Starting phenix.real_space_refine on Thu Jul 24 10:05:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4m_44185/07_2025/9b4m_44185.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4m_44185/07_2025/9b4m_44185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b4m_44185/07_2025/9b4m_44185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4m_44185/07_2025/9b4m_44185.map" model { file = "/net/cci-nas-00/data/ceres_data/9b4m_44185/07_2025/9b4m_44185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4m_44185/07_2025/9b4m_44185.cif" } resolution = 3.1 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 3670 2.51 5 N 1080 2.21 5 O 1110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 3.46, per 1000 atoms: 0.59 Number of scatterers: 5870 At special positions: 0 Unit cell: (147.58, 81.78, 45.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 1110 8.00 N 1080 7.00 C 3670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 770.2 milliseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.268A pdb=" N VAL A 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL D 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL F 309 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE D 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL F 306 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL H 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE F 308 " --> pdb=" O VAL H 309 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL H 306 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL J 309 " --> pdb=" O VAL H 306 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE H 308 " --> pdb=" O VAL J 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 5.908A pdb=" N GLY A 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N HIS D 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLY D 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N HIS F 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLY F 326 " --> pdb=" O ASN H 327 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N HIS H 329 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE F 328 " --> pdb=" O HIS H 329 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLY H 326 " --> pdb=" O ASN J 327 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N HIS J 329 " --> pdb=" O GLY H 326 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE H 328 " --> pdb=" O HIS J 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.550A pdb=" N VAL A 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL F 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL H 337 " --> pdb=" O GLU J 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 removed outlier: 6.458A pdb=" N LEU A 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU F 344 " --> pdb=" O ASP H 345 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU H 344 " --> pdb=" O ASP J 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 362 removed outlier: 6.915A pdb=" N GLY A 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP D 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ILE D 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN A 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N HIS D 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY D 355 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP F 358 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU D 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILE F 360 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N HIS F 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR D 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY F 355 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP H 358 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU F 357 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILE H 360 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN F 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N HIS H 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR F 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY H 355 " --> pdb=" O SER J 356 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP J 358 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU H 357 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ILE J 360 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN H 359 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N HIS J 362 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR H 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 378 Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.267A pdb=" N VAL B 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL E 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL E 306 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL G 309 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE E 308 " --> pdb=" O VAL G 309 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL G 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL I 309 " --> pdb=" O VAL G 306 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE G 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.762A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.756A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.848A pdb=" N GLY C 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN B 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLY B 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N HIS E 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE B 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLY E 326 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N HIS G 329 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE E 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLY G 326 " --> pdb=" O ASN I 327 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N HIS I 329 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE G 328 " --> pdb=" O HIS I 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 337 through 338 removed outlier: 6.550A pdb=" N VAL B 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL G 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.458A pdb=" N LEU B 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU E 344 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU G 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 354 through 362 removed outlier: 6.968A pdb=" N GLY C 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY B 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP E 358 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU B 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILE E 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN B 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N HIS E 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR B 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY E 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP G 358 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU E 357 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ILE G 360 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN E 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N HIS G 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR E 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY G 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP I 358 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU G 357 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ILE I 360 " --> pdb=" O LEU G 357 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN G 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N HIS