Starting phenix.real_space_refine on Wed Sep 17 06:12:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4o_44187/09_2025/9b4o_44187.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4o_44187/09_2025/9b4o_44187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b4o_44187/09_2025/9b4o_44187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4o_44187/09_2025/9b4o_44187.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b4o_44187/09_2025/9b4o_44187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4o_44187/09_2025/9b4o_44187.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.89, per 1000 atoms: 0.15 Number of scatterers: 5870 At special positions: 0 Unit cell: (137.5, 107.8, 46.2, 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: 0.32 Conformation dependent library (CDL) restraints added in 163.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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 18 sheets defined 0.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.223A pdb=" N VAL A 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL D 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL F 306 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL H 306 " --> pdb=" O GLN J 307 " (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 321 through 328 removed outlier: 7.038A pdb=" N CYS D 322 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY A 323 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE D 328 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS F 322 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY D 323 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE F 328 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS H 322 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY F 323 " --> pdb=" O CYS H 322 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE H 328 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS J 322 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY H 323 " --> pdb=" O CYS J 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE J 328 " --> pdb=" O ASN H 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.706A pdb=" N VAL A 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL F 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 6.706A 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 345 through 346 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 362 removed outlier: 7.084A pdb=" N GLY A 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASP D 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ILE D 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN A 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N HIS D 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY D 355 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASP F 358 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU D 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE F 360 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N HIS F 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR D 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY F 355 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASP H 358 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU F 357 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE H 360 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN F 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N HIS H 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR F 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY H 355 " --> pdb=" O SER J 356 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASP J 358 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU H 357 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE J 360 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN H 359 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N HIS J 362 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 6.573A 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 373 removed outlier: 6.524A pdb=" N LYS A 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR D 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU A 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR F 373 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU D 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS F 370 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR H 373 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU F 372 " --> pdb=" O THR H 373 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS H 370 " --> pdb=" O ILE J 371 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR J 373 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU H 372 " --> pdb=" O THR J 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 378 removed outlier: 6.738A pdb=" N LEU A 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU D 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU F 376 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU H 376 " --> pdb=" O THR J 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.223A pdb=" N VAL B 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL E 306 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL G 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.907A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.695A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 321 through 328 removed outlier: 6.056A pdb=" N CYS B 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU C 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER B 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASN C 327 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N GLY B 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS E 322 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY B 323 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE E 328 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS G 322 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY E 323 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE G 328 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS I 322 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY G 323 " --> pdb=" O CYS I 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE I 328 " --> pdb=" O ASN G 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 338 removed outlier: 6.707A pdb=" N VAL B 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL E 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL G 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.499A pdb=" N ASP B 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 362 removed outlier: 7.108A pdb=" N GLY C 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY B 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASP E 358 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE E 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN B 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N HIS E 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR B 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY E 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASP G 358 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU E 357 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ILE G 360 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN E 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N HIS G 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR E 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY G 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASP I 358 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU G 357 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE