Starting phenix.real_space_refine on Sat May 10 09:59:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4m_44185/05_2025/9b4m_44185.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4m_44185/05_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_44185/05_2025/9b4m_44185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4m_44185/05_2025/9b4m_44185.map" model { file = "/net/cci-nas-00/data/ceres_data/9b4m_44185/05_2025/9b4m_44185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4m_44185/05_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-5687/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: 3.26, per 1000 atoms: 0.56 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: 1.24 Conformation dependent library (CDL) restraints added in 685.9 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: 0.82 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: 1.41 Time building geometry restraints manager: 1.49 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: 0.000 Normalize map: mean=0, sd=1: 4.040 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 15.990 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- 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 : 0.731 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: 0.2183 time to fit residues: 108.6473 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 : 0.718 ------------------------------------------------------------------------------- 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 = 32)----------------| | 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: 0.3714 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.692 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8878 (ptpt) cc_final: 0.8493 (ptpp) REVERT: A 331 LYS cc_start: 0.9294 (mtmt) cc_final: 0.8956 (mttp) REVERT: A 340 LYS cc_start: 0.9105 (ttmm) cc_final: 0.8782 (mttp) REVERT: A 343 LYS cc_start: 0.8861 (mttp) cc_final: 0.8528 (mtpp) REVERT: B 317 LYS cc_start: 0.8354 (ptpt) cc_final: 0.7917 (ptpp) REVERT: B 321 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8791 (mttm) REVERT: B 331 LYS cc_start: 0.9224 (mtmt) cc_final: 0.8926 (mttt) REVERT: B 340 LYS cc_start: 0.8846 (ttmm) cc_final: 0.7853 (mttm) REVERT: B 342 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8572 (mp0) REVERT: B 356 SER cc_start: 0.9569 (p) cc_final: 0.9303 (p) REVERT: B 370 LYS cc_start: 0.8992 (tttm) cc_final: 0.8699 (tttm) REVERT: B 375 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8611 (tttt) REVERT: C 317 LYS cc_start: 0.8895 (ptpt) cc_final: 0.8511 (ptpp) REVERT: C 340 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8538 (mttp) REVERT: C 341 SER cc_start: 0.9046 (m) cc_final: 0.8652 (p) REVERT: C 356 SER cc_start: 0.9138 (p) cc_final: 0.8823 (p) REVERT: D 317 LYS cc_start: 0.8169 (ptpt) cc_final: 0.7800 (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: 0.8612 (t80) REVERT: E 317 LYS cc_start: 0.8130 (ptpt) cc_final: 0.7674 (ptpp) REVERT: E 327 ASN cc_start: 0.9122 (t0) cc_final: 0.8704 (t0) REVERT: E 331 LYS cc_start: 0.9242 (mtmt) cc_final: 0.8977 (mttt) REVERT: E 340 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8277 (mttm) REVERT: E 342 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8408 (mp0) REVERT: E 343 LYS cc_start: 0.8746 (mppt) cc_final: 0.8462 (ttmt) REVERT: E 356 SER cc_start: 0.9596 (p) cc_final: 0.9286 (p) REVERT: E 370 LYS cc_start: 0.9002 (tttm) cc_final: 0.8794 (tttm) REVERT: F 317 LYS cc_start: 0.8035 (ptpt) cc_final: 0.7651 (ptpp) REVERT: F 331 LYS cc_start: 0.9219 (mtmt) cc_final: 0.8752 (mttp) REVERT: F 340 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8191 (mttp) REVERT: F 342 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8622 (mp0) REVERT: F 370 LYS cc_start: 0.9132 (tttm) cc_final: 0.8899 (tttp) REVERT: F 372 GLU cc_start: 0.8890 (tt0) cc_final: 0.8627 (tt0) REVERT: G 310 TYR cc_start: 0.9266 (t80) cc_final: 0.8991 (t80) REVERT: G 317 LYS cc_start: 0.8010 (ptpt) cc_final: 0.7622 (ptpp) REVERT: G 331 LYS cc_start: 0.9190 (mtmt) cc_final: 0.8874 (mttp) REVERT: G 342 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: G 356 SER cc_start: 0.9575 (p) cc_final: 0.9316 (p) REVERT: G 378 PHE cc_start: 0.8992 (t80) cc_final: 0.8746 (t80) REVERT: H 317 LYS cc_start: 0.8086 (ptpt) cc_final: 0.7445 (ptpp) REVERT: H 331 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8834 (mttp) REVERT: H 342 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8468 (mp0) REVERT: H 343 LYS cc_start: 0.9031 (mttt) cc_final: 0.8635 (mtpp) REVERT: H 356 SER cc_start: 0.9575 (p) cc_final: 0.9356 (p) REVERT: I 317 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7672 (ptpp) REVERT: I 331 LYS cc_start: 0.9246 (mtmt) cc_final: 0.8810 (mttp) REVERT: I 336 GLN cc_start: 0.9156 (tp40) cc_final: 0.8493 (tp40) REVERT: I 340 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8279 (mttp) REVERT: I 343 LYS cc_start: 0.9037 (mttp) cc_final: 0.8584 (mtpp) REVERT: J 317 LYS cc_start: 0.8302 (ptpt) cc_final: 0.7835 (ptpp) REVERT: J 321 LYS cc_start: 0.9223 (mtmm) cc_final: 0.8909 (mttm) REVERT: J 331 LYS cc_start: 0.9163 (mtmt) cc_final: 0.7377 (tmtt) REVERT: J 340 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8087 (mttm) REVERT: J 356 SER cc_start: 0.9458 (p) cc_final: 0.9132 (p) outliers start: 33 outliers final: 27 residues processed: 409 average time/residue: 0.2086 time to fit residues: 104.0563 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 : 0.816 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.134360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.115644 restraints weight = 9090.862| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.26 r_work: 0.3780 