I 362 " --> pdb=" O ASN G 359 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR G 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.577A pdb=" N LYS B 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLU C 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N HIS C 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR B 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU C 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS B 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE C 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR B 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 285 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: 1.38 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1950 1.34 - 1.46: 822 1.46 - 1.57: 3178 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 5960 Sorted by residual: bond pdb=" CA ASN H 327 " pdb=" C ASN H 327 " ideal model delta sigma weight residual 1.530 1.519 0.011 1.17e-02 7.31e+03 8.79e-01 bond pdb=" CA ASN C 327 " pdb=" C ASN C 327 " ideal model delta sigma weight residual 1.530 1.519 0.011 1.17e-02 7.31e+03 8.48e-01 bond pdb=" CA ASN J 327 " pdb=" C ASN J 327 " ideal model delta sigma weight residual 1.530 1.519 0.011 1.17e-02 7.31e+03 8.42e-01 bond pdb=" CA ASN G 327 " pdb=" C ASN G 327 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.17e-02 7.31e+03 8.23e-01 bond pdb=" CA ASN E 327 " pdb=" C ASN E 327 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.17e-02 7.31e+03 8.21e-01 ... (remaining 5955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 6988 0.83 - 1.65: 810 1.65 - 2.48: 92 2.48 - 3.31: 50 3.31 - 4.14: 30 Bond angle restraints: 7970 Sorted by residual: angle pdb=" C PHE E 346 " pdb=" N LYS E 347 " pdb=" CA LYS E 347 " ideal model delta sigma weight residual 123.24 119.61 3.63 1.54e+00 4.22e-01 5.56e+00 angle pdb=" C PHE F 346 " pdb=" N LYS F 347 " pdb=" CA LYS F 347 " ideal model delta sigma weight residual 123.24 119.61 3.63 1.54e+00 4.22e-01 5.56e+00 angle pdb=" C PHE I 346 " pdb=" N LYS I 347 " pdb=" CA LYS I 347 " ideal model delta sigma weight residual 123.24 119.61 3.63 1.54e+00 4.22e-01 5.56e+00 angle pdb=" C PHE D 346 " pdb=" N LYS D 347 " pdb=" CA LYS D 347 " ideal model delta sigma weight residual 123.24 119.61 3.63 1.54e+00 4.22e-01 5.55e+00 angle pdb=" C PHE H 346 " pdb=" N LYS H 347 " pdb=" CA LYS H 347 " ideal model delta sigma weight residual 123.24 119.61 3.63 1.54e+00 4.22e-01 5.55e+00 ... (remaining 7965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.73: 3090 11.73 - 23.47: 420 23.47 - 35.20: 70 35.20 - 46.93: 30 46.93 - 58.66: 20 Dihedral angle restraints: 3630 sinusoidal: 1520 harmonic: 2110 Sorted by residual: dihedral pdb=" CA LYS B 347 " pdb=" C LYS B 347 " pdb=" N ASP B 348 " pdb=" CA ASP B 348 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA LYS G 347 " pdb=" C LYS G 347 " pdb=" N ASP G 348 " pdb=" CA ASP G 348 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA LYS C 347 " pdb=" C LYS C 347 " pdb=" N ASP C 348 " pdb=" CA ASP C 348 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 477 0.023 - 0.047: 222 0.047 - 0.070: 61 0.070 - 0.094: 20 0.094 - 0.117: 110 Chirality restraints: 890 Sorted by residual: chirality pdb=" CA VAL E 350 " pdb=" N VAL E 350 " pdb=" C VAL E 350 " pdb=" CB VAL E 350 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA VAL A 350 " pdb=" N VAL A 350 " pdb=" C VAL A 350 " pdb=" CB VAL A 350 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.41e-01 chirality pdb=" CA VAL J 350 " pdb=" N VAL J 350 " pdb=" C VAL J 350 " pdb=" CB VAL J 350 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 887 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 331 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO C 332 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 332 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 332 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 331 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO G 332 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO G 332 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 332 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 331 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO I 332 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO I 332 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 332 " 0.018 5.00e-02 4.00e+02 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1703 2.83 - 3.35: 4768 3.35 - 3.86: 9765 3.86 - 4.38: 10129 4.38 - 4.90: 21280 Nonbonded interactions: 47645 Sorted by model distance: nonbonded pdb=" NZ LYS I 370 " pdb=" OE1 GLU I 372 " model vdw 2.311 3.120 nonbonded pdb=" NZ LYS E 370 " pdb=" OE1 GLU E 372 " model vdw 2.311 3.120 nonbonded pdb=" NZ LYS C 370 " pdb=" OE1 GLU C 372 " model vdw 2.311 3.120 nonbonded pdb=" NZ LYS H 370 " pdb=" OE1 GLU H 372 " model vdw 2.311 3.120 nonbonded pdb=" NZ LYS J 370 " pdb=" OE1 GLU J 372 " model vdw 2.311 3.120 ... (remaining 47640 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 0.010 Normalize map: mean=0, sd=1: 8.660 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.600 Find NCS groups from input model: 0.130 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.006 0.025 5960 Z= 0.274 Angle : 0.603 4.136 7970 Z= 0.342 Chirality : 0.046 0.117 890 Planarity : 0.004 0.033 1020 Dihedral : 11.897 58.665 2290 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % 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: -3.19 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 362 PHE 0.007 0.002 PHE F 346 TYR 0.011 0.003 TYR C 310 ARG 0.001 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.15568 ( 95) hydrogen bonds : angle 7.07756 ( 285) covalent geometry : bond 0.00584 ( 5960) covalent geometry : angle 0.60307 ( 7970) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.651 Fit side-chains REVERT: A 317 LYS cc_start: 0.8944 (ptpt) cc_final: 0.8581 (ptpp) REVERT: A 331 LYS cc_start: 0.9215 (mtmt) cc_final: 0.8983 (mttp) REVERT: B 317 LYS cc_start: 0.8504 (ptpt) cc_final: 0.8026 (ptpp) REVERT: B 321 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8844 (mttm) REVERT: B 331 LYS cc_start: 0.9319 (mtmt) cc_final: 0.9055 (mttt) REVERT: B 340 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8213 (mttp) REVERT: B 342 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8413 (mp0) REVERT: B 356 SER cc_start: 0.9570 (p) cc_final: 0.9154 (p) REVERT: B 375 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8605 (tttt) REVERT: C 317 LYS cc_start: 0.9021 (ptpt) cc_final: 0.8559 (ptpp) REVERT: C 340 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8470 (mttp) REVERT: C 356 SER cc_start: 0.9224 (p) cc_final: 0.8952 (p) REVERT: D 317 LYS cc_start: 0.8477 (ptpt) cc_final: 0.8109 (ptpp) REVERT: D 331 LYS cc_start: 0.9282 (mtmt) cc_final: 0.8899 (mttt) REVERT: D 340 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8362 (mttp) REVERT: D 342 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8369 (mm-30) REVERT: D 356 SER cc_start: 0.9553 (p) cc_final: 0.9230 (p) REVERT: D 357 LEU cc_start: 0.9152 (tt) cc_final: 0.8945 (tt) REVERT: E 317 LYS cc_start: 0.8449 (ptpt) cc_final: 0.7999 (ptpp) REVERT: E 327 ASN cc_start: 0.9120 (t0) cc_final: 0.8740 (t0) REVERT: E 331 LYS cc_start: 0.9274 (mtmt) cc_final: 0.8915 (mttp) REVERT: E 338 GLU cc_start: 0.8657 (tt0) cc_final: 0.8385 (tt0) REVERT: E 340 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8326 (mttm) REVERT: E 342 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8231 (mp0) REVERT: E 343 LYS cc_start: 0.8751 (mppt) cc_final: 0.8455 (ttmt) REVERT: E 356 SER cc_start: 0.9564 (p) cc_final: 0.9227 (p) REVERT: E 370 LYS cc_start: 0.9091 (tttm) cc_final: 0.8782 (tttm) REVERT: F 317 LYS cc_start: 0.8423 (ptpt) cc_final: 0.8059 (ptpp) REVERT: F 340 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8358 (mttp) REVERT: F 342 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8139 (mm-30) REVERT: F 343 LYS cc_start: 0.8685 (mppt) cc_final: 0.8439 (mtpp) REVERT: F 356 SER cc_start: 0.9546 (p) cc_final: 0.9172 (p) REVERT: G 317 LYS cc_start: 0.8382 (ptpt) cc_final: 0.7983 (ptpp) REVERT: G 331 LYS cc_start: 0.9327 (mtmt) cc_final: 0.9012 (mttt) REVERT: G 340 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8245 (mttm) REVERT: G 342 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8260 (mp0) REVERT: G 343 LYS cc_start: 0.8721 (mppt) cc_final: 0.8211 (mtpp) REVERT: G 356 SER cc_start: 0.9537 (p) cc_final: 0.9160 (p) REVERT: G 370 LYS cc_start: 0.9077 (tttm) cc_final: 0.8867 (tttm) REVERT: H 317 LYS cc_start: 0.8444 (ptpt) cc_final: 0.8234 (ptmt) REVERT: H 331 LYS cc_start: 0.9280 (mtmt) cc_final: 0.9000 (mttt) REVERT: H 340 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8179 (mttp) REVERT: H 342 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8406 (mp0) REVERT: H 344 LEU cc_start: 0.9471 (mp) cc_final: 0.9174 (mp) REVERT: H 356 SER cc_start: 0.9548 (p) cc_final: 0.9204 (p) REVERT: I 317 LYS cc_start: 0.8558 (ptpt) cc_final: 0.8080 (ptpp) REVERT: I 325 LEU cc_start: 0.8930 (tp) cc_final: 0.8717 (tp) REVERT: I 331 LYS cc_start: 0.9339 (mtmt) cc_final: 0.8949 (mttp) REVERT: I 336 GLN cc_start: 0.9201 (tp40) cc_final: 0.8497 (tp40) REVERT: I 356 SER cc_start: 0.9364 (p) cc_final: 0.8991 (p) REVERT: J 317 LYS cc_start: 0.8617 (ptpt) cc_final: 0.8137 (ptpp) REVERT: J 321 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8891 (mttm) REVERT: J 331 LYS cc_start: 0.9294 (mtmt) cc_final: 0.7438 (tmtt) REVERT: J 340 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8138 (mttm) REVERT: J 343 LYS cc_start: 0.8767 (mppt) cc_final: 0.8390 (ttmt) REVERT: J 356 SER cc_start: 0.9442 (p) cc_final: 0.9106 (p) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.2239 time to fit residues: 111.0635 Evaluate side-chains 371 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN F 368 ASN H 368 ASN J 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.130272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.111766 restraints weight = 9171.551| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.21 r_work: 0.3715 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5960 Z= 0.220 Angle : 0.674 8.663 7970 Z= 0.328 Chirality : 0.050 0.155 890 Planarity : 0.004 0.029 1020 Dihedral : 4.669 16.029 790 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.93 % Allowed : 17.01 % Favored : 78.06 % 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: -3.09 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.012 0.002 PHE G 378 TYR 0.010 0.002 TYR B 310 ARG 0.002 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 95) hydrogen bonds : angle 5.06927 ( 285) covalent geometry : bond 0.00502 ( 5960) covalent geometry : angle 0.67381 ( 7970) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 407 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8880 (ptpt) cc_final: 0.8495 (ptpp) REVERT: A 331 LYS cc_start: 0.9294 (mtmt) cc_final: 0.8956 (mttp) REVERT: A 340 LYS cc_start: 0.9104 (ttmm) cc_final: 0.8781 (mttp) REVERT: A 343 LYS cc_start: 0.8859 (mttp) cc_final: 0.8528 (mtpp) REVERT: B 317 LYS cc_start: 0.8357 (ptpt) cc_final: 0.7919 (ptpp) REVERT: B 321 LYS cc_start: 0.9160 (mtmm) cc_final: 0.8793 (mttm) REVERT: B 331 LYS cc_start: 0.9225 (mtmt) cc_final: 0.8927 (mttt) REVERT: B 340 LYS cc_start: 0.8844 (ttmm) cc_final: 0.7849 (mttm) REVERT: B 342 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8568 (mp0) REVERT: B 356 SER cc_start: 0.9567 (p) cc_final: 0.9301 (p) REVERT: B 370 LYS cc_start: 0.8993 (tttm) cc_final: 0.8700 (tttm) REVERT: B 375 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8614 (tttt) REVERT: C 317 LYS cc_start: 0.8896 (ptpt) cc_final: 0.8512 (ptpp) REVERT: C 340 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8536 (mttp) REVERT: C 341 SER cc_start: 0.9046 (m) cc_final: 0.8653 (p) REVERT: C 356 SER cc_start: 0.9138 (p) cc_final: 0.8824 (p) REVERT: D 317 LYS cc_start: 0.8171 (ptpt) cc_final: 0.7802 (ptpp) REVERT: D 331 LYS cc_start: 0.9198 (mtmt) cc_final: 0.8790 (mttt) REVERT: D 340 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8288 (mttp) REVERT: E 310 TYR cc_start: 0.9218 (t80) cc_final: 0.8613 (t80) REVERT: E 317 LYS cc_start: 0.8135 (ptpt) cc_final: 0.7675 (ptpp) REVERT: E 327 ASN cc_start: 0.9122 (t0) cc_final: 0.8704 (t0) REVERT: E 331 LYS cc_start: 0.9243 (mtmt) cc_final: 0.8980 (mttt) REVERT: E 340 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8276 (mttm) REVERT: E 342 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8409 (mp0) REVERT: E 343 LYS cc_start: 0.8748 (mppt) cc_final: 0.8463 (ttmt) REVERT: E 356 SER cc_start: 0.9597 (p) cc_final: 0.9288 (p) REVERT: E 370 LYS cc_start: 0.9004 (tttm) cc_final: 0.8794 (tttm) REVERT: F 317 LYS cc_start: 0.8037 (ptpt) cc_final: 0.7651 (ptpp) REVERT: F 331 LYS cc_start: 0.9218 (mtmt) cc_final: 0.8751 (mttp) REVERT: F 340 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8191 (mttp) REVERT: F 342 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8619 (mp0) REVERT: F 370 LYS cc_start: 0.9133 (tttm) cc_final: 0.8900 (tttp) REVERT: F 372 GLU cc_start: 0.8887 (tt0) cc_final: 0.8625 (tt0) REVERT: G 310 TYR cc_start: 0.9267 (t80) cc_final: 0.8993 (t80) REVERT: G 317 LYS cc_start: 0.8014 (ptpt) cc_final: 0.7623 (ptpp) REVERT: G 331 LYS cc_start: 0.9190 (mtmt) cc_final: 0.8875 (mttp) REVERT: G 342 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: G 356 SER cc_start: 0.9576 (p) cc_final: 0.9317 (p) REVERT: G 378 PHE cc_start: 0.8991 (t80) cc_final: 0.8746 (t80) REVERT: H 317 LYS cc_start: 0.8088 (ptpt) cc_final: 0.7446 (ptpp) REVERT: H 331 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8834 (mttp) REVERT: H 342 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8466 (mp0) REVERT: H 343 LYS cc_start: 0.9032 (mttt) cc_final: 0.8635 (mtpp) REVERT: H 356 SER cc_start: 0.9574 (p) cc_final: 0.9354 (p) REVERT: I 317 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7674 (ptpp) REVERT: I 331 LYS cc_start: 0.9248 (mtmt) cc_final: 0.8812 (mttp) REVERT: I 336 GLN cc_start: 0.9158 (tp40) cc_final: 0.8496 (tp40) REVERT: I 340 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8281 (mttp) REVERT: I 343 LYS cc_start: 0.9036 (mttp) cc_final: 0.8583 (mtpp) REVERT: J 317 LYS cc_start: 0.8306 (ptpt) cc_final: 0.7837 (ptpp) REVERT: J 321 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8908 (mttm) REVERT: J 331 LYS cc_start: 0.9165 (mtmt) cc_final: 0.7377 (tmtt) REVERT: J 340 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8087 (mttm) REVERT: J 356 SER cc_start: 0.9456 (p) cc_final: 0.9130 (p) outliers start: 33 outliers final: 27 residues processed: 409 average time/residue: 0.2213 time to fit residues: 110.2771 Evaluate side-chains 416 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 388 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN G 368 ASN H 368 ASN J 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.134063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.115260 restraints weight = 9094.111| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.29 