I 360 " --> pdb=" O LEU G 357 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN G 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N HIS I 362 " --> pdb=" O ASN G 359 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR G 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.525A pdb=" N LYS B 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR E 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU B 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS E 370 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR G 373 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU E 372 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS G 370 " --> pdb=" O ILE I 371 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR I 373 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU G 372 " --> pdb=" O THR I 373 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 376 through 378 removed outlier: 6.737A pdb=" N LEU B 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU E 376 " --> pdb=" O THR G 377 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU G 376 " --> pdb=" O THR I 377 " (cutoff:3.500A) 65 hydrogen bonds defined for protein. 195 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: 0.95 Time building geometry restraints manager: 0.50 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 - 1.45: 668 1.45 - 1.57: 3332 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 5960 Sorted by residual: bond pdb=" N LYS G 370 " pdb=" CA LYS G 370 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.20e-02 6.94e+03 4.76e+00 bond pdb=" N LYS B 370 " pdb=" CA LYS B 370 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.20e-02 6.94e+03 4.73e+00 bond pdb=" N LYS E 370 " pdb=" CA LYS E 370 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.20e-02 6.94e+03 4.66e+00 bond pdb=" N LYS F 370 " pdb=" CA LYS F 370 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.20e-02 6.94e+03 4.65e+00 bond pdb=" N LYS D 370 " pdb=" CA LYS D 370 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.20e-02 6.94e+03 4.63e+00 ... (remaining 5955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 7138 1.23 - 2.47: 702 2.47 - 3.70: 100 3.70 - 4.94: 20 4.94 - 6.17: 10 Bond angle restraints: 7970 Sorted by residual: angle pdb=" C LYS C 370 " pdb=" CA LYS C 370 " pdb=" CB LYS C 370 " ideal model delta sigma weight residual 110.24 105.83 4.41 1.46e+00 4.69e-01 9.14e+00 angle pdb=" C LYS I 370 " pdb=" CA LYS I 370 " pdb=" CB LYS I 370 " ideal model delta sigma weight residual 110.24 105.84 4.40 1.46e+00 4.69e-01 9.08e+00 angle pdb=" C LYS D 370 " pdb=" CA LYS D 370 " pdb=" CB LYS D 370 " ideal model delta sigma weight residual 110.24 105.85 4.39 1.46e+00 4.69e-01 9.05e+00 angle pdb=" C LYS J 370 " pdb=" CA LYS J 370 " pdb=" CB LYS J 370 " ideal model delta sigma weight residual 110.24 105.85 4.39 1.46e+00 4.69e-01 9.04e+00 angle pdb=" C LYS A 370 " pdb=" CA LYS A 370 " pdb=" CB LYS A 370 " ideal model delta sigma weight residual 110.24 105.85 4.39 1.46e+00 4.69e-01 9.03e+00 ... (remaining 7965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.97: 2634 6.97 - 13.94: 525 13.94 - 20.91: 281 20.91 - 27.88: 160 27.88 - 34.85: 30 Dihedral angle restraints: 3630 sinusoidal: 1520 harmonic: 2110 Sorted by residual: 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 180.00 164.20 15.80 0 5.00e+00 4.00e-02 9.98e+00 dihedral pdb=" CA LYS I 347 " pdb=" C LYS I 347 " pdb=" N ASP I 348 " pdb=" CA ASP I 348 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.97e+00 dihedral pdb=" CA LYS D 347 " pdb=" C LYS D 347 " pdb=" N ASP D 348 " pdb=" CA ASP D 348 " ideal model delta harmonic sigma weight residual 180.00 164.22 15.78 0 5.00e+00 4.00e-02 9.96e+00 ... (remaining 3627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 515 0.033 - 0.065: 205 0.065 - 0.098: 46 0.098 - 0.130: 104 0.130 - 0.163: 20 Chirality restraints: 890 Sorted by residual: chirality pdb=" CA GLU G 372 " pdb=" N GLU G 372 " pdb=" C GLU G 372 " pdb=" CB GLU G 372 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA GLU B 372 " pdb=" N GLU B 372 " pdb=" C GLU B 372 " pdb=" CB GLU B 372 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA GLU J 372 " pdb=" N GLU J 372 " pdb=" C GLU J 372 " pdb=" CB GLU J 372 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 887 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 331 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO H 332 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO H 332 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 332 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 331 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO E 332 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO E 332 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 332 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 331 " 0.021 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO I 332 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO I 332 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 332 " 0.017 5.00e-02 4.00e+02 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 1788 2.85 - 3.36: 4924 3.36 - 3.87: 8663 3.87 - 4.39: 8823 4.39 - 4.90: 16939 Nonbonded interactions: 41137 Sorted by model distance: nonbonded pdb=" OD1 ASP I 348 " pdb=" N ARG I 349 " model vdw 2.333 3.120 nonbonded pdb=" OD1 ASP B 348 " pdb=" N ARG B 349 " model vdw 2.333 3.120 nonbonded pdb=" OD1 ASP C 348 " pdb=" N ARG C 349 " model vdw 2.333 3.120 nonbonded pdb=" OD1 ASP H 348 " pdb=" N ARG H 349 " model vdw 2.333 3.120 nonbonded pdb=" OD1 ASP J 348 " pdb=" N ARG J 349 " model vdw 2.333 3.120 ... (remaining 41132 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 0.035 5960 Z= 0.281 Angle : 0.771 6.169 7970 Z= 0.440 Chirality : 0.054 0.163 890 Planarity : 0.004 0.031 1020 Dihedral : 11.064 34.846 2290 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.02 (0.20), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.15), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.014 0.004 TYR B 310 PHE 0.008 0.002 PHE D 346 HIS 0.002 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00601 ( 5960) covalent geometry : angle 0.77067 ( 7970) hydrogen bonds : bond 0.38848 ( 65) hydrogen bonds : angle 9.78238 ( 195) *********************** 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 341 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.9282 (mp) cc_final: 0.8823 (tt) REVERT: A 340 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8337 (mtpt) REVERT: A 343 LYS cc_start: 0.8040 (tppt) cc_final: 0.7684 (pttm) REVERT: A 351 GLN cc_start: 0.9409 (tt0) cc_final: 0.9118 (tt0) REVERT: A 379 ARG cc_start: 0.7543 (mmt90) cc_final: 0.7283 (pmt-80) REVERT: B 340 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8425 (tttt) REVERT: B 344 LEU cc_start: 0.9486 (mt) cc_final: 0.9278 (mt) REVERT: B 345 ASP cc_start: 0.8726 (m-30) cc_final: 0.8306 (t0) REVERT: B 370 LYS cc_start: 0.8893 (tttm) cc_final: 0.8670 (ttmm) REVERT: B 372 GLU cc_start: 0.8628 (tt0) cc_final: 0.8390 (mt-10) REVERT: C 308 ILE cc_start: 0.8967 (mt) cc_final: 0.8733 (mt) REVERT: C 315 LEU cc_start: 0.9260 (mp) cc_final: 0.8825 (tt) REVERT: C 343 LYS cc_start: 0.8188 (tppt) cc_final: 0.7871 (pttp) REVERT: C 379 ARG cc_start: 0.7346 (mmt90) cc_final: 0.6968 (pmt-80) REVERT: D 311 LYS cc_start: 0.8861 (mttt) cc_final: 0.8644 (mttt) REVERT: D 314 ASP cc_start: 0.8463 (t0) cc_final: 0.8208 (t0) REVERT: D 315 LEU cc_start: 0.9443 (mp) cc_final: 0.8918 (tt) REVERT: D 343 LYS cc_start: 0.8249 (tppt) cc_final: 0.8014 (mmmm) REVERT: D 345 ASP cc_start: 