: 0.6564 (mtt180) cc_final: 0.5918 (mtm110) REVERT: E 314 ASP cc_start: 0.8256 (t70) cc_final: 0.7930 (t0) REVERT: E 317 LYS cc_start: 0.8475 (tttt) cc_final: 0.8214 (tmtp) REVERT: E 321 LYS cc_start: 0.7903 (ptpt) cc_final: 0.6983 (pmtt) REVERT: E 369 LYS cc_start: 0.8673 (ptpt) cc_final: 0.7985 (pptt) REVERT: F 311 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7933 (mttt) REVERT: F 349 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7800 (mtp85) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 1.3075 time to fit residues: 157.9150 Evaluate side-chains 116 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 0.0570 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.176164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164313 restraints weight = 12607.609| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.71 r_work: 0.3992 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.6545 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= 0.090 Angle : 0.533 5.685 4500 Z= 0.258 Chirality : 0.051 0.124 504 Planarity : 0.006 0.094 570 Dihedral : 4.495 16.111 444 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.26 % Allowed : 28.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (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 ARG 0.012 0.001 ARG F 379 TYR 0.008 0.001 TYR A 310 PHE 0.006 0.001 PHE C 346 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 3366) covalent geometry : angle 0.53326 ( 4500) hydrogen bonds : bond 0.01804 ( 60) hydrogen bonds : angle 3.65708 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3878.66 seconds wall clock time: 66 minutes 16.05 seconds (3976.05 seconds total)