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2275 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= 0.144 Angle : 0.640 7.640 7970 Z= 0.303 Chirality : 0.050 0.158 890 Planarity : 0.004 0.035 1020 Dihedral : 4.540 15.114 790 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.33 % Allowed : 20.45 % 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: -3.04 (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 0.000 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 B 349 Details of bonding type rmsd hydrogen bonds : bond 0.02865 ( 95) hydrogen bonds : angle 4.74890 ( 285) covalent geometry : bond 0.00337 ( 5960) covalent geometry : angle 0.64044 ( 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 436 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 407 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8894 (ptpt) cc_final: 0.8467 (ptpp) REVERT: A 331 LYS cc_start: 0.9272 (mtmt) cc_final: 0.8944 (mttp) REVERT: A 343 LYS cc_start: 0.8674 (mttp) cc_final: 0.8390 (mtpp) REVERT: A 357 LEU cc_start: 0.9183 (tt) cc_final: 0.8975 (tt) REVERT: B 317 LYS cc_start: 0.8270 (ptpt) cc_final: 0.7825 (ptpp) REVERT: B 321 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8773 (mttp) REVERT: B 331 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8939 (mttt) REVERT: B 340 LYS cc_start: 0.8812 (ttmm) cc_final: 0.7898 (mttm) REVERT: B 342 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8526 (mp0) REVERT: B 370 LYS cc_start: 0.8962 (tttm) cc_final: 0.8635 (tttm) REVERT: B 375 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8604 (tttt) REVERT: C 317 LYS cc_start: 0.8916 (ptpt) cc_final: 0.8510 (ptpp) REVERT: C 340 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8509 (mttm) REVERT: C 341 SER cc_start: 0.9059 (m) cc_final: 0.8809 (p) REVERT: C 343 LYS cc_start: 0.8626 (ttmt) cc_final: 0.8233 (mtpp) REVERT: C 356 SER cc_start: 0.9016 (p) cc_final: 0.8806 (p) REVERT: D 317 LYS cc_start: 0.8135 (ptpt) cc_final: 0.7764 (ptpp) REVERT: D 331 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8768 (mttt) REVERT: D 340 LYS cc_start: 0.8826 (ttmm) cc_final: 0.7993 (mttp) REVERT: D 343 LYS cc_start: 0.9153 (mttt) cc_final: 0.8567 (mtpp) REVERT: E 310 TYR cc_start: 0.9202 (t80) cc_final: 0.8684 (t80) REVERT: E 327 ASN cc_start: 0.9131 (t0) cc_final: 0.8795 (t0) REVERT: E 331 LYS cc_start: 0.9212 (mtmt) cc_final: 0.8990 (mttt) REVERT: E 338 GLU cc_start: 0.8827 (tt0) cc_final: 0.8393 (tt0) REVERT: E 340 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8261 (mttm) REVERT: E 342 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8395 (mp0) REVERT: E 343 LYS cc_start: 0.8672 (mppt) cc_final: 0.8360 (ttmt) REVERT: E 356 SER cc_start: 0.9623 (p) cc_final: 0.9357 (p) REVERT: F 317 LYS cc_start: 0.8073 (ptpt) cc_final: 0.7667 (ptpp) REVERT: F 331 LYS cc_start: 0.9155 (mtmt) cc_final: 0.8747 (mttp) REVERT: F 340 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8194 (mttp) REVERT: F 342 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8474 (mm-30) REVERT: F 370 LYS cc_start: 0.9100 (tttm) cc_final: 0.8815 (tttp) REVERT: F 372 GLU cc_start: 0.8831 (tt0) cc_final: 0.8538 (tt0) REVERT: G 317 LYS cc_start: 0.7955 (ptpt) cc_final: 0.7540 (ptpp) REVERT: G 331 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8851 (mttp) REVERT: G 342 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8377 (mp0) REVERT: G 356 SER cc_start: 0.9596 (p) cc_final: 0.9365 (p) REVERT: G 378 PHE cc_start: 0.8994 (t80) cc_final: 0.8741 (t80) REVERT: H 317 LYS cc_start: 0.8055 (ptpt) cc_final: 0.7648 (ptpp) REVERT: H 331 LYS cc_start: 0.9116 (mtmt) cc_final: 0.8900 (mtmm) REVERT: H 342 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8346 (mp0) REVERT: H 343 LYS cc_start: 0.9062 (mttt) cc_final: 0.8629 (mtpp) REVERT: H 345 ASP cc_start: 0.8435 (t0) cc_final: 0.8215 (t0) REVERT: I 317 LYS cc_start: 0.8099 (ptpt) cc_final: 0.7628 (ptpp) REVERT: I 331 LYS cc_start: 0.9187 (mtmt) cc_final: 0.8811 (mttp) REVERT: I 336 GLN cc_start: 0.9147 (tp40) cc_final: 0.8575 (tp40) REVERT: I 340 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8264 (mttp) REVERT: I 343 LYS cc_start: 0.9086 (mttp) cc_final: 0.8632 (mtpp) REVERT: J 317 LYS cc_start: 0.8218 (ptpt) cc_final: 0.7822 (ptpp) REVERT: J 321 LYS cc_start: 0.9228 (mtmm) cc_final: 0.8904 (mttp) REVERT: J 331 LYS cc_start: 0.9154 (mtmt) cc_final: 0.7358 (tmtt) REVERT: J 340 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8111 (mttm) REVERT: J 356 SER cc_start: 0.9451 (p) cc_final: 0.9246 (p) outliers start: 29 outliers final: 27 residues processed: 411 average time/residue: 0.2124 time to fit residues: 106.7536 Evaluate side-chains 419 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 392 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.130627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.111956 restraints weight = 9342.753| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.29 r_work: 0.3729 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5960 Z= 0.125 Angle : 0.609 9.074 7970 Z= 0.290 Chirality : 0.049 0.125 890 Planarity : 0.004 0.042 1020 Dihedral : 4.399 14.789 790 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.48 % Allowed : 21.79 % Favored : 73.73 % 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: -3.01 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 330 PHE 0.008 0.002 PHE J 378 TYR 0.016 0.002 TYR G 310 ARG 0.001 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.02492 ( 95) hydrogen bonds : angle 4.61729 ( 285) covalent geometry : bond 0.00296 ( 5960) covalent geometry : angle 0.60934 ( 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 439 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 409 