r_work: 0.3775 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5960 Z= 0.146 Angle : 0.642 7.693 7970 Z= 0.304 Chirality : 0.050 0.157 890 Planarity : 0.004 0.036 1020 Dihedral : 4.545 15.183 790 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.48 % Allowed : 20.30 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.05 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 374 PHE 0.009 0.002 PHE J 378 TYR 0.018 0.002 TYR A 310 ARG 0.001 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 95) hydrogen bonds : angle 4.76882 ( 285) covalent geometry : bond 0.00344 ( 5960) covalent geometry : angle 0.64171 ( 7970) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 405 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8893 (ptpt) cc_final: 0.8466 (ptpp) REVERT: A 331 LYS cc_start: 0.9272 (mtmt) cc_final: 0.8943 (mttp) REVERT: A 340 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8675 (mttp) REVERT: A 343 LYS cc_start: 0.8683 (mttp) cc_final: 0.8392 (mtpp) REVERT: A 357 LEU cc_start: 0.9181 (tt) cc_final: 0.8968 (tt) REVERT: B 317 LYS cc_start: 0.8287 (ptpt) cc_final: 0.7843 (ptpp) REVERT: B 321 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8778 (mttp) REVERT: B 331 LYS cc_start: 0.9227 (mtmt) cc_final: 0.8937 (mttt) REVERT: B 340 LYS cc_start: 0.8809 (ttmm) cc_final: 0.7836 (mttm) REVERT: B 342 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8533 (mp0) REVERT: B 370 LYS cc_start: 0.8965 (tttm) cc_final: 0.8635 (tttm) REVERT: B 375 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8606 (tttt) REVERT: C 317 LYS cc_start: 0.8915 (ptpt) cc_final: 0.8508 (ptpp) REVERT: C 340 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8510 (mttm) REVERT: C 341 SER cc_start: 0.9059 (m) cc_final: 0.8809 (p) REVERT: C 343 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8231 (mtpp) REVERT: C 356 SER cc_start: 0.8988 (p) cc_final: 0.8781 (p) REVERT: D 317 LYS cc_start: 0.8133 (ptpt) cc_final: 0.7762 (ptpp) REVERT: D 331 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8768 (mttt) REVERT: D 340 LYS cc_start: 0.8828 (ttmm) cc_final: 0.8212 (mttp) REVERT: D 343 LYS cc_start: 0.9154 (mttt) cc_final: 0.8566 (mtpp) REVERT: E 310 TYR cc_start: 0.9203 (t80) cc_final: 0.8680 (t80) REVERT: E 327 ASN cc_start: 0.9133 (t0) cc_final: 0.8800 (t0) REVERT: E 331 LYS cc_start: 0.9215 (mtmt) cc_final: 0.8990 (mttt) REVERT: E 338 GLU cc_start: 0.8830 (tt0) cc_final: 0.8392 (tt0) REVERT: E 340 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8264 (mttm) REVERT: E 342 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8392 (mp0) REVERT: E 343 LYS cc_start: 0.8670 (mppt) cc_final: 0.8359 (ttmt) REVERT: E 356 SER cc_start: 0.9636 (p) cc_final: 0.9379 (p) REVERT: E 370 LYS cc_start: 0.8985 (tttm) cc_final: 0.8783 (tttm) REVERT: F 317 LYS cc_start: 0.8059 (ptpt) cc_final: 0.7657 (ptpp) REVERT: F 331 LYS cc_start: 0.9153 (mtmt) cc_final: 0.8741 (mttp) REVERT: F 340 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8191 (mttp) REVERT: F 342 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8472 (mm-30) REVERT: F 370 LYS cc_start: 0.9104 (tttm) cc_final: 0.8820 (tttp) REVERT: F 372 GLU cc_start: 0.8834 (tt0) cc_final: 0.8541 (tt0) REVERT: G 317 LYS cc_start: 0.7946 (ptpt) cc_final: 0.7530 (ptpp) REVERT: G 331 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8849 (mttp) REVERT: G 342 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8376 (mp0) REVERT: G 356 SER cc_start: 0.9597 (p) cc_final: 0.9354 (p) REVERT: G 378 PHE cc_start: 0.8996 (t80) cc_final: 0.8741 (t80) REVERT: H 317 LYS cc_start: 0.8056 (ptpt) cc_final: 0.7647 (ptpp) REVERT: H 331 LYS cc_start: 0.9118 (mtmt) cc_final: 0.8898 (mtmm) REVERT: H 342 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8308 (mp0) REVERT: H 343 LYS cc_start: 0.9063 (mttt) cc_final: 0.8629 (mtpp) REVERT: I 317 LYS cc_start: 0.8098 (ptpt) cc_final: 0.7627 (ptpp) REVERT: I 331 LYS cc_start: 0.9190 (mtmt) cc_final: 0.8811 (mttp) REVERT: I 336 GLN cc_start: 0.9149 (tp40) cc_final: 0.8578 (tp40) REVERT: I 340 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8267 (mttp) REVERT: I 343 LYS cc_start: 0.9081 (mttp) cc_final: 0.8626 (mtpp) REVERT: J 317 LYS cc_start: 0.8197 (ptpt) cc_final: 0.7805 (ptpp) REVERT: J 321 LYS cc_start: 0.9228 (mtmm) cc_final: 0.8904 (mttp) REVERT: J 331 LYS cc_start: 0.9157 (mtmt) cc_final: 0.7357 (tmtt) REVERT: J 340 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8112 (mttm) REVERT: J 356 SER cc_start: 0.9452 (p) cc_final: 0.9243 (p) outliers start: 30 outliers final: 29 residues processed: 409 average time/residue: 0.2340 time to fit residues: 116.9628 Evaluate side-chains 421 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 392 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 352 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 66 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN I 359 ASN J 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.129517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.110989 restraints weight = 9437.158| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.22 r_work: 0.3712 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 5960 Z= 0.298 Angle : 0.696 8.683 7970 Z= 0.345 Chirality : 0.051 0.125 890 Planarity : 0.005 0.045 1020 Dihedral : 4.814 15.834 790 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.22 % Allowed : 21.19 % Favored : 73.58 % 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: -3.10 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.010 0.002 PHE J 378 TYR 0.021 0.003 TYR A 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 95) hydrogen bonds : angle 5.08615 ( 285) covalent geometry : bond 0.00685 ( 5960) covalent geometry : angle 0.69587 ( 7970) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 389 time to evaluate : 0.789 Fit side-chains REVERT: A 317 LYS cc_start: 0.8934 (ptpt) cc_final: 0.8518 (ptpp) REVERT: A 331 LYS cc_start: 0.9328 (mtmt) cc_final: 0.8952 (mttp) REVERT: A 340 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8793 (mttp) REVERT: A 343 LYS cc_start: 0.8710 (mttp) cc_final: 0.8444 (mtpp) REVERT: A 357 LEU cc_start: 0.9174 (tt) cc_final: 0.8925 (tt) REVERT: B 317 LYS cc_start: 0.8351 (ptpt) cc_final: 0.7937 (ptpp) REVERT: B 331 LYS cc_start: 0.9260 (mtmt) cc_final: 0.8912 (mttt) REVERT: B 340 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8075 (mttm) REVERT: B 370 LYS cc_start: 0.9030 (tttm) cc_final: 0.8667 (tttm) REVERT: B 375 LYS cc_start: 0.8948 (ttmm) cc_final: 0.8586 (tttt) REVERT: C 310 TYR cc_start: 0.9067 (t80) cc_final: 0.8679 (t80) REVERT: C 317 LYS cc_start: 0.8924 (ptpt) cc_final: 0.8519 (ptpp) REVERT: C 340 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8524 (mttm) REVERT: C 343 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8289 (mtpp) REVERT: C 356 SER cc_start: 0.9094 (p) cc_final: 0.8868 (p) REVERT: D 317 LYS cc_start: 0.8154 (ptpt) cc_final: 0.7768 (ptpp) REVERT: D 331 LYS cc_start: 0.9204 (mtmt) cc_final: 0.8744 (mttt) REVERT: D 340 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8371 (mttp) REVERT: D 343 LYS cc_start: 0.9167 (mttt) cc_final: 0.8594 (mtpp) REVERT: E 310 TYR cc_start: 0.9189 (t80) cc_final: 0.8614 (t80) REVERT: E 327 ASN cc_start: 0.9138 (t0) cc_final: 0.8663 (t0) REVERT: E 331 LYS cc_start: 0.9263 (mtmt) cc_final: 0.8987 (mttt) REVERT: E 338 GLU cc_start: 0.8870 (tt0) cc_final: 0.8457 (tt0) REVERT: E 340 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8368 (mttm) REVERT: E 342 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8429 (mp0) REVERT: E 343 LYS cc_start: 0.8734 (mppt) cc_final: 0.8410 (ttmt) REVERT: E 356 SER cc_start: 0.9590 (p) cc_final: 0.9347 (p) REVERT: E 370 LYS cc_start: 0.9013 (tttm) cc_final: 0.8764 (tttm) REVERT: F 317 LYS cc_start: 0.8166 (ptpt) cc_final: 0.7788 (ptpp) REVERT: F 331 LYS cc_start: 0.9212 (mtmt) cc_final: 0.8768 (mttp) REVERT: F 340 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8356 (mttp) REVERT: F 342 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8434 (mm-30) REVERT: F 370 LYS cc_start: 0.9146 (tttm) cc_final: 0.8784 (tttp) REVERT: F 372 GLU cc_start: 0.8887 (tt0) cc_final: 0.8529 (tt0) REVERT: G 310 TYR cc_start: 0.9293 (t80) cc_final: 0.8803 (t80) REVERT: G 317 LYS cc_start: 0.8089 (ptpt) cc_final: 0.7607 (ptpp) REVERT: G 331 LYS cc_start: 0.9214 (mtmt) cc_final: 0.8858 (mttp) REVERT: G 341 SER cc_start: 0.9084 (m) cc_final: 0.8771 (p) REVERT: G 356 SER cc_start: 0.9616 (p) cc_final: 0.9402 (p) REVERT: G 378 PHE cc_start: 0.8983 (t80) cc_final: 0.8546 (t80) REVERT: H 317 LYS cc_start: 0.8086 (ptpt) cc_final: 0.7679 (ptpp) REVERT: H 331 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8854 (mtmm) REVERT: H 340 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8177 (mttp) REVERT: H 342 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8373 (mp0) REVERT: H 343 LYS cc_start: 0.9095 (mttt) cc_final: 0.8689 (mtpp) REVERT: H 345 ASP cc_start: 0.8492 (t0) cc_final: 0.8240 (t0) REVERT: I 317 LYS cc_start: 0.8145 (ptpt) cc_final: 0.7648 (ptpp) REVERT: I 331 LYS cc_start: 0.9250 (mtmt) cc_final: 0.8889 (mttp) REVERT: I 336 GLN cc_start: 0.9142 (tp40) cc_final: 0.8583 (tp40) REVERT: I 340 LYS cc_start: 0.9000 (ttmm) cc_final: 0.8100 (mmtp) REVERT: J 317 LYS cc_start: 0.8282 (ptpt) cc_final: 0.7849 (ptpp) REVERT: J 321 LYS cc_start: 0.9231 (mtmm) cc_final: 0.8890 (mttm) REVERT: J 331 LYS cc_start: 0.9165 (mtmt) cc_final: 0.7408 (tmtt) REVERT: J 340 LYS cc_start: 0.8842 (ttmm) cc_final: 0.8156 (mttm) REVERT: J 345 ASP cc_start: 0.8622 (t0) cc_final: 0.8307 (t0) outliers start: 35 outliers final: 33 residues processed: 391 average time/residue: 0.2267 time to fit residues: 107.7337 Evaluate side-chains 413 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 380 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 352 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.134717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.116065 restraints weight = 9033.814| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.28 r_work: 0.3788 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5960 Z= 0.148 Angle : 0.639 9.162 7970 Z= 0.306 Chirality : 0.050 0.192 890 Planarity : 0.005 0.043 1020 Dihedral : 4.588 14.735 790 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.93 % Allowed : 22.24 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 330 PHE 0.008 0.002 PHE C 346 TYR 0.016 0.002 TYR A 310 ARG 0.001 0.000 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.02754 ( 95) hydrogen bonds : angle 4.67296 ( 285) covalent geometry : bond 0.00350 ( 5960) covalent geometry : angle 0.63911 ( 7970) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 392 time to evaluate : 1.382 Fit side-chains REVERT: A 317 LYS cc_start: 0.8934 (ptpt) cc_final: 0.8478 (ptpp) REVERT: A 331 LYS cc_start: 0.9297 (mtmt) cc_final: 0.8940 (mttp) REVERT: A 341 SER cc_start: 0.9085 (m) cc_final: 0.8841 (p) REVERT: A 357 LEU cc_start: 0.9163 (tt) cc_final: 0.8887 (tt) REVERT: B 317 LYS cc_start: 0.8324 (ptpt) cc_final: 0.7924 (ptpp) REVERT: B 331 LYS cc_start: 0.9247 (mtmt) cc_final: 0.8933 (mttt) REVERT: B 340 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8013 (mttm) REVERT: B 342 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8486 (mp0) REVERT: B 375 LYS cc_start: 0.8929 (ttmm) cc_final: 0.8576 (tttt) REVERT: C 310 TYR cc_start: 0.9030 (t80) cc_final: 0.8495 (t80) REVERT: C 317 LYS cc_start: 0.8878 (ptpt) cc_final: 0.8450 (ptpp) REVERT: C 340 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8480 (mttp) REVERT: C 343 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8248 (mtpp) REVERT: C 356 SER cc_start: 0.9016 (p) cc_final: 0.8803 (p) REVERT: D 317 LYS cc_start: 0.8132 (ptpt) cc_final: 0.7747 (ptpp) REVERT: D 331 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8762 (mttt) REVERT: D 340 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8002 (mttp) REVERT: D 343 LYS cc_start: 0.9137 (mttt) cc_final: 0.8574 (mtpp) REVERT: E 310 TYR cc_start: 0.9210 (t80) cc_final: 0.8686 (t80) REVERT: E 327 ASN cc_start: 0.9132 (t0) cc_final: 0.8717 (t0) REVERT: E 331 LYS cc_start: 0.9220 (mtmt) cc_final: 0.9000 (mttt) REVERT: E 338 GLU cc_start: 0.8841 (tt0) cc_final: 0.8346 (tt0) REVERT: E 340 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8147 (mttm) REVERT: E 342 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8436 (mp0) REVERT: E 343 LYS cc_start: 0.8678 (mppt) cc_final: 0.8420 (ttmt) REVERT: E 356 SER cc_start: 0.9574 (p) cc_final: 0.9336 (p) REVERT: E 370 LYS cc_start: 0.8962 (tttm) cc_final: 0.8738 (tttm) REVERT: F 317 LYS cc_start: 0.8146 (ptpt) cc_final: 0.7780 (ptpp) REVERT: F 331 LYS cc_start: 0.9152 (mtmt) cc_final: 0.8737 (mttp) REVERT: F 340 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8254 (mttp) REVERT: F 342 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8614 (mp0) REVERT: F 370 LYS cc_start: 0.9096 (tttm) cc_final: 0.8765 (tttp) REVERT: F 372 GLU cc_start: 0.8832 (tt0) cc_final: 0.8529 (tt0) REVERT: G 310 TYR cc_start: 0.9233 (t80) cc_final: 0.8999 (t80) REVERT: G 317 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7547 (ptpp) REVERT: G 331 LYS cc_start: 0.9150 (mtmt) cc_final: 0.8891 (mttt) REVERT: G 372 GLU cc_start: 0.8616 (tt0) cc_final: 0.8402 (tt0) REVERT: G 378 PHE cc_start: 0.8976 (t80) cc_final: 0.8598 (t80) REVERT: H 317 LYS cc_start: 0.8073 (ptpt) cc_final: 0.7648 (ptpp) REVERT: H 331 LYS cc_start: 0.9119 (mtmt) cc_final: 0.8904 (mtmm) REVERT: H 340 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8152 (mttm) REVERT: H 342 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8504 (mp0) REVERT: H 343 LYS cc_start: 0.9080 (mttt) cc_final: 0.8688 (mtpp) REVERT: H 345 ASP cc_start: 0.8525 (t0) cc_final: 0.8257 (t0) REVERT: I 317 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7634 (ptpp) REVERT: I 331 LYS cc_start: 0.9202 (mtmt) cc_final: 0.8827 (mttp) REVERT: I 336 GLN cc_start: 0.9115 (tp40) cc_final: 0.8627 (tp40) REVERT: I 340 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8293 (mmtp) REVERT: I 343 LYS cc_start: 0.9119 (mttp) cc_final: 0.8687 (mmmt) REVERT: J 321 LYS cc_start: 0.9227 (mtmm) cc_final: 0.8881 (mttm) REVERT: J 340 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8194 (mttm) REVERT: J 345 ASP cc_start: 0.8693 (t0) cc_final: 0.8424 (t0) outliers start: 33 outliers final: 31 residues processed: 396 average time/residue: 0.2417 time to fit residues: 116.9602 Evaluate side-chains 414 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 383 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 352 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 0.0270 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.129136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.110421 restraints weight = 9180.932| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.26 r_work: 0.3729 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5960 Z= 0.164 Angle : 0.651 9.215 7970 Z= 0.311 Chirality : 0.050 0.148 890 Planarity : 0.005 0.045 1020 Dihedral : 4.571 15.102 790 