0.8785 (m-30) cc_final: 0.8394 (t0) REVERT: D 351 GLN cc_start: 0.9347 (tt0) cc_final: 0.9118 (tt0) REVERT: D 370 LYS cc_start: 0.8873 (tttm) cc_final: 0.8392 (ttmm) REVERT: E 315 LEU cc_start: 0.9335 (mp) cc_final: 0.8800 (tt) REVERT: E 343 LYS cc_start: 0.8242 (tppt) cc_final: 0.8013 (mmmm) REVERT: E 345 ASP cc_start: 0.8603 (m-30) cc_final: 0.8196 (t0) REVERT: E 370 LYS cc_start: 0.8952 (tttm) cc_final: 0.8599 (tttm) REVERT: E 372 GLU cc_start: 0.8763 (tt0) cc_final: 0.8525 (tt0) REVERT: E 379 ARG cc_start: 0.7405 (mmt90) cc_final: 0.7038 (mmm-85) REVERT: F 315 LEU cc_start: 0.9351 (mp) cc_final: 0.8760 (tt) REVERT: F 345 ASP cc_start: 0.8729 (m-30) cc_final: 0.8251 (t0) REVERT: F 379 ARG cc_start: 0.7314 (mmt90) cc_final: 0.7027 (mmm-85) REVERT: G 311 LYS cc_start: 0.8853 (mttt) cc_final: 0.8570 (mtmt) REVERT: G 345 ASP cc_start: 0.8844 (m-30) cc_final: 0.8341 (t0) REVERT: G 372 GLU cc_start: 0.8701 (tt0) cc_final: 0.8389 (mt-10) REVERT: G 379 ARG cc_start: 0.7221 (mmt90) cc_final: 0.6894 (mmm-85) REVERT: H 311 LYS cc_start: 0.8964 (mttt) cc_final: 0.8730 (mttt) REVERT: H 314 ASP cc_start: 0.8585 (t0) cc_final: 0.8279 (t0) REVERT: H 315 LEU cc_start: 0.9394 (mp) cc_final: 0.8790 (tt) REVERT: H 343 LYS cc_start: 0.8267 (tppt) cc_final: 0.7932 (mmmm) REVERT: H 344 LEU cc_start: 0.9471 (mt) cc_final: 0.9213 (mt) REVERT: H 345 ASP cc_start: 0.8853 (m-30) cc_final: 0.8343 (t0) REVERT: H 347 LYS cc_start: 0.8892 (pttm) cc_final: 0.8688 (ptpp) REVERT: H 351 GLN cc_start: 0.9430 (tt0) cc_final: 0.9185 (tt0) REVERT: H 379 ARG cc_start: 0.7540 (mmt90) cc_final: 0.7292 (mmm-85) REVERT: I 315 LEU cc_start: 0.9265 (mp) cc_final: 0.8777 (tt) REVERT: I 331 LYS cc_start: 0.9334 (mtmt) cc_final: 0.9039 (mttt) REVERT: I 345 ASP cc_start: 0.8795 (m-30) cc_final: 0.8152 (t0) REVERT: I 358 ASP cc_start: 0.7976 (m-30) cc_final: 0.7697 (m-30) REVERT: I 378 PHE cc_start: 0.8372 (t80) cc_final: 0.8169 (t80) REVERT: I 379 ARG cc_start: 0.7274 (mmt90) cc_final: 0.6652 (mmp-170) REVERT: J 331 LYS cc_start: 0.9321 (mtmt) cc_final: 0.9118 (mttt) REVERT: J 340 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8464 (mtpt) REVERT: J 345 ASP cc_start: 0.8810 (m-30) cc_final: 0.8271 (t0) REVERT: J 379 ARG cc_start: 0.7060 (mmt90) cc_final: 0.6678 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1253 time to fit residues: 50.5016 Evaluate side-chains 281 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN B 336 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN F 307 GLN F 327 ASN G 327 ASN H 327 ASN I 327 ASN I 330 HIS J 307 GLN J 330 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.149233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.128336 restraints weight = 9921.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.131292 restraints weight = 4577.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.133111 restraints weight = 2752.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.134312 restraints weight = 1950.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.135096 restraints weight = 1539.109| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5960 Z= 0.131 Angle : 0.643 6.456 7970 Z= 0.335 Chirality : 0.049 0.150 890 Planarity : 0.004 0.034 1020 Dihedral : 5.311 16.884 790 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.34 % Allowed : 15.82 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.54 (0.22), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.17), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.008 0.001 TYR I 310 PHE 0.017 0.003 PHE A 378 HIS 0.002 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5960) covalent geometry : angle 0.64329 ( 7970) hydrogen bonds : bond 0.06422 ( 65) hydrogen bonds : angle 6.79532 ( 195) *********************** 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 331 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 322 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8587 (ptpp) REVERT: A 315 LEU cc_start: 0.9021 (mp) cc_final: 0.8691 (tt) REVERT: A 340 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8393 (mtpt) REVERT: A 379 ARG cc_start: 0.7616 (mmt90) cc_final: 0.7065 (pmt-80) REVERT: B 315 LEU cc_start: 0.9226 (mp) cc_final: 0.8814 (tt) REVERT: B 340 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8103 (tttt) REVERT: B 345 ASP cc_start: 0.8584 (m-30) cc_final: 0.8348 (t0) REVERT: C 311 LYS cc_start: 0.8700 (mttt) cc_final: 0.8094 (mtmm) REVERT: C 315 LEU cc_start: 0.9236 (mp) cc_final: 0.8814 (tt) REVERT: C 343 LYS cc_start: 0.8420 (tppt) cc_final: 0.7394 (pptt) REVERT: C 379 ARG cc_start: 0.7405 (mmt90) cc_final: 0.6784 (pmt-80) REVERT: D 311 LYS cc_start: 0.9024 (mttt) cc_final: 0.8445 (mtmm) REVERT: D 315 LEU cc_start: 0.9336 (mp) cc_final: 0.8865 (tt) REVERT: D 342 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7721 (mm-30) REVERT: D 345 ASP cc_start: 0.8775 (m-30) cc_final: 0.8259 (t0) REVERT: E 315 LEU cc_start: 0.9205 (mp) cc_final: 0.8767 (tt) REVERT: E 342 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7399 (mm-30) REVERT: E 345 ASP cc_start: 0.8374 (m-30) cc_final: 0.7963 (t0) REVERT: E 370 LYS cc_start: 0.8845 (tttm) cc_final: 0.8220 (tttm) REVERT: E 372 GLU cc_start: 0.8709 (tt0) cc_final: 0.8388 (mt-10) REVERT: E 375 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8729 (ttmm) REVERT: E 379 ARG cc_start: 0.7355 (mmt90) cc_final: 0.6897 (mmm-85) REVERT: F 310 TYR cc_start: 0.8140 (t80) cc_final: 0.7841 (t80) REVERT: F 315 LEU cc_start: 0.9321 (mp) cc_final: 0.8842 (tt) REVERT: F 345 ASP cc_start: 0.8525 (m-30) cc_final: 0.8212 (t0) REVERT: F 379 ARG cc_start: 0.7478 (mmt90) cc_final: 0.6939 (mmm-85) REVERT: G 311 LYS cc_start: 0.8918 (mttt) cc_final: 0.8484 (mtmt) REVERT: G 315 LEU cc_start: 0.9291 (mp) cc_final: 0.8838 (tt) REVERT: G 340 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8239 (tttt) REVERT: G 345 ASP cc_start: 0.8683 (m-30) cc_final: 0.8174 (t0) REVERT: G 379 ARG cc_start: 0.7257 (mmt90) cc_final: 0.6747 (mmm-85) REVERT: H 311 LYS cc_start: 0.8903 (mttt) cc_final: 0.8503 (mtmm) REVERT: H 315 LEU cc_start: 0.9344 (mp) cc_final: 0.8932 (tt) REVERT: H 342 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7665 (mm-30) REVERT: H 344 LEU cc_start: 0.9421 (mt) cc_final: 0.9141 (mt) REVERT: H 345 ASP cc_start: 0.8684 (m-30) cc_final: 0.8107 (t0) REVERT: H 379 ARG cc_start: 0.7348 (mmt90) cc_final: 0.6965 (mmm-85) REVERT: I 311 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8703 (mmtt) REVERT: I 315 LEU cc_start: 0.9208 (mp) cc_final: 0.8699 (tt) REVERT: I 358 ASP cc_start: 0.7959 (m-30) cc_final: 0.7672 (m-30) REVERT: I 375 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8587 (ttmm) REVERT: I 378 PHE cc_start: 0.8382 (t80) cc_final: 0.8169 (t80) REVERT: I 379 ARG cc_start: 0.7155 (mmt90) cc_final: 0.6412 (mmp-170) REVERT: J 311 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8722 (mmtt) REVERT: J 315 LEU cc_start: 0.9245 (mp) cc_final: 0.8727 (tt) REVERT: J 340 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8321 (mtpt) REVERT: J 379 ARG cc_start: 0.7141 (mmt90) cc_final: 0.6520 (mmp-170) outliers start: 9 outliers final: 6 residues processed: 324 average time/residue: 0.1110 time to fit residues: 43.1350 Evaluate side-chains 289 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 283 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** C 336 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN E 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.147265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.125648 restraints weight = 9837.