time to evaluate : 0.596 Fit side-chains REVERT: A 317 LYS cc_start: 0.8888 (ptpt) cc_final: 0.8458 (ptpp) REVERT: A 331 LYS cc_start: 0.9264 (mtmt) cc_final: 0.8944 (mttp) REVERT: A 343 LYS cc_start: 0.8573 (mttp) cc_final: 0.8301 (mtpp) REVERT: A 353 LYS cc_start: 0.9157 (tttp) cc_final: 0.8956 (tttm) REVERT: A 357 LEU cc_start: 0.9163 (tt) cc_final: 0.8854 (tt) REVERT: B 317 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7699 (ptpp) REVERT: B 331 LYS cc_start: 0.9220 (mtmt) cc_final: 0.8951 (mttt) REVERT: B 340 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8129 (mttm) REVERT: B 342 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8553 (mp0) REVERT: B 375 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8570 (tttt) REVERT: C 310 TYR cc_start: 0.9012 (t80) cc_final: 0.8461 (t80) REVERT: C 317 LYS cc_start: 0.8846 (ptpt) cc_final: 0.8437 (ptpp) REVERT: C 340 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8555 (mttm) REVERT: C 343 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8219 (mtpp) REVERT: C 356 SER cc_start: 0.8973 (p) cc_final: 0.8741 (p) REVERT: D 317 LYS cc_start: 0.8088 (ptpt) cc_final: 0.7707 (ptpp) REVERT: D 331 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8795 (mttt) REVERT: D 340 LYS cc_start: 0.8709 (ttmm) cc_final: 0.8119 (mttp) REVERT: D 343 LYS cc_start: 0.9169 (mttt) cc_final: 0.8558 (mtpp) REVERT: E 310 TYR cc_start: 0.9199 (t80) cc_final: 0.8752 (t80) REVERT: E 327 ASN cc_start: 0.9094 (t0) cc_final: 0.8790 (t0) REVERT: E 331 LYS cc_start: 0.9198 (mtmt) cc_final: 0.8994 (mttt) REVERT: E 338 GLU cc_start: 0.8842 (tt0) cc_final: 0.8430 (tt0) REVERT: E 340 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8188 (mttm) REVERT: E 342 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8456 (mp0) REVERT: E 343 LYS cc_start: 0.8591 (mppt) cc_final: 0.8256 (mmmm) REVERT: E 356 SER cc_start: 0.9527 (p) cc_final: 0.9278 (p) REVERT: F 317 LYS cc_start: 0.8090 (ptpt) cc_final: 0.7698 (ptpp) REVERT: F 331 LYS cc_start: 0.9154 (mtmt) cc_final: 0.8762 (mttp) REVERT: F 340 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8209 (mttp) REVERT: F 342 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8634 (mp0) REVERT: F 372 GLU cc_start: 0.8831 (tt0) cc_final: 0.8595 (tt0) REVERT: G 310 TYR cc_start: 0.9246 (t80) cc_final: 0.9001 (t80) REVERT: G 317 LYS cc_start: 0.7916 (ptpt) cc_final: 0.7482 (ptpp) REVERT: G 331 LYS cc_start: 0.9152 (mtmt) cc_final: 0.8903 (mttt) REVERT: G 356 SER cc_start: 0.9575 (p) cc_final: 0.9325 (p) REVERT: G 372 GLU cc_start: 0.8671 (tt0) cc_final: 0.8456 (tt0) REVERT: G 378 PHE cc_start: 0.8973 (t80) cc_final: 0.8753 (t80) REVERT: H 317 LYS cc_start: 0.8027 (ptpt) cc_final: 0.7521 (ptpp) REVERT: H 331 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8857 (mttm) REVERT: H 340 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8130 (mttm) REVERT: H 342 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8549 (mp0) REVERT: H 343 LYS cc_start: 0.9031 (mttt) cc_final: 0.8594 (mtpp) REVERT: H 345 ASP cc_start: 0.8456 (t0) cc_final: 0.8223 (t0) REVERT: I 317 LYS cc_start: 0.8141 (ptpt) cc_final: 0.7625 (ptpp) REVERT: I 331 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8824 (mttp) REVERT: I 336 GLN cc_start: 0.9132 (tp40) cc_final: 0.8550 (tp40) REVERT: I 340 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8384 (mttp) REVERT: I 343 LYS cc_start: 0.9047 (mttp) cc_final: 0.8625 (mmmt) REVERT: I 353 LYS cc_start: 0.9096 (tttp) cc_final: 0.8857 (tttm) REVERT: J 317 LYS cc_start: 0.8204 (ptpt) cc_final: 0.7788 (ptpp) REVERT: J 321 LYS cc_start: 0.9217 (mtmm) cc_final: 0.8889 (mttp) REVERT: J 331 LYS cc_start: 0.9114 (mtmt) cc_final: 0.7360 (tmtt) REVERT: J 340 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8165 (mttm) REVERT: J 345 ASP cc_start: 0.8736 (t0) cc_final: 0.8447 (t0) outliers start: 30 outliers final: 28 residues processed: 411 average time/residue: 0.2136 time to fit residues: 107.3273 Evaluate side-chains 426 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 398 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 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 344 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 319 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 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 = 0.4071 r_free = 0.4071 target = 0.127837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.109382 restraints weight = 9212.911| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.19 r_work: 0.3690 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.054 5960 Z= 0.444 Angle : 0.782 8.651 7970 Z= 0.396 Chirality : 0.053 0.209 890 Planarity : 0.006 0.048 1020 Dihedral : 5.066 16.608 790 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 5.37 % Allowed : 21.19 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (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 0.005 0.001 HIS A 330 PHE 0.019 0.003 PHE H 346 TYR 0.023 0.004 TYR A 310 ARG 0.002 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 95) hydrogen bonds : angle 5.09498 ( 285) covalent geometry : bond 0.01018 ( 5960) covalent geometry : angle 0.78197 ( 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 412 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 376 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8944 (ptpt) cc_final: 0.8509 (ptpp) REVERT: A 331 LYS cc_start: 0.9344 (mtmt) cc_final: 0.8954 (mttp) REVERT: A 343 LYS cc_start: 0.8719 (mttp) cc_final: 0.8478 (mtpp) REVERT: A 357 LEU cc_start: 0.9138 (tt) cc_final: 0.8897 (tt) REVERT: B 317 LYS cc_start: 0.8332 (ptpt) cc_final: 0.7935 (ptpp) REVERT: B 331 LYS cc_start: 0.9300 (mtmt) cc_final: 0.8920 (mttt) REVERT: B 340 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8180 (mttm) REVERT: B 342 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8387 (mp0) REVERT: B 370 LYS cc_start: 0.9071 (tttm) cc_final: 0.8719 (tttm) REVERT: B 375 LYS cc_start: 0.8939 (ttmm) cc_final: 0.8548 (tttt) REVERT: C 310 TYR cc_start: 0.9076 (t80) cc_final: 0.8839 (t80) REVERT: C 317 LYS cc_start: 0.8973 (ptpt) cc_final: 0.8571 (ptpp) REVERT: C 340 LYS cc_start: 0.9193 (ttmm) cc_final: 0.8601 (mttp) REVERT: C 356 SER cc_start: 0.9075 (p) cc_final: 0.8840 (p) REVERT: D 317 LYS cc_start: 0.8148 (ptpt) cc_final: 0.7770 (ptpp) REVERT: D 331 LYS cc_start: 0.9230 (mtmt) cc_final: 0.8726 (mttt) REVERT: D 340 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8266 (mttp) REVERT: D 343 LYS cc_start: 0.9156 (mttt) cc_final: 0.8589 (mtpp) REVERT: E 310 TYR cc_start: 0.9240 (t80) cc_final: 0.8592 (t80) REVERT: E 327 ASN cc_start: 0.9163 (t0) cc_final: 0.8634 (t0) REVERT: E 331 LYS cc_start: 0.9276 (mtmt) cc_final: 0.8969 (mttt) REVERT: E 338 GLU cc_start: 0.8881 (tt0) cc_final: 0.8495 (tt0) REVERT: E 340 LYS cc_start: 0.8991 (ttmm) cc_final: 0.8396 (mttm) REVERT: E 342 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: E 343 LYS cc_start: 0.8774 (mppt) cc_final: 0.8482 (ttmt) REVERT: E 370 LYS cc_start: 0.9120 (tttm) cc_final: 0.8640 (tttm) REVERT: E 372 GLU cc_start: 0.8975 (tt0) cc_final: 0.8612 (tt0) REVERT: F 317 LYS cc_start: 0.8218 (ptpt) cc_final: 0.7856 (ptpp) REVERT: F 331 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8744 (mttp) REVERT: F 340 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8411 (mttp) REVERT: F 342 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8395 (mm-30) REVERT: F 343 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8515 (mtpt) REVERT: F 372 GLU cc_start: 0.8961 (tt0) cc_final: 0.8703 (tt0) REVERT: G 310 TYR cc_start: 0.9281 (t80) cc_final: 0.8966 (t80) REVERT: G 317 LYS cc_start: 0.8176 (ptpt) cc_final: 0.7707 (ptpp) REVERT: G 331 LYS cc_start: 0.9221 (mtmt) cc_final: 0.8838 (mttp) REVERT: G 356 SER cc_start: 0.9597 (p) cc_final: 0.9367 (p) REVERT: H 317 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7719 (ptpp) REVERT: H 331 LYS cc_start: 0.9137 (mtmt) cc_final: 0.8833 (mtmm) REVERT: H 340 LYS cc_start: 0.8870 (ttmm) cc_final: 0.8242 (mttp) REVERT: H 342 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8295 (mp0) REVERT: H 343 LYS cc_start: 0.9086 (mttt) cc_final: 0.8699 (mtpp) REVERT: H 345 ASP cc_start: 0.8526 (t0) cc_final: 0.8247 (t0) REVERT: I 317 LYS cc_start: 0.8195 (ptpt) cc_final: 0.7699 (ptpp) REVERT: I 331 LYS cc_start: 0.9262 (mtmt) cc_final: 0.8881 (mttp) REVERT: I 336 GLN cc_start: 0.9184 (tp40) cc_final: 0.8592 (tp40) REVERT: I 340 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8328 (mmtp) REVERT: I 343 LYS cc_start: 0.9074 (mttp) cc_final: 0.8637 (mmmt) REVERT: J 317 LYS cc_start: 0.8307 (ptpt) cc_final: 0.7876 (ptpp) REVERT: J 321 LYS cc_start: 0.9227 (mtmm) cc_final: 0.8865 (mttm) REVERT: J 331 LYS cc_start: 0.9192 (mtmt) cc_final: 0.7448 (tmtt) REVERT: J 345 ASP cc_start: 0.8649 (t0) cc_final: 0.8357 (t0) outliers start: 36 outliers final: 33 residues processed: 382 average time/residue: 0.2237 time to fit residues: 103.5468 Evaluate side-chains 401 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 366 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 328 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.129633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.110923 restraints weight = 9139.804| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.27 r_work: 0.3719 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5960 Z= 0.143 Angle : 0.642 8.251 7970 Z= 0.306 Chirality : 0.050 0.148 890 Planarity : 0.005 0.042 1020 Dihedral : 4.620 15.189 790 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.03 % Allowed : 24.03 % Favored : 71.94 % 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: -3.01 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 374 PHE 0.014 0.002 PHE H 346 TYR 0.015 0.002 TYR A 310 ARG 0.001 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.02576 ( 95) hydrogen bonds : angle 4.60348 ( 285) covalent geometry : bond 0.00335 ( 5960) covalent geometry : angle 0.64202 ( 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 425 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 398 time to evaluate : 0.770 Fit side-chains REVERT: A 317 LYS cc_start: 0.8920 (ptpt) cc_final: 0.8425 (ptpp) REVERT: A 331 LYS cc_start: 0.9297 (mtmt) cc_final: 0.8940 (mttp) REVERT: A 357 LEU cc_start: 0.9096 (tt) cc_final: 0.8826 (tt) REVERT: B 317 LYS cc_start: 0.8264 (ptpt) cc_final: 0.7887 (ptpp) REVERT: B 331 LYS cc_start: 0.9235 (mtmt) cc_final: 0.8918 (mttt) REVERT: B 340 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8051 (mttm) REVERT: B 342 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8465 (mp0) REVERT: B 370 LYS cc_start: 0.9013 (tttm) cc_final: 0.8729 (tttm) REVERT: B 375 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8554 (tttt) REVERT: C 310 TYR cc_start: 0.9002 (t80) cc_final: 0.8541 (t80) REVERT: C 317 LYS cc_start: 0.8879 (ptpt) cc_final: 0.8474 (ptpp) REVERT: C 325 LEU cc_start: 0.8648 (tp) cc_final: 0.8307 (tp) REVERT: C 340 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8563 (mttp) REVERT: C 343 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8269 (mtpp) REVERT: C 356 SER cc_start: 0.8959 (p) cc_final: 0.8740 (p) REVERT: D 317 LYS cc_start: 0.8054 (ptpt) cc_final: 0.7670 (ptpp) REVERT: D 331 LYS cc_start: 0.9198 (mtmt) cc_final: 0.8739 (mttt) REVERT: D 340 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8138 (mttp) REVERT: D 343 LYS cc_start: 0.9111 (mttt) cc_final: 0.8472 (mtpp) REVERT: E 310 TYR cc_start: 0.9239 (t80) cc_final: 0.8690 (t80) REVERT: E 327 ASN cc_start: 0.9184 (t0) cc_final: 0.8635 (t0) REVERT: E 331 LYS cc_start: 0.9223 (mtmt) cc_final: 0.9007 (mttt) REVERT: E 338 GLU cc_start: 0.8869 (tt0) cc_final: 0.8402 (tt0) REVERT: E 340 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8161 (mttm) REVERT: E 342 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8327 (mp0) REVERT: E 343 LYS cc_start: 0.8620 (mppt) cc_final: 0.8394 (ttmt) REVERT: E 370 LYS cc_start: 0.9060 (tttm) cc_final: 0.8853 (tttm) REVERT: F 317 LYS cc_start: 0.8100 (ptpt) cc_final: 0.7721 (ptpp) REVERT: F 331 LYS cc_start: 0.9146 (mtmt) cc_final: 0.8761 (mttp) REVERT: F 340 LYS cc_start: 0.8807 (ttmm) cc_final: 0.8245 (mttp) REVERT: F 342 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8479 (mp0) REVERT: F 343 LYS cc_start: 0.8810 (mmtp) cc_final: 0.8392 (mtpt) REVERT: F 372 GLU cc_start: 0.8904 (tt0) cc_final: 0.8663 (tt0) REVERT: G 310 TYR cc_start: 0.9227 (t80) cc_final: 0.8981 (t80) REVERT: G 317 LYS cc_start: 0.7968 (ptpt) cc_final: 0.7476 (ptpp) REVERT: G 331 LYS cc_start: 0.9142 (mtmt) cc_final: 0.8891 (mttt) REVERT: G 378 PHE cc_start: 0.8974 (t80) cc_final: 0.8544 (t80) REVERT: H 317 LYS cc_start: 0.8055 (ptpt) cc_final: 0.7619 (ptpp) REVERT: H 331 LYS cc_start: 0.9127 (mtmt) cc_final: 0.8842 (mttm) REVERT: H 340 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8154 (mttm) REVERT: H 342 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8599 (mp0) REVERT: H 343 LYS cc_start: 0.9011 (mttt) cc_final: 0.8631 (mtpp) REVERT: H 345 ASP cc_start: 0.8544 (t0) cc_final: 0.8257 (t0) REVERT: I 317 LYS cc_start: 0.8058 (ptpt) cc_final: 0.7539 (ptpp) REVERT: I 331 LYS cc_start: 0.9210 (mtmt) cc_final: 0.8828 (mttp) REVERT: I 336 GLN cc_start: 0.9105 (tp40) cc_final: 0.8494 (tp40) REVERT: I 340 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8409 (mttp) REVERT: I 343 LYS cc_start: 0.9084 (mttp) cc_final: 0.8670 (mmmt) REVERT: I 353 LYS cc_start: 0.9063 (tttp) cc_final: 0.8816 (tttp) REVERT: J 317 LYS cc_start: 0.8190 (ptpt) cc_final: 0.7746 (ptpp) REVERT: J 321 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8832 (mttm) REVERT: J 331 LYS cc_start: 0.9128 (mtmt) cc_final: 0.7345 (tmtt) REVERT: J 340 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8198 (mttm) REVERT: J 345 ASP cc_start: 0.8720 (t0) cc_final: 0.8448 (t0) outliers start: 27 outliers final: 26 residues processed: 402 average time/residue: 0.2335 time to fit residues: 115.1682 Evaluate side-chains 412 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 386 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 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 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 318 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.122732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.104195 restraints weight = 9606.276| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.35 r_work: 0.3653 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 5960 Z= 0.345 Angle : 0.737 9.136 7970 Z= 0.363 Chirality : 0.051 0.147 890 Planarity : 0.005 0.050 1020 Dihedral : 4.945 16.003 790 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 5.82 % Allowed : 24.93 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 330 PHE 0.013 0.003 PHE H 346 TYR 0.021 0.003 TYR A 310 ARG 0.002 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 95) hydrogen bonds : angle 4.97415 ( 285) covalent geometry : bond 0.00789 ( 5960) covalent geometry : angle 0.73740 ( 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: 39 poor density : 387 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8691 (ptpt) cc_final: 0.8219 (ptpp) REVERT: A 331 LYS cc_start: 0.9207 (mtmt) cc_final: 0.8779 (mttp) REVERT: A 357 LEU cc_start: 0.8688 (tt) cc_final: 0.8417 (tt) REVERT: B 317 LYS cc_start: 0.7761 (ptpt) cc_final: 0.7407 (ptpp) REVERT: B 331 LYS cc_start: 0.8944 (mtmt) cc_final: 0.8589 (mttt) REVERT: B 340 LYS cc_start: 0.8666 (ttmm) cc_final: 0.7821 (mttm) REVERT: B 370 LYS cc_start: 0.8817 (tttm) cc_final: 0.8461 (tttm) REVERT: B 375 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8317 (tttt) REVERT: C 310 TYR cc_start: 0.8937 (t80) cc_final: 0.8560 (t80) REVERT: C 317 LYS cc_start: 0.8714 (ptpt) cc_final: 0.8295 (ptpp) REVERT: C 340 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8468 (mttp) REVERT: C 356 SER cc_start: 0.8741 (p) cc_final: 0.8513 (p) REVERT: D 317 LYS cc_start: 0.7507 (ptpt) cc_final: 0.7163 (ptpp) REVERT: D 331 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8390 (mttt) REVERT: D 340 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8008 (mttp) REVERT: D 343 LYS cc_start: 0.9006 (mttt) cc_final: 0.8399 (mtpp) REVERT: E 310 TYR cc_start: 0.9226 (t80) cc_final: 0.8540 (t80) REVERT: E 327 ASN cc_start: 0.8862 (t0) cc_final: 0.8336 (t0) REVERT: E 331 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8662 (mttt) REVERT: E 338 GLU cc_start: 0.8878 (tt0) cc_final: 0.8518 (tt0) REVERT: E 340 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8219 (mttm) REVERT: E 342 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8091 (mm-30) REVERT: E 343 LYS cc_start: 0.8471 (mppt) cc_final: 0.8268 (ttmt) REVERT: E 370 LYS cc_start: 0.8808 (tttm) cc_final: 0.8573 (tttm) REVERT: F 317 LYS cc_start: 0.7608 (ptpt) cc_final: 0.7245 (ptpp) REVERT: F 331 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8389 (mttp) REVERT: F 340 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8156 (mttp) REVERT: F 342 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8371 (mm-30) REVERT: F 343 LYS cc_start: 0.8633 (mmtp) cc_final: 0.8197 (mtpt) REVERT: F 372 GLU cc_start: 0.9009 (tt0) cc_final: 0.8711 (tt0) REVERT: G 310 TYR cc_start: 0.9279 (t80) cc_final: 0.8945 (t80) REVERT: G 317 LYS cc_start: 0.7448 (ptpt) cc_final: 0.7037 (ptpp) REVERT: G 331 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8494 (mttp) REVERT: G 378 PHE cc_start: 0.8812 (t80) cc_final: 0.8363 (t80) REVERT: H 317 LYS cc_start: 0.7543 (ptpt) cc_final: 0.7179 (ptpp) REVERT: H 331 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8502 (mtmm) REVERT: H 340 LYS cc_start: 0.8607 (ttmm) cc_final: 0.7998 (mttp) REVERT: H 342 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: H 343 LYS cc_start: 0.8875 (mttt) cc_final: 0.8474 (mtpp) REVERT: H 345 ASP cc_start: 0.8212 (t0) cc_final: 0.7977 (t0) REVERT: I 317 LYS cc_start: 0.7589 (ptpt) cc_final: 0.7110 (ptpp) REVERT: I 331 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8465 (mttp) REVERT: I 336 GLN cc_start: 0.9099 (tp40) cc_final: 0.8357 (tp40) REVERT: I 340 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8150 (mttp) REVERT: I 343 LYS cc_start: 0.8861 (mttp) cc_final: 0.8416 (mmmt) REVERT: I 353 LYS cc_start: 0.8835 (tttp) cc_final: 0.8500 (tttp) REVERT: J 317 LYS cc_start: 0.7743 (ptpt) cc_final: 0.7338 (ptpp) REVERT: J 321 LYS cc_start: 0.9009 (mtmm) cc_final: 0.8626 (mttm) REVERT: J 331 LYS cc_start: 0.8866 (mtmt) cc_final: 0.6979 (tmtt) REVERT: J 345 ASP cc_start: 0.8399 (t0) cc_final: 0.8116 (t0) outliers start: 39 outliers final: 34 residues processed: 392 average time/residue: 0.2197 time to fit residues: 105.3740 Evaluate side-chains 413 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 378 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 373 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 328 ILE 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 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 H residue 342 GLU Chi-restraints excluded: chain H residue 352 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4108 r_free = 0.4108 target = 0.129533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.110589 restraints weight = 9288.609| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.39 r_work: 0.3745 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5960 Z= 0.141 Angle : 0.666 9.224 7970 Z= 0.315 Chirality : 0.050 0.137 890 Planarity : 0.005 0.042 1020 Dihedral : 4.652 15.129 790 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.93 % Allowed : 25.97 % Favored : 69.10 % 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: -2.98 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 330 PHE 0.012 0.002 PHE H 346 TYR 0.017 0.002 TYR A 310 ARG 0.001 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.02562 ( 95) hydrogen bonds : angle 4.63086 ( 285) covalent geometry : bond 0.00334 ( 5960) covalent geometry : angle 0.66632 ( 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 426 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 393 time to evaluate : 0.669 Fit side-chains REVERT: A 317 LYS cc_start: 0.8669 (ptpt) cc_final: 0.8175 (ptpp) REVERT: A 331 LYS cc_start: 0.9137 (mtmt) cc_final: 0.8737 (mttp) REVERT: A 357 LEU cc_start: 0.8588 (tt) cc_final: 0.8270 (tt) REVERT: B 317 LYS cc_start: 0.7659 (ptpt) cc_final: 0.7328 (ptpp) REVERT: B 325 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8931 (pt) REVERT: B 331 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8525 (mttt) REVERT: B 340 LYS cc_start: 0.8555 (ttmm) cc_final: 0.7755 (mttm) REVERT: B 370 LYS cc_start: 0.8709 (tttm) cc_final: 0.8415 (tttm) REVERT: B 375 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8283 (tttt) REVERT: C 310 TYR cc_start: 0.8876 (t80) cc_final: 0.8300 (t80) REVERT: C 317 LYS cc_start: 0.8617 (ptpt) cc_final: 0.8195 (ptpp) REVERT: C 340 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8445 (mttp) REVERT: C 356 SER cc_start: 0.8597 (p) cc_final: 0.8368 (p) REVERT: D 317 LYS cc_start: 0.7422 (ptpt) cc_final: 0.7078 (ptpp) REVERT: D 331 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8326 (mttt) REVERT: D 340 LYS cc_start: 0.8508 (ttmm) cc_final: 0.7908 (mttp) REVERT: D 343 LYS cc_start: 0.8930 (mttt) cc_final: 0.8291 (mtpp) REVERT: E 310 TYR cc_start: 0.9231 (t80) cc_final: 0.8548 (t80) REVERT: E 327 ASN cc_start: 0.8830 (t0) cc_final: 0.8334 (t0) REVERT: E 331 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8631 (mttt) REVERT: E 338 GLU cc_start: 0.8856 (tt0) cc_final: 0.8412 (tt0) REVERT: E 340 LYS cc_start: 0.8528 (ttmm) cc_final: 0.7811 (mttm) REVERT: E 342 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8206 (mp0) REVERT: E 370 LYS cc_start: 0.8654 (tttm) cc_final: 0.8439 (tttm) REVERT: F 317 LYS cc_start: 0.7540 (ptpt) cc_final: 0.7200 (ptpp) REVERT: F 331 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8345 (mttp) REVERT: F 340 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8047 (mttp) REVERT: F 342 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8338 (mp0) REVERT: F 343 LYS cc_start: 0.8545 (mmtp) cc_final: 0.8107 (mtpt) REVERT: F 372 GLU cc_start: 0.8942 (tt0) cc_final: 0.8670 (tt0) REVERT: G 310 TYR cc_start: 0.9237 (t80) cc_final: 0.8885 (t80) REVERT: G 331 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8495 (mttt) REVERT: G 372 GLU cc_start: 0.8806 (tt0) cc_final: 0.8522 (tt0) REVERT: G 378 PHE cc_start: 0.8777 (t80) cc_final: 0.8372 (t80) REVERT: H 317 LYS cc_start: 0.7495 (ptpt) cc_final: 0.7087 (ptpp) REVERT: H 331 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8464 (mttm) REVERT: H 340 LYS cc_start: 0.8519 (ttmm) cc_final: 0.7896 (mttm) REVERT: H 342 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8485 (mp0) REVERT: H 343 LYS cc_start: 0.8798 (mttt) cc_final: 0.8439 (mtpp) REVERT: H 345 ASP cc_start: 0.8221 (t0) cc_final: 0.7999 (t0) REVERT: I 317 LYS cc_start: 0.7415 (ptpt) cc_final: 0.6882 (ptpp) REVERT: I 331 LYS cc_start: 0.8886 (mtmt) cc_final: 0.8470 (mttp) REVERT: I 336 GLN cc_start: 0.9026 (tp40) cc_final: 0.8201 (tp40) REVERT: I 340 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8254 (mttp) REVERT: I 343 LYS cc_start: 0.8899 (mttp) cc_final: 0.8461 (mmmt) REVERT: I 353 LYS cc_start: 0.8766 (tttp) cc_final: 0.8454 (tttp) REVERT: J 317 LYS cc_start: 0.7595 (ptpt) cc_final: 0.7198 (ptpp) REVERT: J 321 LYS cc_start: 0.8947 (mtmm) cc_final: 0.8572 (mttm) REVERT: J 331 LYS cc_start: 0.8787 (mtmt) cc_final: 0.6891 (tmtt) REVERT: J 340 LYS cc_start: 0.8650 (ttmm) cc_final: 0.7995 (mttm) REVERT: J 345 ASP cc_start: 0.8427 (t0) cc_final: 0.8160 (t0) outliers start: 33 outliers final: 32 residues processed: 397 average time/residue: 0.2168 time to fit residues: 104.9804 Evaluate side-chains 423 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 390 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 325 LEU 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 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 H residue 352 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 67 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.127708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.108821 restraints weight = 9346.422| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.42 r_work: 0.3719 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5960 Z= 0.196 Angle : 0.669 9.750 7970 Z= 0.322 Chirality : 0.050 0.128 890 Planarity : 0.005 0.048 1020 Dihedral : 4.688 15.429 790 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 4.78 % Allowed : 26.72 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.002 0.001 HIS C 330 PHE 0.012 0.002 PHE H 346 TYR 0.019 0.003 TYR A 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 95) hydrogen bonds : angle 4.69737 ( 285) covalent geometry : bond 0.00459 ( 5960) covalent geometry : angle 0.66918 ( 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 426 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 394 time to evaluate : 0.717 Fit side-chains REVERT: A 317 LYS cc_start: 0.8688 (ptpt) cc_final: 0.8188 (ptpp) REVERT: A 331 LYS cc_start: 0.9153 (mtmt) cc_final: 0.8747 (mttp) REVERT: A 357 LEU cc_start: 0.8721 (tt) cc_final: 0.8449 (tt) REVERT: B 317 LYS cc_start: 0.7698 (ptpt) cc_final: 0.7358 (ptpp) REVERT: B 331 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8531 (mttt) REVERT: B 340 LYS cc_start: 0.8588 (ttmm) cc_final: 0.7776 (mttm) REVERT: B 370 LYS cc_start: 0.8724 (tttm) cc_final: 0.8413 (tttm) REVERT: B 375 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8282 (tttt) REVERT: C 310 TYR cc_start: 0.8924 (t80) cc_final: 0.8418 (t80) REVERT: C 317 LYS cc_start: 0.8639 (ptpt) cc_final: 0.8209 (ptpp) REVERT: C 340 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8442 (mttp) REVERT: C 356 SER cc_start: 0.8596 (p) cc_final: 0.8388 (p) REVERT: D 317 LYS cc_start: 0.7441 (ptpt) cc_final: 0.7093 (ptpp) REVERT: D 331 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8344 (mttt) REVERT: D 340 LYS cc_start: 0.8546 (ttmm) cc_final: 0.7956 (mttp) REVERT: D 343 LYS cc_start: 0.8944 (mttt) cc_final: 0.8316 (mtpp) REVERT: E 310 TYR cc_start: 0.9219 (t80) cc_final: 0.8614 (t80) REVERT: E 327 ASN cc_start: 0.8875 (t0) cc_final: 0.8322 (t0) REVERT: E 331 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8620 (mttt) REVERT: E 338 GLU cc_start: 0.8883 (tt0) cc_final: 0.8508 (tt0) REVERT: E 340 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8025 (mttm) REVERT: E 370 LYS cc_start: 0.8702 (tttm) cc_final: 0.8482 (tttm) REVERT: F 317 LYS cc_start: 0.7550 (ptpt) cc_final: 0.7195 (ptpp) REVERT: F 331 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8325 (mttp) REVERT: F 340 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8125 (mttp) REVERT: F 342 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8306 (mp0) REVERT: F 343 LYS cc_start: 0.8545 (mmtp) cc_final: 0.8047 (mtpt) REVERT: F 372 GLU cc_start: 0.8948 (tt0) cc_final: 0.8691 (tt0) REVERT: G 310 TYR cc_start: 0.9225 (t80) cc_final: 0.8988 (t80) REVERT: G 331 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8426 (mttp) REVERT: G 372 GLU cc_start: 0.8838 (tt0) cc_final: 0.8535 (tt0) REVERT: G 378 PHE cc_start: 0.8775 (t80) cc_final: 0.8347 (t80) REVERT: H 317 LYS cc_start: 0.7495 (ptpt) cc_final: 0.7086 (ptpp) REVERT: H 331 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8426 (mttm) REVERT: H 340 LYS cc_start: 0.8549 (ttmm) cc_final: 0.7932 (mttm) REVERT: H 342 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8433 (mp0) REVERT: H 343 LYS cc_start: 0.8810 (mttt) cc_final: 0.8420 (mtpp) REVERT: I 317 LYS cc_start: 0.7508 (ptpt) cc_final: 0.7150 (ptpp) REVERT: I 331 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8433 (mttp) REVERT: I 336 GLN cc_start: 0.9049 (tp40) cc_final: 0.8222 (tp40) REVERT: I 340 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8255 (mttp) REVERT: I 343 LYS cc_start: 0.8897 (mttp) cc_final: 0.8467 (mmmt) REVERT: J 317 LYS cc_start: 0.7695 (ptpt) cc_final: 0.7274 (ptpp) REVERT: J 321 LYS cc_start: 0.8976 (mtmm) cc_final: 0.8604 (mttm) REVERT: J 331 LYS cc_start: 0.8805 (mtmt) cc_final: 0.6939 (tmtt) REVERT: J 340 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8030 (mttm) REVERT: J 345 ASP cc_start: 0.8455 (t0) cc_final: 0.8183 (t0) outliers start: 32 outliers final: 30 residues processed: 396 average time/residue: 0.2181 time to fit residues: 105.5013 Evaluate side-chains 420 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 390 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 