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 5.37 % Allowed : 23.28 % Favored : 71.34 % 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: -2.99 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 330 PHE 0.008 0.002 PHE J 378 TYR 0.017 0.003 TYR A 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.02804 ( 95) hydrogen bonds : angle 4.66198 ( 285) covalent geometry : bond 0.00386 ( 5960) covalent geometry : angle 0.65068 ( 7970) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 390 time to evaluate : 0.731 Fit side-chains REVERT: A 317 LYS cc_start: 0.8908 (ptpt) cc_final: 0.8515 (ptpp) REVERT: A 331 LYS cc_start: 0.9286 (mtmt) cc_final: 0.8944 (mttp) REVERT: A 357 LEU cc_start: 0.9145 (tt) cc_final: 0.8850 (tt) REVERT: B 317 LYS cc_start: 0.8271 (ptpt) cc_final: 0.7804 (ptpp) REVERT: B 321 LYS cc_start: 0.9184 (mttp) cc_final: 0.8962 (mttp) REVERT: B 331 LYS cc_start: 0.9253 (mtmt) cc_final: 0.8942 (mttt) REVERT: B 340 LYS cc_start: 0.8795 (ttmm) cc_final: 0.8081 (mttm) REVERT: B 342 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8471 (mp0) REVERT: B 370 LYS cc_start: 0.9020 (tttm) cc_final: 0.8713 (tttm) REVERT: B 375 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8552 (tttt) REVERT: C 310 TYR cc_start: 0.9051 (t80) cc_final: 0.8650 (t80) REVERT: C 317 LYS cc_start: 0.8863 (ptpt) cc_final: 0.8433 (ptpp) REVERT: C 340 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8434 (mttp) REVERT: C 356 SER cc_start: 0.8957 (p) cc_final: 0.8742 (p) REVERT: D 317 LYS cc_start: 0.8099 (ptpt) cc_final: 0.7702 (ptpp) REVERT: D 331 LYS cc_start: 0.9167 (mtmt) cc_final: 0.8729 (mttt) REVERT: D 340 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8337 (mttp) REVERT: D 343 LYS cc_start: 0.9163 (mttt) cc_final: 0.8561 (mtpp) REVERT: E 310 TYR cc_start: 0.9223 (t80) cc_final: 0.8673 (t80) REVERT: E 327 ASN cc_start: 0.9157 (t0) cc_final: 0.8629 (t0) REVERT: E 331 LYS cc_start: 0.9228 (mtmt) cc_final: 0.8996 (mttt) REVERT: E 338 GLU cc_start: 0.8850 (tt0) cc_final: 0.8462 (tt0) REVERT: E 340 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8219 (mttm) REVERT: E 342 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: E 343 LYS cc_start: 0.8720 (mppt) cc_final: 0.8461 (ttmt) REVERT: E 370 LYS cc_start: 0.8977 (tttm) cc_final: 0.8758 (tttm) REVERT: F 317 LYS cc_start: 0.8121 (ptpt) cc_final: 0.7740 (ptpp) REVERT: F 331 LYS cc_start: 0.9155 (mtmt) cc_final: 0.8736 (mttp) REVERT: F 340 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8287 (mttp) REVERT: F 342 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8425 (mm-30) REVERT: F 372 GLU cc_start: 0.8835 (tt0) cc_final: 0.8575 (tt0) REVERT: G 331 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8838 (mttp) REVERT: G 378 PHE cc_start: 0.8952 (t80) cc_final: 0.8652 (t80) REVERT: H 317 LYS cc_start: 0.8037 (ptpt) cc_final: 0.7587 (ptpp) REVERT: H 340 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8151 (mttm) REVERT: H 342 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8308 (mp0) REVERT: H 343 LYS cc_start: 0.9058 (mttt) cc_final: 0.8647 (mtpp) REVERT: H 345 ASP cc_start: 0.8522 (t0) cc_final: 0.8223 (t0) REVERT: I 317 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7615 (ptpp) REVERT: I 331 LYS cc_start: 0.9207 (mtmt) cc_final: 0.8877 (mttp) REVERT: I 336 GLN cc_start: 0.9083 (tp40) cc_final: 0.8603 (tp40) REVERT: I 340 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8451 (mttm) REVERT: I 343 LYS cc_start: 0.9045 (mttp) cc_final: 0.8648 (mmmt) REVERT: J 321 LYS cc_start: 0.9212 (mtmm) cc_final: 0.8854 (mttm) REVERT: J 340 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8211 (mttm) REVERT: J 345 ASP cc_start: 0.8702 (t0) cc_final: 0.8442 (t0) outliers start: 36 outliers final: 33 residues processed: 392 average time/residue: 0.2206 time to fit residues: 105.7879 Evaluate side-chains 418 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 383 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 352 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 20 optimal weight: 0.0470 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.130233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.111786 restraints weight = 9285.921| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.29 r_work: 0.3759 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5960 Z= 0.147 Angle : 0.637 9.461 7970 Z= 0.306 Chirality : 0.049 0.130 890 Planarity : 0.005 0.044 1020 Dihedral : 4.542 14.837 790 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.22 % Allowed : 24.03 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.96 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 374 PHE 0.008 0.002 PHE I 378 TYR 0.016 0.003 TYR A 310 ARG 0.001 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02591 ( 95) hydrogen bonds : angle 4.55568 ( 285) covalent geometry : bond 0.00348 ( 5960) covalent geometry : angle 0.63692 ( 7970) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 391 time to evaluate : 0.718 Fit side-chains REVERT: A 317 LYS cc_start: 0.8880 (ptpt) cc_final: 0.8478 (ptpp) REVERT: A 331 LYS cc_start: 0.9293 (mtmt) cc_final: 0.8931 (mttp) REVERT: A 357 LEU cc_start: 0.9199 (tt) cc_final: 0.8971 (tt) REVERT: B 317 LYS cc_start: 0.8272 (ptpt) cc_final: 0.7802 (ptpp) REVERT: B 321 LYS cc_start: 0.9188 (mttp) cc_final: 0.8979 (mttp) REVERT: B 331 LYS cc_start: 0.9218 (mtmt) cc_final: 0.8917 (mttt) REVERT: B 340 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8052 (mttm) REVERT: B 375 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8542 (tttt) REVERT: C 310 TYR cc_start: 0.8997 (t80) cc_final: 0.8567 (t80) REVERT: C 317 LYS cc_start: 0.8868 (ptpt) cc_final: 0.8431 (ptpp) REVERT: C 340 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8415 (mttp) REVERT: C 356 SER cc_start: 0.8945 (p) cc_final: 0.8735 (p) REVERT: D 317 LYS cc_start: 0.8080 (ptpt) cc_final: 0.7682 (ptpp) REVERT: D 331 LYS cc_start: 0.9174 (mtmt) cc_final: 0.8752 (mttt) REVERT: D 340 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8330 (mttp) REVERT: D 343 LYS cc_start: 0.9100 (mttt) cc_final: 0.8509 (mtpp) REVERT: E 310 TYR cc_start: 0.9230 (t80) cc_final: 0.8663 (t80) REVERT: E 327 ASN cc_start: 0.9120 (t0) cc_final: 0.8701 (t0) REVERT: E 331 LYS cc_start: 0.9215 (mtmt) cc_final: 0.8978 (mttt) REVERT: E 338 GLU cc_start: 0.8840 (tt0) cc_final: 0.8383 (tt0) REVERT: E 340 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8113 (mttm) REVERT: E 342 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: E 343 LYS cc_start: 0.8638 (mppt) cc_final: 0.8388 (ttmt) REVERT: F 317 LYS cc_start: 0.8095 (ptpt) cc_final: 0.7695 (ptpp) REVERT: F 331 LYS cc_start: 0.9141 (mtmt) cc_final: 0.8713 (mttp) REVERT: F 340 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8253 (mttp) REVERT: F 342 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8447 (mp0) REVERT: F 372 GLU cc_start: 0.8830 (tt0) cc_final: 0.8568 (tt0) REVERT: G 310 TYR cc_start: 0.9301 (t80) cc_final: 0.8879 (t80) REVERT: G 331 LYS cc_start: 0.9139 (mtmt) cc_final: 0.8883 (mttt) REVERT: G 378 PHE cc_start: 0.8953 (t80) cc_final: 0.8622 (t80) REVERT: H 317 LYS cc_start: 0.8041 (ptpt) cc_final: 0.7593 (ptpp) REVERT: H 340 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8173 (mttm) REVERT: H 342 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8569 (mp0) REVERT: H 343 LYS cc_start: 0.9046 (mttt) cc_final: 0.8637 (mtpp) REVERT: H 345 ASP cc_start: 0.8504 (t0) cc_final: 0.8236 (t0) REVERT: I 317 LYS cc_start: 0.8143 (ptpt) cc_final: 0.7739 (ptpp) REVERT: I 331 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8868 (mttp) REVERT: I 336 GLN cc_start: 0.9047 (tp40) cc_final: 0.8627 (tp40) REVERT: I 340 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8536 (mttm) REVERT: I 343 LYS cc_start: 0.9088 (mttp) cc_final: 0.8713 (mmmt) REVERT: J 321 LYS cc_start: 0.9205 (mtmm) cc_final: 0.8850 (mttm) REVERT: J 340 LYS cc_start: 0.8851 (ttmm) cc_final: 0.8234 (mttm) REVERT: J 345 ASP cc_start: 0.8706 (t0) cc_final: 0.8454 (t0) outliers start: 35 outliers final: 31 residues processed: 395 average time/residue: 0.2138 time to fit residues: 103.0867 Evaluate side-chains 421 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 388 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 352 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 0.0070 chunk 53 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.133388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.114772 restraints weight = 9123.672| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.35 r_work: 0.3806 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5960 Z= 0.108 Angle : 0.643 9.751 7970 Z= 0.300 Chirality : 0.049 0.124 890 Planarity : 0.004 0.043 1020 Dihedral : 4.417 14.714 790 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.69 % Allowed : 27.46 % Favored : 69.85 % 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: -2.91 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 329 PHE 0.009 0.002 PHE I 378 TYR 0.016 0.002 TYR A 310 ARG 0.001 0.000 ARG I 349 Details of bonding type rmsd hydrogen bonds : bond 0.02040 ( 95) hydrogen bonds : angle 4.36742 ( 285) covalent geometry : bond 0.00262 ( 5960) covalent geometry : angle 0.64347 ( 7970) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 397 time to evaluate : 0.753 Fit side-chains REVERT: A 317 LYS cc_start: 0.8860 (ptpt) cc_final: 0.8459 (ptpp) REVERT: A 331 LYS cc_start: 0.9254 (mtmt) cc_final: 0.8893 (mttp) REVERT: A 357 LEU cc_start: 0.9134 (tt) cc_final: 0.8888 (tt) REVERT: B 317 LYS cc_start: 0.8183 (ptpt) cc_final: 0.7695 (ptpp) REVERT: B 331 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8936 (mttt) REVERT: B 340 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8075 (mttm) REVERT: B 370 LYS cc_start: 0.8940 (tttm) cc_final: 0.8683 (tttm) REVERT: B 375 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8516 (tttt) REVERT: C 310 TYR cc_start: 0.9023 (t80) cc_final: 0.8559 (t80) REVERT: C 317 LYS cc_start: 0.8847 (ptpt) cc_final: 0.8407 (ptpp) REVERT: C 325 LEU cc_start: 0.8435 (tp) cc_final: 0.8183 (tp) REVERT: C 340 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8398 (mttp) REVERT: C 356 SER cc_start: 0.8833 (p) cc_final: 0.8631 (p) REVERT: D 317 LYS cc_start: 0.8014 (ptpt) cc_final: 0.7628 (ptpp) REVERT: D 331 LYS cc_start: 0.9173 (mtmt) cc_final: 0.8719 (mttt) REVERT: D 340 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8295 (mttp) REVERT: D 343 LYS cc_start: 0.9111 (mttt) cc_final: 0.8573 (mtpp) REVERT: E 310 TYR cc_start: 0.9233 (t80) cc_final: 0.8682 (t80) REVERT: E 331 LYS cc_start: 0.9188 (mtmt) cc_final: 0.8976 (mttt) REVERT: E 338 GLU cc_start: 0.8802 (tt0) cc_final: 0.8357 (tt0) REVERT: E 340 LYS cc_start: 0.8808 (ttmm) cc_final: 0.8113 (mttm) REVERT: E 342 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8379 (mp0) REVERT: E 343 LYS cc_start: 0.8624 (mppt) cc_final: 0.8373 (ttmt) REVERT: F 317 LYS cc_start: 0.8095 (ptpt) cc_final: 0.7691 (ptpp) REVERT: F 331 LYS cc_start: 0.9109 (mtmt) cc_final: 0.8716 (mttp) REVERT: F 340 LYS cc_start: 0.8848 (ttmm) cc_final: 0.8297 (mttp) REVERT: F 342 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8439 (mp0) REVERT: F 372 GLU cc_start: 0.8838 (tt0) cc_final: 0.8554 (tt0) REVERT: G 310 TYR cc_start: 0.9219 (t80) cc_final: 0.8834 (t80) REVERT: G 331 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8877 (mttt) REVERT: G 372 GLU cc_start: 0.8640 (tt0) cc_final: 0.8376 (tt0) REVERT: G 378 PHE cc_start: 0.8936 (t80) cc_final: 0.8579 (t80) REVERT: H 317 LYS cc_start: 0.8055 (ptpt) cc_final: 0.7627 (ptpp) REVERT: H 340 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8174 (mttm) REVERT: H 342 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8592 (mp0) REVERT: H 343 LYS cc_start: 0.9007 (mttt) cc_final: 0.8604 (mtpp) REVERT: H 345 ASP cc_start: 0.8497 (t0) cc_final: 0.8263 (t0) REVERT: I 317 LYS cc_start: 0.8159 (ptpt) cc_final: 0.7752 (ptpp) REVERT: I 331 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8878 (mttp) REVERT: I 336 GLN cc_start: 0.9049 (tp40) cc_final: 0.8534 (tp40) REVERT: I 340 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8624 (mttp) REVERT: I 343 LYS cc_start: 0.9091 (mttp) cc_final: 0.8725 (mmmt) REVERT: J 317 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7733 (ptpp) REVERT: J 321 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8848 (mttm) REVERT: J 331 LYS cc_start: 0.9073 (mtmt) cc_final: 0.7329 (tmtt) REVERT: J 340 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8233 (mttm) REVERT: J 345 ASP cc_start: 0.8701 (t0) cc_final: 0.8473 (t0) outliers start: 18 outliers final: 17 residues processed: 401 average time/residue: 0.2209 time to fit residues: 108.1609 Evaluate side-chains 408 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 391 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 352 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.125900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.107359 restraints weight = 9468.452| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 3.29 r_work: 0.3687 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 5960 Z= 0.304 Angle : 0.745 9.635 7970 Z= 0.361 Chirality : 0.051 0.135 890 Planarity : 0.005 0.052 1020 Dihedral : 4.815 15.153 790 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 3.88 % Allowed : 26.42 % Favored : 69.70 % 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: -2.92 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.010 0.002 PHE I 346 TYR 0.020 0.004 TYR A 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 95) hydrogen bonds : angle 4.83745 ( 285) covalent geometry : bond 0.00706 ( 5960) covalent geometry : angle 0.74461 ( 7970) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 384 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8660 (ptpt) cc_final: 0.8172 (ptpp) REVERT: A 331 LYS cc_start: 0.9125 (mtmt) cc_final: 0.8697 (mttp) REVERT: A 357 LEU cc_start: 0.8737 (tt) cc_final: 0.8511 (tt) REVERT: B 317 LYS cc_start: 0.7700 (ptpt) cc_final: 0.7344 (ptpp) REVERT: B 331 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8523 (mttt) REVERT: B 340 LYS cc_start: 0.8614 (ttmm) cc_final: 0.7817 (mttm) REVERT: B 342 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8530 (mp0) REVERT: B 370 LYS cc_start: 0.8724 (tttm) cc_final: 0.8376 (tttm) REVERT: B 375 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8262 (tttt) REVERT: C 310 TYR cc_start: 0.8896 (t80) cc_final: 0.8489 (t80) REVERT: C 317 LYS cc_start: 0.8667 (ptpt) cc_final: 0.8233 (ptpp) REVERT: C 340 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8467 (mttp) REVERT: C 356 SER cc_start: 0.8643 (p) cc_final: 0.8426 (p) REVERT: D 317 LYS cc_start: 0.7429 (ptpt) cc_final: 0.7073 (ptpp) REVERT: D 331 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8307 (mttt) REVERT: D 340 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8199 (mttp) REVERT: D 343 LYS cc_start: 0.8939 (mttt) cc_final: 0.8310 (mtpp) REVERT: E 310 TYR cc_start: 0.9174 (t80) cc_final: 0.8419 (t80) REVERT: E 331 LYS cc_start: 