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.128577 restraints weight = 4723.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.130483 restraints weight = 2895.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.131698 restraints weight = 2059.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.132505 restraints weight = 1631.157| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5960 Z= 0.157 Angle : 0.651 5.602 7970 Z= 0.340 Chirality : 0.048 0.138 890 Planarity : 0.004 0.045 1020 Dihedral : 5.560 18.187 790 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.84 % Allowed : 19.25 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.22), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.17), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.014 0.003 TYR I 310 PHE 0.016 0.003 PHE A 346 HIS 0.004 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 5960) covalent geometry : angle 0.65090 ( 7970) hydrogen bonds : bond 0.06593 ( 65) hydrogen bonds : angle 6.45638 ( 195) *********************** 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 307 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 288 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.9125 (mp) cc_final: 0.8780 (tt) REVERT: A 379 ARG cc_start: 0.7522 (mmt90) cc_final: 0.6982 (pmt-80) REVERT: B 315 LEU cc_start: 0.9238 (mp) cc_final: 0.8795 (tt) REVERT: B 340 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8273 (tttt) REVERT: B 345 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8370 (t0) REVERT: C 315 LEU cc_start: 0.9223 (mp) cc_final: 0.8729 (tt) REVERT: C 343 LYS cc_start: 0.8511 (tppt) cc_final: 0.7466 (pptt) REVERT: C 375 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8839 (tttm) REVERT: C 379 ARG cc_start: 0.7481 (mmt90) cc_final: 0.6846 (pmt-80) REVERT: D 311 LYS cc_start: 0.9045 (mttt) cc_final: 0.8436 (mtmm) REVERT: D 315 LEU cc_start: 0.9361 (mp) cc_final: 0.8828 (tt) REVERT: D 345 ASP cc_start: 0.8761 (m-30) cc_final: 0.8293 (t0) REVERT: D 375 LYS cc_start: 0.9007 (tttt) cc_final: 0.8757 (tttp) REVERT: E 315 LEU cc_start: 0.9202 (mp) cc_final: 0.8768 (tt) REVERT: E 343 LYS cc_start: 0.8115 (tppt) cc_final: 0.7843 (mmmm) REVERT: E 345 ASP cc_start: 0.8584 (m-30) cc_final: 0.8110 (t0) REVERT: E 370 LYS cc_start: 0.8857 (tttm) cc_final: 0.8079 (tttm) REVERT: E 372 GLU cc_start: 0.8665 (tt0) cc_final: 0.8412 (mt-10) REVERT: E 379 ARG cc_start: 0.7307 (mmt90) cc_final: 0.6802 (mmm-85) REVERT: F 315 LEU cc_start: 0.9291 (mp) cc_final: 0.8851 (tt) REVERT: F 345 ASP cc_start: 0.8633 (m-30) cc_final: 0.8325 (t0) REVERT: F 379 ARG cc_start: 0.7359 (mmt90) cc_final: 0.6886 (mmm-85) REVERT: G 311 LYS cc_start: 0.8913 (mttt) cc_final: 0.8547 (mtmt) REVERT: G 315 LEU cc_start: 0.9393 (mp) cc_final: 0.8867 (tt) REVERT: G 340 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8250 (tttt) REVERT: G 345 ASP cc_start: 0.8659 (m-30) cc_final: 0.8114 (t0) REVERT: G 379 ARG cc_start: 0.7307 (mmt90) cc_final: 0.6747 (mmm-85) REVERT: H 315 LEU cc_start: 0.9336 (mp) cc_final: 0.8955 (tt) REVERT: H 343 LYS cc_start: 0.8262 (tppt) cc_final: 0.8023 (mmmm) REVERT: H 345 ASP cc_start: 0.8745 (m-30) cc_final: 0.8078 (t0) REVERT: H 379 ARG cc_start: 0.7413 (mmt90) cc_final: 0.7006 (mmm-85) REVERT: I 315 LEU cc_start: 0.9271 (mp) cc_final: 0.8734 (tt) REVERT: I 342 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6900 (mm-30) REVERT: I 358 ASP cc_start: 0.7925 (m-30) cc_final: 0.7528 (m-30) REVERT: I 375 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8521 (ttmm) REVERT: I 379 ARG cc_start: 0.7246 (mmt90) cc_final: 0.6486 (mmp-170) REVERT: J 311 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8796 (mmtt) REVERT: J 315 LEU cc_start: 0.9306 (mp) cc_final: 0.8746 (tt) REVERT: J 340 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8282 (mtpt) REVERT: J 379 ARG cc_start: 0.7194 (mmt90) cc_final: 0.6571 (mmp-170) outliers start: 19 outliers final: 16 residues processed: 295 average time/residue: 0.1178 time to fit residues: 41.3087 Evaluate side-chains 295 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 278 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain H residue 322 CYS Chi-restraints excluded: chain J residue 331 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 375 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN E 327 ASN E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.146008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.124284 restraints weight = 9916.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.127256 restraints weight = 4775.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.129221 restraints weight = 2925.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.130427 restraints weight = 2061.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.131227 restraints weight = 1630.501| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5960 Z= 0.200 Angle : 0.701 6.774 7970 Z= 0.368 Chirality : 0.049 0.137 890 Planarity : 0.004 0.037 1020 Dihedral : 5.883 18.847 790 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 3.43 % Allowed : 20.30 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.21), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.16), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.018 0.003 TYR F 310 PHE 0.015 0.003 PHE F 346 HIS 0.004 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 5960) covalent geometry : angle 0.70055 ( 7970) hydrogen bonds : bond 0.06887 ( 65) hydrogen bonds : angle 6.38908 ( 195) *********************** 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 302 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 279 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.9108 (mp) cc_final: 0.8741 (tt) REVERT: A 340 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8208 (mtpt) REVERT: A 343 LYS cc_start: 0.8626 (tppt) cc_final: 0.7480 (pttp) REVERT: A 379 ARG cc_start: 0.7547 (mmt90) cc_final: 0.6959 (pmt-80) REVERT: B 315 LEU cc_start: 0.9273 (mp) cc_final: 0.8813 (tt) REVERT: B 342 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7957 (mm-30) REVERT: B 343 LYS cc_start: 0.8360 (mmmm) cc_final: 0.8066 (mmmm) REVERT: B 345 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8447 (t0) REVERT: C 311 LYS cc_start: 0.9005 (mttt) cc_final: 0.8489 (mtmm) REVERT: C 314 ASP cc_start: 0.8433 (t0) cc_final: 0.8158 (t0) REVERT: C 315 LEU cc_start: 0.9233 (mp) cc_final: 0.8751 (tt) REVERT: C 343 LYS cc_start: 0.8415 (tppt) cc_final: 0.7528 (pttp) REVERT: C 379 ARG cc_start: 0.7499 (mmt90) cc_final: 0.6899 (pmt-80) REVERT: D 311 LYS cc_start: 0.8978 (mttt) cc_final: 0.8538 (mtmm) REVERT: D 315 LEU cc_start: 0.9367 (mp) cc_final: 0.8825 (tt) REVERT: D 345 ASP cc_start: 0.8756 (m-30) cc_final: 0.8301 (t0) REVERT: D 375 LYS cc_start: 0.9039 (tttt) cc_final: 0.8719 (tttp) REVERT: E 314 ASP cc_start: 0.8371 (t0) cc_final: 0.7884 (t0) REVERT: E 315 LEU cc_start: 0.9203 (mp) cc_final: 0.8809 (tt) REVERT: E 343 LYS cc_start: 0.8129 (tppt) cc_final: 0.7844 (mmmm) REVERT: E 345 ASP cc_start: 0.8550 (m-30) cc_final: 0.8108 (t0) REVERT: E 370 LYS cc_start: 0.8853 (tttm) cc_final: 0.8250 (tttm) REVERT: E 372 GLU cc_start: 0.8748 (tt0) cc_final: 0.8500 (mt-10) REVERT: E 379 ARG cc_start: 0.7301 (mmt90) cc_final: 0.6779 (mmm-85) REVERT: F 315 LEU cc_start: 0.9298 (mp) cc_final: 0.8834 (tt) REVERT: F 345 ASP cc_start: 0.8682 (m-30) cc_final: 0.8298 (t0) REVERT: F 379 ARG cc_start: 0.7448 (mmt90) cc_final: 0.6938 (mmm-85) REVERT: G 311 LYS cc_start: 0.8931 (mttt) cc_final: 0.8536 (mtmt) REVERT: G 315 LEU cc_start: 0.9418 (mp) cc_final: 0.8897 (tt) REVERT: G 340 