H residue 352 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.132063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.112971 restraints weight = 9285.534| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 3.49 r_work: 0.3804 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5960 Z= 0.118 Angle : 0.655 9.932 7970 Z= 0.309 Chirality : 0.049 0.124 890 Planarity : 0.005 0.044 1020 Dihedral : 4.546 15.122 790 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.03 % Allowed : 27.46 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 330 PHE 0.015 0.002 PHE H 346 TYR 0.020 0.003 TYR A 310 ARG 0.001 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.02249 ( 95) hydrogen bonds : angle 4.45676 ( 285) covalent geometry : bond 0.00284 ( 5960) covalent geometry : angle 0.65486 ( 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 421 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 394 time to evaluate : 0.725 Fit side-chains REVERT: A 317 LYS cc_start: 0.8731 (ptpt) cc_final: 0.8294 (ptpp) REVERT: A 331 LYS cc_start: 0.9152 (mtmt) cc_final: 0.8731 (mttp) REVERT: A 357 LEU cc_start: 0.8769 (tt) cc_final: 0.8493 (tt) REVERT: B 317 LYS cc_start: 0.7773 (ptpt) cc_final: 0.7334 (ptpp) REVERT: B 331 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8607 (mttt) REVERT: B 340 LYS cc_start: 0.8578 (ttmm) cc_final: 0.7789 (mttm) REVERT: B 370 LYS cc_start: 0.8762 (tttm) cc_final: 0.8458 (tttm) REVERT: B 375 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8352 (tttt) REVERT: C 310 TYR cc_start: 0.8939 (t80) cc_final: 0.8395 (t80) REVERT: C 317 LYS cc_start: 0.8645 (ptpt) cc_final: 0.8198 (ptpp) REVERT: C 340 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8403 (mttp) REVERT: C 356 SER cc_start: 0.8559 (p) cc_final: 0.8358 (p) REVERT: D 317 LYS cc_start: 0.7545 (ptpt) cc_final: 0.7176 (ptpp) REVERT: D 331 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8371 (mttp) REVERT: D 340 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8007 (mttp) REVERT: D 343 LYS cc_start: 0.8965 (mttt) cc_final: 0.8379 (mtpp) REVERT: E 310 TYR cc_start: 0.9251 (t80) cc_final: 0.8614 (t80) REVERT: E 327 ASN cc_start: 0.8925 (t0) cc_final: 0.8389 (t0) REVERT: E 331 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8686 (mttt) REVERT: E 338 GLU cc_start: 0.8864 (tt0) cc_final: 0.8369 (tt0) REVERT: E 340 LYS cc_start: 0.8608 (ttmm) cc_final: 0.7851 (mttm) REVERT: F 317 LYS cc_start: 0.7633 (ptpt) cc_final: 0.7256 (ptpp) REVERT: F 331 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8362 (mttp) REVERT: F 340 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8108 (mttp) REVERT: F 342 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8328 (mp0) REVERT: F 372 GLU cc_start: 0.8881 (tt0) cc_final: 0.8576 (tt0) REVERT: G 310 TYR cc_start: 0.9243 (t80) cc_final: 0.8988 (t80) REVERT: G 331 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8566 (mttt) REVERT: G 372 GLU cc_start: 0.8781 (tt0) cc_final: 0.8486 (tt0) REVERT: G 378 PHE cc_start: 0.8823 (t80) cc_final: 0.8353 (t80) REVERT: H 317 LYS cc_start: 0.7609 (ptpt) cc_final: 0.7170 (ptpp) REVERT: H 331 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8514 (mttm) REVERT: H 340 LYS cc_start: 0.8603 (ttmm) cc_final: 0.7979 (mttm) REVERT: H 342 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8469 (mp0) REVERT: H 343 LYS cc_start: 0.8786 (mttt) cc_final: 0.8391 (mtpp) REVERT: I 317 LYS cc_start: 0.7578 (ptpt) cc_final: 0.7213 (ptpp) REVERT: I 331 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8544 (mttp) REVERT: I 336 GLN cc_start: 0.9087 (tp40) cc_final: 0.8252 (tp40) REVERT: I 340 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8289 (mttp) REVERT: I 343 LYS cc_start: 0.8995 (mttp) cc_final: 0.8580 (mmmt) REVERT: J 317 LYS cc_start: 0.7771 (ptpt) cc_final: 0.7322 (ptpp) REVERT: J 321 LYS cc_start: 0.9022 (mtmm) cc_final: 0.8649 (mttm) REVERT: J 331 LYS cc_start: 0.8844 (mtmt) cc_final: 0.6982 (tmtt) REVERT: J 340 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8090 (mttm) REVERT: J 345 ASP cc_start: 0.8576 (t0) cc_final: 0.8274 (t0) outliers start: 27 outliers final: 26 residues processed: 397 average time/residue: 0.2167 time to fit residues: 105.1889 Evaluate side-chains 415 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 389 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 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 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 320 SER Chi-restraints excluded: chain E residue 373 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 H residue 319 THR Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 328 ILE 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: 4.9990 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.127430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.108443 restraints weight = 9439.971| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 3.41 r_work: 0.3710 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5960 Z= 0.227 Angle : 0.712 9.812 7970 Z= 0.341 Chirality : 0.050 0.139 890 Planarity : 0.005 0.050 1020 Dihedral : 4.707 15.671 790 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 4.03 % Allowed : 28.21 % Favored : 67.76 % 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: -2.89 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 374 PHE 0.013 0.002 PHE H 346 TYR 0.019 0.004 TYR I 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 95) hydrogen bonds : angle 4.71974 ( 285) covalent geometry : bond 0.00533 ( 5960) covalent geometry : angle 0.71204 ( 7970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3451.11 seconds wall clock time: 61 minutes 45.16 seconds (3705.16 seconds total)