0.8908 (mtmt) cc_final: 0.8611 (mttt) REVERT: E 338 GLU cc_start: 0.8860 (tt0) cc_final: 0.8498 (tt0) REVERT: E 340 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8202 (mttm) REVERT: E 342 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.7998 (mm-30) REVERT: E 372 GLU cc_start: 0.9003 (tt0) cc_final: 0.8561 (tt0) REVERT: F 317 LYS cc_start: 0.7594 (ptpt) cc_final: 0.7195 (ptpp) REVERT: F 331 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8305 (mttp) REVERT: F 340 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8136 (mttp) REVERT: F 342 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8316 (mm-30) REVERT: F 343 LYS cc_start: 0.8508 (mmtp) cc_final: 0.8046 (mtpp) REVERT: F 372 GLU cc_start: 0.9017 (tt0) cc_final: 0.8645 (tt0) REVERT: G 310 TYR cc_start: 0.9327 (t80) cc_final: 0.8848 (t80) REVERT: G 331 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8452 (mttp) REVERT: G 378 PHE cc_start: 0.8774 (t80) cc_final: 0.8330 (t80) REVERT: H 317 LYS cc_start: 0.7514 (ptpt) cc_final: 0.7138 (ptpp) REVERT: H 340 LYS cc_start: 0.8554 (ttmm) cc_final: 0.7958 (mttp) REVERT: H 342 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8184 (mp0) REVERT: H 343 LYS cc_start: 0.8816 (mttt) cc_final: 0.8431 (mtpp) REVERT: H 345 ASP cc_start: 0.8252 (t0) cc_final: 0.8004 (t0) REVERT: I 317 LYS cc_start: 0.7567 (ptpt) cc_final: 0.7087 (ptpp) REVERT: I 331 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8418 (mttp) REVERT: I 336 GLN cc_start: 0.8947 (tp40) cc_final: 0.8298 (tp40) REVERT: I 340 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8235 (mttp) REVERT: I 343 LYS cc_start: 0.8915 (mttp) cc_final: 0.8497 (mmmt) REVERT: J 317 LYS cc_start: 0.7640 (ptpt) cc_final: 0.7238 (ptpp) REVERT: J 321 LYS cc_start: 0.8976 (mtmm) cc_final: 0.8620 (mttm) REVERT: J 331 LYS cc_start: 0.8782 (mtmt) cc_final: 0.6908 (tmtt) REVERT: J 345 ASP cc_start: 0.8347 (t0) cc_final: 0.8094 (t0) outliers start: 26 outliers final: 24 residues processed: 386 average time/residue: 0.2187 time to fit residues: 102.6579 Evaluate side-chains 406 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 381 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.131422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.112595 restraints weight = 9302.972| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.42 r_work: 0.3755 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5960 Z= 0.131 Angle : 0.681 10.073 7970 Z= 0.319 Chirality : 0.050 0.162 890 Planarity : 0.005 0.047 1020 Dihedral : 4.593 14.675 790 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.69 % Allowed : 28.36 % Favored : 68.96 % 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: -2.93 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 330 PHE 0.008 0.002 PHE J 378 TYR 0.021 0.003 TYR A 310 ARG 0.001 0.000 ARG I 349 Details of bonding type rmsd hydrogen bonds : bond 0.02310 ( 95) hydrogen bonds : angle 4.47893 ( 285) covalent geometry : bond 0.00312 ( 5960) covalent geometry : angle 0.68135 ( 7970) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 391 time to evaluate : 1.026 Fit side-chains REVERT: A 317 LYS cc_start: 0.8675 (ptpt) cc_final: 0.8239 (ptpp) REVERT: A 331 LYS cc_start: 0.9065 (mtmt) cc_final: 0.8685 (mttp) REVERT: A 357 LEU cc_start: 0.8754 (tt) cc_final: 0.8466 (tt) REVERT: B 317 LYS cc_start: 0.7642 (ptpt) cc_final: 0.7236 (ptpp) REVERT: B 331 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8552 (mttt) REVERT: B 340 LYS cc_start: 0.8587 (ttmm) cc_final: 0.7792 (mttm) REVERT: B 370 LYS cc_start: 0.8640 (tttm) cc_final: 0.8375 (tttm) REVERT: B 375 LYS cc_start: 0.8761 (ttmm) cc_final: 0.8299 (tttt) REVERT: C 310 TYR cc_start: 0.8882 (t80) cc_final: 0.8282 (t80) REVERT: C 317 LYS cc_start: 0.8603 (ptpt) cc_final: 0.8168 (ptpp) REVERT: C 340 LYS cc_start: 0.9010 (ttmm) cc_final: 0.8398 (mttp) REVERT: C 356 SER cc_start: 0.8566 (p) cc_final: 0.8363 (p) REVERT: D 317 LYS cc_start: 0.7414 (ptpt) cc_final: 0.7051 (ptpp) REVERT: D 331 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8336 (mttt) REVERT: D 340 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8137 (mttp) REVERT: D 343 LYS cc_start: 0.8914 (mttt) cc_final: 0.8326 (mtpp) REVERT: E 310 TYR cc_start: 0.9232 (t80) cc_final: 0.8635 (t80) REVERT: E 331 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8617 (mttt) REVERT: E 338 GLU cc_start: 0.8884 (tt0) cc_final: 0.8446 (tt0) REVERT: E 340 LYS cc_start: 0.8599 (ttmm) cc_final: 0.7973 (mttm) REVERT: E 342 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8230 (mp0) REVERT: E 372 GLU cc_start: 0.8957 (tt0) cc_final: 0.8571 (tt0) REVERT: F 317 LYS cc_start: 0.7480 (ptpt) cc_final: 0.7120 (ptpp) REVERT: F 331 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8327 (mttp) REVERT: F 340 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8066 (mttp) REVERT: F 342 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8277 (mp0) REVERT: F 372 GLU cc_start: 0.8915 (tt0) cc_final: 0.8579 (tt0) REVERT: G 310 TYR cc_start: 0.9258 (t80) cc_final: 0.8844 (t80) REVERT: G 331 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8481 (mttt) REVERT: G 372 GLU cc_start: 0.8733 (tt0) cc_final: 0.8510 (tt0) REVERT: G 378 PHE cc_start: 0.8746 (t80) cc_final: 0.8276 (t80) REVERT: H 317 LYS cc_start: 0.7461 (ptpt) cc_final: 0.7058 (ptpp) REVERT: H 340 LYS cc_start: 0.8539 (ttmm) cc_final: 0.7926 (mttm) REVERT: H 342 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8445 (mp0) REVERT: H 343 LYS cc_start: 0.8716 (mttt) cc_final: 0.8345 (mtpp) REVERT: H 345 ASP cc_start: 0.8174 (t0) cc_final: 0.7895 (t0) REVERT: I 317 LYS cc_start: 0.7446 (ptpt) cc_final: 0.7102 (ptpp) REVERT: I 331 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8488 (mttp) REVERT: I 336 GLN cc_start: 0.8922 (tp40) cc_final: 0.8289 (tp40) REVERT: I 340 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8413 (mttp) REVERT: I 343 LYS cc_start: 0.8985 (mttp) cc_final: 0.8545 (mmmt) REVERT: J 317 LYS cc_start: 0.7561 (ptpt) cc_final: 0.7197 (ptpp) REVERT: J 321 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8593 (mttm) REVERT: J 331 LYS cc_start: 0.8782 (mtmt) cc_final: 0.6909 (tmtt) REVERT: J 340 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8075 (mttm) outliers start: 18 outliers final: 18 residues processed: 391 average time/residue: 0.2226 time to fit residues: 105.9901 Evaluate side-chains 405 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 387 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 0.5980 chunk 4 optimal weight: 0.0370 chunk 12 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.130870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.112004 restraints weight = 9420.532| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.44 r_work: 0.3772 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5960 Z= 0.143 Angle : 0.685 9.925 7970 Z= 0.323 Chirality : 0.050 0.148 890 Planarity : 0.005 0.049 1020 Dihedral : 4.541 15.071 790 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.13 % Allowed : 28.66 % Favored : 68.21 % 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: -2.84 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 374 PHE 0.007 0.002 PHE J 378 TYR 0.019 0.004 TYR I 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.02449 ( 95) hydrogen bonds : angle 4.49980 ( 285) covalent geometry : bond 0.00342 ( 5960) covalent geometry : angle 0.68485 ( 7970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3571.42 seconds wall clock time: 63 minutes 32.27 seconds (3812.27 seconds total)