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8289 (tttt) REVERT: G 345 ASP cc_start: 0.8683 (m-30) cc_final: 0.8130 (t0) REVERT: G 379 ARG cc_start: 0.7349 (mmt90) cc_final: 0.6763 (mmm-85) REVERT: H 315 LEU cc_start: 0.9336 (mp) cc_final: 0.8896 (tt) REVERT: H 343 LYS cc_start: 0.8292 (tppt) cc_final: 0.8030 (mmmm) REVERT: H 345 ASP cc_start: 0.8721 (m-30) cc_final: 0.8113 (t0) REVERT: H 379 ARG cc_start: 0.7393 (mmt90) cc_final: 0.6975 (mmm-85) REVERT: I 315 LEU cc_start: 0.9261 (mp) cc_final: 0.8731 (tt) REVERT: I 358 ASP cc_start: 0.7941 (m-30) cc_final: 0.7559 (m-30) REVERT: I 375 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8459 (ttmm) REVERT: I 379 ARG cc_start: 0.7286 (mmt90) cc_final: 0.6506 (mmp-170) REVERT: J 311 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8822 (mmtt) REVERT: J 340 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8302 (mtpt) REVERT: J 379 ARG cc_start: 0.7229 (mmt90) cc_final: 0.6721 (mmp-170) outliers start: 23 outliers final: 18 residues processed: 287 average time/residue: 0.1180 time to fit residues: 40.2096 Evaluate side-chains 292 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 273 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain H residue 322 CYS Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain J residue 331 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN G 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.148454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.126470 restraints weight = 9961.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.129530 restraints weight = 4804.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.131539 restraints weight = 2952.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.132753 restraints weight = 2081.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.133441 restraints weight = 1641.767| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5960 Z= 0.149 Angle : 0.650 6.384 7970 Z= 0.342 Chirality : 0.048 0.132 890 Planarity : 0.003 0.032 1020 Dihedral : 5.543 17.372 790 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 2.99 % Allowed : 21.94 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.43 (0.22), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.17), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.012 0.002 TYR I 310 PHE 0.013 0.002 PHE F 346 HIS 0.003 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5960) covalent geometry : angle 0.65020 ( 7970) hydrogen bonds : bond 0.05610 ( 65) hydrogen bonds : angle 6.22724 ( 195) *********************** 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 300 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 280 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.9076 (mp) cc_final: 0.8747 (tt) REVERT: A 379 ARG cc_start: 0.7543 (mmt90) cc_final: 0.6920 (pmt-80) REVERT: B 311 LYS cc_start: 0.9127 (pttt) cc_final: 0.8812 (ptpp) REVERT: B 315 LEU cc_start: 0.9257 (mp) cc_final: 0.8845 (tt) REVERT: B 340 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8258 (tttt) REVERT: B 345 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8362 (t0) REVERT: C 311 LYS cc_start: 0.8971 (mttt) cc_final: 0.8451 (mtmm) REVERT: C 314 ASP cc_start: 0.8433 (t0) cc_final: 0.8130 (t0) REVERT: C 315 LEU cc_start: 0.9241 (mp) cc_final: 0.8787 (tt) REVERT: C 343 LYS cc_start: 0.8471 (tppt) cc_final: 0.7480 (pttm) REVERT: C 375 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8793 (tttm) REVERT: C 379 ARG cc_start: 0.7480 (mmt90) cc_final: 0.6810 (pmt-80) REVERT: D 311 LYS cc_start: 0.9012 (mttt) cc_final: 0.8450 (mtmm) REVERT: D 315 LEU cc_start: 0.9409 (mp) cc_final: 0.8858 (tt) REVERT: D 345 ASP cc_start: 0.8748 (m-30) cc_final: 0.8283 (t0) REVERT: D 375 LYS cc_start: 0.9015 (tttt) cc_final: 0.8672 (tttp) REVERT: E 315 LEU cc_start: 0.9194 (mp) cc_final: 0.8789 (tt) REVERT: E 345 ASP cc_start: 0.8557 (m-30) cc_final: 0.8077 (t0) REVERT: E 370 LYS cc_start: 0.8844 (tttm) cc_final: 0.8385 (tttm) REVERT: E 372 GLU cc_start: 0.8723 (tt0) cc_final: 0.8385 (mt-10) REVERT: E 379 ARG cc_start: 0.7337 (mmt90) cc_final: 0.6782 (mmm-85) REVERT: F 314 ASP cc_start: 0.8307 (t0) cc_final: 0.7974 (t0) REVERT: F 315 LEU cc_start: 0.9306 (mp) cc_final: 0.8857 (tt) REVERT: F 336 GLN cc_start: 0.8894 (tp40) cc_final: 0.8260 (tp40) REVERT: F 345 ASP cc_start: 0.8642 (m-30) cc_final: 0.8278 (t0) REVERT: F 379 ARG cc_start: 0.7467 (mmt90) cc_final: 0.6968 (mmm-85) REVERT: G 311 LYS cc_start: 0.8909 (mttt) cc_final: 0.8493 (mtmt) REVERT: G 315 LEU cc_start: 0.9393 (mp) cc_final: 0.8936 (tt) REVERT: G 340 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8167 (tttt) REVERT: G 345 ASP cc_start: 0.8656 (m-30) cc_final: 0.8098 (t0) REVERT: G 379 ARG cc_start: 0.7361 (mmt90) cc_final: 0.6712 (mmm-85) REVERT: H 315 LEU cc_start: 0.9323 (mp) cc_final: 0.8892 (tt) REVERT: H 343 LYS cc_start: 0.8257 (tppt) cc_final: 0.7956 (mmmm) REVERT: H 345 ASP cc_start: 0.8716 (m-30) cc_final: 0.8125 (t0) REVERT: H 379 ARG cc_start: 0.7406 (mmt90) cc_final: 0.7007 (mmm-85) REVERT: I 315 LEU cc_start: 0.9223 (mp) cc_final: 0.8711 (tt) REVERT: I 358 ASP cc_start: 0.7936 (m-30) cc_final: 0.7576 (m-30) REVERT: I 375 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8430 (ttmm) REVERT: I 379 ARG cc_start: 0.7288 (mmt90) cc_final: 0.6470 (mmp-170) REVERT: J 311 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8791 (mmtt) REVERT: J 315 LEU cc_start: 0.9303 (mp) cc_final: 0.8663 (tt) REVERT: J 340 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8153 (tttt) REVERT: J 379 ARG cc_start: 0.7250 (mmt90) cc_final: 0.6747 (mmp-170) outliers start: 20 outliers final: 15 residues processed: 288 average time/residue: 0.1127 time to fit residues: 38.8481 Evaluate side-chains 293 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 277 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain H residue 322 CYS Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain J residue 331 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 358 ASP Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 29 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.148474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.126284 restraints weight = 9833.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.129341 restraints weight = 4789.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.131341 restraints weight = 2964.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.132594 restraints weight = 2106.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.133438 restraints weight = 1661.118| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5960 Z= 0.153 Angle : 0.657 6.201 7970 Z= 0.346 Chirality : 0.048 0.131 890 Planarity : 0.004 0.036 1020 Dihedral : 5.572 17.272 790 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 3.28 % Allowed : 21.79 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.36 (0.23), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.17), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.015 0.002 TYR F 310 PHE 0.013 0.003 PHE F 346 HIS 0.003 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 5960) covalent geometry : angle 0.65748 ( 7970) hydrogen bonds : bond 0.05716 ( 65) hydrogen bonds : angle 6.20315 ( 195) *********************** 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 301 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 279 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.9083 (mp) cc_final: 0.8697 (tt) REVERT: A 340 LYS cc_start: 0.8547 (ttmm) cc_final: 0.8266 (mtpt) REVERT: A 378 PHE cc_start: 0.8500 (t80) cc_final: 0.8291 (t80) REVERT: A 379 ARG cc_start: 0.7507 (mmt90) cc_final: 0.6973 (pmt-80) REVERT: B 315 LEU cc_start: 0.9255 (mp) cc_final: 0.8867 (tt) REVERT: B 340 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8226 (tttt) REVERT: B 345 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8373 (t0) REVERT: C 310 TYR cc_start: 0.8249 (t80) cc_final: 0.8010 (t80) REVERT: C 311 LYS cc_start: 0.8953 (mttt) cc_final: 0.8482 (mtmm) REVERT: C 314 ASP cc_start: 0.8416 (t0) cc_final: 0.8132 (t0) REVERT: C 315 LEU cc_start: 0.9239 (mp) cc_final: 0.8796 (tt) REVERT: C 343 LYS cc_start: 0.8421 (tppt) cc_final: 0.7468 (pttp) REVERT: C 379 ARG cc_start: 0.7480 (mmt90) cc_final: 0.6829 (pmt-80) REVERT: D 311 LYS cc_start: 0.9020 (mttt) cc_final: 0.8691 (mtmm) REVERT: D 315 LEU cc_start: 0.9386 (mp) cc_final: 0.8850 (tt) REVERT: D 345 ASP cc_start: 0.8746 (m-30) cc_final: 0.8278 (t0) REVERT: D 375 LYS cc_start: 0.9040 (tttt) cc_final: 0.8739 (tttp) REVERT: E 315 LEU cc_start: 0.9197 (mp) cc_final: 0.8806 (tt) REVERT: E 342 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7599 (mm-30) REVERT: E 345 ASP cc_start: 0.8453 (m-30) cc_final: 0.8052 (t0) REVERT: E 370 LYS cc_start: 0.8843 (tttm) cc_final: 0.8395 (tttm) REVERT: E 372 GLU cc_start: 0.8711 (tt0) cc_final: 0.8400 (mt-10) REVERT: E 379 ARG cc_start: 0.7328 (mmt90) cc_final: 0.6723 (mmm-85) REVERT: F 314 ASP cc_start: 0.8351 (t0) cc_final: 0.8053 (t0) REVERT: F 315 LEU cc_start: 0.9300 (mp) cc_final: 0.8848 (tt) REVERT: F 336 GLN cc_start: 0.8896 (tp40) cc_final: 0.8294 (tp40) REVERT: F 342 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7717 (mm-30) REVERT: F 343 LYS cc_start: 0.8721 (mmmm) cc_final: 0.7891 (mmmm) REVERT: F 379 ARG cc_start: 0.7409 (mmt90) cc_final: 0.6927 (mmm-85) REVERT: G 311 LYS cc_start: 0.8905 (mttt) cc_final: 0.8536 (mtmt) REVERT: G 315 LEU cc_start: 0.9387 (mp) cc_final: 0.8924 (tt) REVERT: G 340 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8210 (tttt) REVERT: G 345 ASP cc_start: 0.8636 (m-30) cc_final: 0.8106 (t0) REVERT: G 379 ARG cc_start: 0.7396 (mmt90) cc_final: 0.6726 (mmm-85) REVERT: H 315 LEU cc_start: 0.9324 (mp) cc_final: 0.8909 (tt) REVERT: H 343 LYS cc_start: 0.8231 (tppt) cc_final: 0.7888 (mmmm) REVERT: H 345 ASP cc_start: 0.8689 (m-30) cc_final: 0.8093 (t0) REVERT: H 379 ARG cc_start: 0.7426 (mmt90) cc_final: 0.7000 (mmm-85) REVERT: I 315 LEU cc_start: 0.9302 (mp) cc_final: 0.8749 (tt) REVERT: I 342 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7092 (mm-30) REVERT: I 358 ASP cc_start: 0.7904 (m-30) cc_final: 0.7573 (m-30) REVERT: I 379 ARG cc_start: 0.7311 (mmt90) cc_final: 0.6496 (mmp-170) REVERT: J 311 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8825 (mmtt) REVERT: J 315 LEU cc_start: 0.9300 (mp) cc_final: 0.8654 (tt) REVERT: J 340 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8286 (mtpt) REVERT: J 379 ARG cc_start: 0.7299 (mmt90) cc_final: 0.6794 (mmp-170) outliers start: 22 outliers final: 15 residues processed: 289 average time/residue: 0.1132 time to fit residues: 39.0318 Evaluate side-chains 291 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain H residue 322 CYS Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain J residue 331 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 358 ASP Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.145914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.123642 restraints weight = 9978.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.126615 restraints weight = 4829.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.128521 restraints weight = 2992.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.129777 restraints weight = 2141.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.130637 restraints weight = 1699.666| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5960 Z= 0.219 Angle : 0.723 7.229 7970 Z= 0.381 Chirality : 0.049 0.148 890 Planarity : 0.004 0.041 1020 Dihedral : 5.991 19.148 790 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 3.13 % Allowed : 22.84 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.45 (0.23), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.17), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.021 0.004 TYR F 310 PHE 0.016 0.003 PHE F 346 HIS 0.004 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 5960) covalent geometry : angle 0.72281 ( 7970) hydrogen bonds : bond 0.06813 ( 65) hydrogen bonds : angle 6.42126 ( 195) *********************** 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 294 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 273 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.9117 (mp) cc_final: 0.8728 (tt) REVERT: A 340 LYS cc_start: 0.8311 (ttmm) cc_final: 0.8056 (mtpt) REVERT: A 379 ARG cc_start: 0.7477 (mmt90) cc_final: 0.7028 (pmt-80) REVERT: B 311 LYS cc_start: 0.9133 (pttt) cc_final: 0.8829 (ptpp) REVERT: B 315 LEU cc_start: 0.9254 (mp) cc_final: 0.8897 (tt) REVERT: B 340 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8314 (tttt) REVERT: B 345 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8396 (t0) REVERT: C 314 ASP cc_start: 0.8435 (t0) cc_final: 0.8160 (t0) REVERT: C 315 LEU cc_start: 0.9258 (mp) cc_final: 0.8825 (tt) REVERT: C 343 LYS cc_start: 0.8353 (tppt) cc_final: 0.8022 (mmmm) REVERT: C 379 ARG cc_start: 0.7539 (mmt90) cc_final: 0.6920 (pmt-80) REVERT: D 311 LYS cc_start: 0.9016 (mttt) cc_final: 0.8551 (mtmm) REVERT: D 315 LEU cc_start: 0.9398 (mp) cc_final: 0.8923 (tt) REVERT: D 345 ASP cc_start: 0.8782 (m-30) cc_final: 0.8345 (t0) REVERT: D 375 LYS cc_start: 0.9086 (tttt) cc_final: 0.8795 (tttp) REVERT: E 314 ASP cc_start: 0.8362 (t0) cc_final: 0.7911 (t0) REVERT: E 315 LEU cc_start: 0.9188 (mp) cc_final: 0.8819 (tt) REVERT: E 342 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7659 (mm-30) REVERT: E 345 ASP cc_start: 0.8603 (m-30) cc_final: 0.8155 (t0) REVERT: E 370 LYS cc_start: 0.8876 (tttm) cc_final: 0.8447 (tttm) REVERT: E 372 GLU cc_start: 0.8731 (tt0) cc_final: 0.8482 (mt-10) REVERT: E 379 ARG cc_start: 0.7409 (mmt90) cc_final: 0.6866 (mmm-85) REVERT: F 314 ASP cc_start: 0.8254 (t0) cc_final: 0.7965 (t0) REVERT: F 315 LEU cc_start: 0.9320 (mp) cc_final: 0.8848 (tt) REVERT: F 342 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7823 (mm-30) REVERT: F 343 LYS cc_start: 0.8785 (mmmm) cc_final: 0.7993 (mmmm) REVERT: F 379 ARG cc_start: 0.7440 (mmt90) cc_final: 0.6956 (mmm-85) REVERT: G 311 LYS cc_start: 0.8918 (mttt) cc_final: 0.8547 (mtmt) REVERT: G 315 LEU cc_start: 0.9409 (mp) cc_final: 0.8944 (tt) REVERT: G 340 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8289 (tttt) REVERT: G 345 ASP cc_start: 0.8622 (m-30) cc_final: 0.8171 (t0) REVERT: G 379 ARG cc_start: 0.7391 (mmt90) cc_final: 0.6743 (mmm-85) REVERT: H 315 LEU cc_start: 0.9350 (mp) cc_final: 0.8909 (tt) REVERT: H 343 LYS cc_start: 0.8323 (tppt) cc_final: 0.8000 (mmmm) REVERT: H 345 ASP cc_start: 0.8844 (m-30) cc_final: 0.8167 (t0) REVERT: H 379 ARG cc_start: 0.7469 (mmt90) cc_final: 0.7055 (mmm-85) REVERT: I 315 LEU cc_start: 0.9301 (mp) cc_final: 0.8777 (tt) REVERT: I 343 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8145 (mmmt) REVERT: I 358 ASP cc_start: 0.8044 (m-30) cc_final: 0.7670 (m-30) REVERT: I 379 ARG cc_start: 0.7322 (mmt90) cc_final: 0.6536 (mmp-170) REVERT: J 311 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8863 (mmtt) REVERT: J 315 LEU cc_start: 0.9337 (mp) cc_final: 0.8726 (tt) REVERT: J 340 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8237 (tttt) REVERT: J 379 ARG cc_start: 0.7334 (mmt90) cc_final: 0.6799 (mmp-170) outliers start: 21 outliers final: 18 residues processed: 281 average time/residue: 0.1196 time to fit residues: 40.1187 Evaluate side-chains 286 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 267 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain H residue 322 CYS Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain J residue 331 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 0.0070 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 ASN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.153088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.131078 restraints weight = 9662.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.134185 restraints weight = 4685.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.136160 restraints weight = 2869.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.137474 restraints weight = 2040.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.138296 restraints weight = 1609.093| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5960 Z= 0.122 Angle : 0.631 6.313 7970 Z= 0.334 Chirality : 0.048 0.123 890 Planarity : 0.004 0.033 1020 Dihedral : 5.161 17.045 790 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.24 % Allowed : 23.43 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.29 (0.23), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.006 0.001 TYR F 310 PHE 0.013 0.003 PHE B 378 HIS 0.001 0.000 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5960) covalent geometry : angle 0.63132 ( 7970) hydrogen bonds : bond 0.03955 ( 65) hydrogen bonds : angle 5.97578 ( 195) *********************** 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 319 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 304 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.9041 (mp) cc_final: 0.8703 (tt) REVERT: A 340 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8243 (mtpt) REVERT: A 379 ARG cc_start: 0.7586 (mmt90) cc_final: 0.6889 (pmt-80) REVERT: B 311 LYS cc_start: 0.9074 (pttt) cc_final: 0.8862 (ptpp) REVERT: B 315 LEU cc_start: 0.9202 (mp) cc_final: 0.8820 (tt) REVERT: B 340 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7918 (tttt) REVERT: B 345 ASP cc_start: 0.8738 (m-30) cc_final: 0.8431 (t0) REVERT: B 379 ARG cc_start: 0.7872 (mmm-85) cc_final: 0.7250 (mmm-85) REVERT: C 310 TYR cc_start: 0.8220 (t80) cc_final: 0.7906 (t80) REVERT: C 314 ASP cc_start: 0.8413 (t0) cc_final: 0.8163 (t0) REVERT: C 315 LEU cc_start: 0.9228 (mp) cc_final: 0.8813 (tt) REVERT: C 375 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8815 (tttm) REVERT: C 379 ARG cc_start: 0.7405 (mmt90) cc_final: 0.6765 (pmt-80) REVERT: D 311 LYS cc_start: 0.8959 (mttt) cc_final: 0.8492 (mtmm) REVERT: D 315 LEU cc_start: 0.9371 (mp) cc_final: 0.8952 (tt) REVERT: D 345 ASP cc_start: 0.8772 (m-30) cc_final: 0.8395 (t0) REVERT: D 356 SER cc_start: 0.8804 (p) cc_final: 0.8562 (p) REVERT: D 375 LYS cc_start: 0.9029 (tttt) cc_final: 0.8691 (tttp) REVERT: E 315 LEU cc_start: 0.9204 (mp) cc_final: 0.8815 (tt) REVERT: E 343 LYS cc_start: 0.7945 (mmmm) cc_final: 0.7720 (mmmm) REVERT: E 345 ASP cc_start: 0.8441 (m-30) cc_final: 0.7961 (t0) REVERT: E 370 LYS cc_start: 0.8806 (tttm) cc_final: 0.8312 (tttm) REVERT: E 372 GLU cc_start: 0.8711 (tt0) cc_final: 0.8478 (mt-10) REVERT: E 379 ARG cc_start: 0.7339 (mmt90) cc_final: 0.6701 (mmm-85) REVERT: F 314 ASP cc_start: 0.8258 (t0) cc_final: 0.8039 (t0) REVERT: F 315 LEU cc_start: 0.9283 (mp) cc_final: 0.8920 (tt) REVERT: F 336 GLN cc_start: 0.8741 (tp40) cc_final: 0.8304 (tp40) REVERT: F 349 ARG cc_start: 0.7372 (mtm180) cc_final: 0.7161 (mtp-110) REVERT: F 372 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8692 (mm-30) REVERT: F 379 ARG cc_start: 0.7458 (mmt90) cc_final: 0.6940 (mmm-85) REVERT: G 311 LYS cc_start: 0.8894 (mttt) cc_final: 0.8421 (mtmt) REVERT: G 315 LEU cc_start: 0.9331 (mp) cc_final: 0.8883 (tt) REVERT: G 340 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8145 (tttt) REVERT: G 345 ASP cc_start: 0.8575 (m-30) cc_final: 0.8138 (t0) REVERT: G 379 ARG cc_start: 0.7322 (mmt90) cc_final: 0.6632 (mmm-85) REVERT: H 315 LEU cc_start: 0.9245 (mp) cc_final: 0.8907 (tt) REVERT: H 343 LYS cc_start: 0.8171 (tppt) cc_final: 0.7900 (mmmm) REVERT: H 345 ASP cc_start: 0.8755 (m-30) cc_final: 0.8156 (t0) REVERT: H 351 GLN cc_start: 0.9317 (tt0) cc_final: 0.9091 (mt0) REVERT: H 379 ARG cc_start: 0.7472 (mmt90) cc_final: 0.7030 (mmm-85) REVERT: I 311 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8475 (mmtt) REVERT: I 315 LEU cc_start: 0.9266 (mp) cc_final: 0.8743 (tt) REVERT: I 358 ASP cc_start: 0.7879 (m-30) cc_final: 0.7624 (m-30) REVERT: I 379 ARG cc_start: 0.7247 (mmt90) cc_final: 0.6503 (mmp-170) REVERT: J 311 LYS cc_start: 0.9058 (mtmt) cc_final: 0.8787 (mmtt) REVERT: J 315 LEU cc_start: 0.9214 (mp) cc_final: 0.8605 (tt) REVERT: J 349 ARG cc_start: 0.7393 (mtm180) cc_final: 0.6668 (mmm160) REVERT: J 379 ARG cc_start: 0.7344 (mmt90) cc_final: 0.6842 (mmp-170) outliers start: 15 outliers final: 10 residues processed: 311 average time/residue: 0.1106 time to fit residues: 41.2548 Evaluate side-chains 292 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 282 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain H residue 322 CYS Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain J residue 331 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.147102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.124932 restraints weight = 10004.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.127954 restraints weight = 4789.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.129904 restraints weight = 2919.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.131132 restraints weight = 2086.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.131991 restraints weight = 1659.170| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5960 Z= 0.191 Angle : 0.719 6.439 7970 Z= 0.379 Chirality : 0.049 0.154 890 Planarity : 0.006 0.054 1020 Dihedral : 5.837 19.391 790 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 1.64 % Allowed : 26.27 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.013 0.003 TYR E 310 PHE 0.014 0.003 PHE F 346 HIS 0.004 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 5960) covalent geometry : angle 0.71873 ( 7970) hydrogen bonds : bond 0.06305 ( 65) hydrogen bonds : angle 6.28888 ( 195) *********************** 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 290 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 279 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.9098 (mp) cc_final: 0.8726 (tt) REVERT: A 340 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8159 (mtpt) REVERT: A 379 ARG cc_start: 0.7590 (mmt90) cc_final: 0.6878 (pmt-80) REVERT: B 315 LEU cc_start: 0.9269 (mp) cc_final: 0.8886 (tt) REVERT: B 340 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8142 (tttt) REVERT: B 345 ASP cc_start: 0.8765 (m-30) cc_final: 0.8369 (t0) REVERT: C 311 LYS cc_start: 0.8927 (mttt) cc_final: 0.8539 (mtmp) REVERT: C 314 ASP cc_start: 0.8276 (t0) cc_final: 0.8019 (t0) REVERT: C 315 LEU cc_start: 0.9259 (mp) cc_final: 0.8835 (tt) REVERT: C 379 ARG cc_start: 0.7515 (mmt90) cc_final: 0.6881 (pmt-80) REVERT: D 315 LEU cc_start: 0.9381 (mp) cc_final: 0.8904 (tt) REVERT: D 345 ASP cc_start: 0.8776 (m-30) cc_final: 0.8391 (t0) REVERT: D 375 LYS cc_start: 0.9052 (tttt) cc_final: 0.8763 (tttp) REVERT: E 314 ASP cc_start: 0.8246 (t0) cc_final: 0.7823 (t0) REVERT: E 315 LEU cc_start: 0.9191 (mp) cc_final: 0.8830 (tt) REVERT: E 345 ASP cc_start: 0.8503 (m-30) cc_final: 0.7971 (t0) REVERT: E 370 LYS cc_start: 0.8878 (tttm) cc_final: 0.8466 (tttm) REVERT: E 372 GLU cc_start: 0.8734 (tt0) cc_final: 0.8465 (mt-10) REVERT: E 379 ARG cc_start: 0.7408 (mmt90) cc_final: 0.6829 (mmm-85) REVERT: F 314 ASP cc_start: 0.8321 (t0) cc_final: 0.8044 (t0) REVERT: F 315 LEU cc_start: 0.9320 (mp) cc_final: 0.8839 (tt) REVERT: F 343 LYS cc_start: 0.8709 (mmmm) cc_final: 0.7972 (mmmm) REVERT: F 347 LYS cc_start: 0.8953 (ptpp) cc_final: 0.8748 (ptpp) REVERT: F 379 ARG cc_start: 0.7500 (mmt90) cc_final: 0.6929 (mmm-85) REVERT: G 311 LYS cc_start: 0.8922 (mttt) cc_final: 0.8346 (mtmt) REVERT: G 315 LEU cc_start: 0.9350 (mp) cc_final: 0.8906 (tt) REVERT: G 340 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8192 (tttt) REVERT: G 345 ASP cc_start: 0.8602 (m-30) cc_final: 0.8161 (t0) REVERT: G 379 ARG cc_start: 0.7343 (mmt90) cc_final: 0.6695 (mmm-85) REVERT: H 315 LEU cc_start: 0.9301 (mp) cc_final: 0.8910 (tt) REVERT: H 343 LYS cc_start: 0.8300 (tppt) cc_final: 0.7956 (mmmm) REVERT: H 345 ASP cc_start: 0.8815 (m-30) cc_final: 0.8182 (t0) REVERT: H 379 ARG cc_start: 0.7480 (mmt90) cc_final: 0.7073 (mmm-85) REVERT: I 311 LYS cc_start: 0.9078 (mtmm) cc_final: 0.8823 (mmtt) REVERT: I 315 LEU cc_start: 0.9415 (mp) cc_final: 0.8864 (tt) REVERT: I 343 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8148 (mmmt) REVERT: I 358 ASP cc_start: 0.7872 (m-30) cc_final: 0.7559 (m-30) REVERT: I 379 ARG cc_start: 0.7334 (mmt90) cc_final: 0.6554 (mmp-170) REVERT: J 311 LYS cc_start: 0.9126 (mtmt) cc_final: 0.8833 (mmtt) REVERT: J 315 LEU cc_start: 0.9336 (mp) cc_final: 0.8646 (tt) REVERT: J 340 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8279 (tttt) REVERT: J 379 ARG cc_start: 0.7423 (mmt90) cc_final: 0.6945 (mmp-170) outliers start: 11 outliers final: 9 residues processed: 285 average time/residue: 0.1114 time to fit residues: 37.8827 Evaluate side-chains 282 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 273 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain H residue 322 CYS Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 331 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN G 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.151595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.129453 restraints weight = 9849.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.132517 restraints weight = 4745.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.134523 restraints weight = 2898.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.135717 restraints weight = 2057.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.136599 restraints weight = 1641.571| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5960 Z= 0.135 Angle : 0.678 6.362 7970 Z= 0.359 Chirality : 0.048 0.124 890 Planarity : 0.005 0.048 1020 Dihedral : 5.458 20.910 790 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.49 % Allowed : 28.21 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.23 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.017 0.002 TYR F 310 PHE 0.012 0.003 PHE B 378 HIS 0.002 0.000 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5960) covalent geometry : angle 0.67756 ( 7970) hydrogen bonds : bond 0.04628 ( 65) hydrogen bonds : angle 6.04781 ( 195) ********************** 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 289 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 279 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.9072 (mp) cc_final: 0.8730 (tt) REVERT: A 340 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8186 (tttt) REVERT: A 379 ARG cc_start: 0.7600 (mmt90) cc_final: 0.6835 (pmt-80) REVERT: B 311 LYS cc_start: 0.9093 (pttt) cc_final: 0.8798 (ptpp) REVERT: B 315 LEU cc_start: 0.9224 (mp) cc_final: 0.8839 (tt) REVERT: B 340 LYS cc_start: 0.8362 (ttmm) cc_final: 0.7946 (tttt) REVERT: B 345 ASP cc_start: 0.8773 (m-30) cc_final: 0.8424 (t0) REVERT: C 310 TYR cc_start: 0.8253 (t80) cc_final: 0.7943 (t80) REVERT: C 314 ASP cc_start: 0.8270 (t0) cc_final: 0.8030 (t0) REVERT: C 315 LEU cc_start: 0.9227 (mp) cc_final: 0.8841 (tt) REVERT: C 375 LYS cc_start: 0.9056 (ttmt) cc_final: 0.8798 (tttm) REVERT: C 379 ARG cc_start: 0.7306 (mmt90) cc_final: 0.6705 (pmt-80) REVERT: D 315 LEU cc_start: 0.9371 (mp) cc_final: 0.8925 (tt) REVERT: D 345 ASP cc_start: 0.8772 (m-30) cc_final: 0.8419 (t0) REVERT: D 375 LYS cc_start: 0.9045 (tttt) cc_final: 0.8744 (tttp) REVERT: E 314 ASP cc_start: 0.8275 (t0) cc_final: 0.7861 (t0) REVERT: E 315 LEU cc_start: 0.9224 (mp) cc_final: 0.8851 (tt) REVERT: E 345 ASP cc_start: 0.8366 (m-30) cc_final: 0.7951 (t0) REVERT: E 370 LYS cc_start: 0.8868 (tttm) cc_final: 0.8347 (tttm) REVERT: E 379 ARG cc_start: 0.7363 (mmt90) cc_final: 0.6800 (mmm-85) REVERT: F 315 LEU cc_start: 0.9286 (mp) cc_final: 0.8848 (tt) REVERT: F 379 ARG cc_start: 0.7477 (mmt90) cc_final: 0.6931 (mmm-85) REVERT: G 311 LYS cc_start: 0.8912 (mttt) cc_final: 0.8331 (mtmt) REVERT: G 315 LEU cc_start: 0.9344 (mp) cc_final: 0.8853 (tt) REVERT: G 340 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8157 (tttt) REVERT: G 345 ASP cc_start: 0.8579 (m-30) cc_final: 0.8153 (t0) REVERT: G 379 ARG cc_start: 0.7272 (mmt90) cc_final: 0.6623 (mmm-85) REVERT: H 315 LEU cc_start: 0.9278 (mp) cc_final: 0.8921 (tt) REVERT: H 343 LYS cc_start: 0.8180 (tppt) cc_final: 0.7929 (mmmm) REVERT: H 345 ASP cc_start: 0.8784 (m-30) cc_final: 0.8217 (t0) REVERT: H 379 ARG cc_start: 0.7479 (mmt90) cc_final: 0.7017 (mmm-85) REVERT: I 311 LYS cc_start: 0.9079 (mtmm) cc_final: 0.8698 (mmtt) REVERT: I 315 LEU cc_start: 0.9354 (mp) cc_final: 0.8828 (tt) REVERT: I 358 ASP cc_start: 0.7958 (m-30) cc_final: 0.7700 (m-30) REVERT: I 379 ARG cc_start: 0.7270 (mmt90) cc_final: 0.6529 (mmp-170) REVERT: J 311 LYS cc_start: 0.9081 (mtmt) cc_final: 0.8823 (mmtt) REVERT: J 340 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8248 (tttt) REVERT: J 349 ARG cc_start: 0.7421 (mtm180) cc_final: 0.6743 (mmm160) REVERT: J 379 ARG cc_start: 0.7412 (mmt90) cc_final: 0.6969 (mmp-170) outliers start: 10 outliers final: 9 residues processed: 285 average time/residue: 0.1206 time to fit residues: 40.8806 Evaluate side-chains 281 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 272 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain H residue 322 CYS Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain J residue 331 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.146724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.124709 restraints weight = 9894.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.127632 restraints weight = 4776.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.129564 restraints weight = 2944.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.130818 restraints weight = 2105.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.131590 restraints weight = 1666.731| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5960 Z= 0.198 Angle : 0.740 6.599 7970 Z= 0.388 Chirality : 0.049 0.162 890 Planarity : 0.006 0.052 1020 Dihedral : 5.947 20.465 790 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 1.19 % Allowed : 27.31 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.32 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.018 0.003 TYR A 310 PHE 0.013 0.003 PHE F 346 HIS 0.003 0.001 HIS J 330 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 5960) covalent geometry : angle 0.73976 ( 7970) hydrogen bonds : bond 0.06315 ( 65) hydrogen bonds : angle 6.31570 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1377.21 seconds wall clock time: 24 minutes 43.70 seconds (1483.70 seconds total)