Starting phenix.real_space_refine on Mon Aug 25 08:47:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fug_29458/08_2025/8fug_29458_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fug_29458/08_2025/8fug_29458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fug_29458/08_2025/8fug_29458_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fug_29458/08_2025/8fug_29458_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fug_29458/08_2025/8fug_29458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fug_29458/08_2025/8fug_29458.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 23 5.16 5 C 8464 2.51 5 N 2415 2.21 5 O 2392 1.98 5 F 23 1.80 5 H 13317 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26634 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W Time building chain proxies: 2.32, per 1000 atoms: 0.09 Number of scatterers: 26634 At special positions: 0 Unit cell: (115.926, 129.27, 75.894, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 23 16.00 F 23 9.00 O 2392 8.00 N 2415 7.00 C 8464 6.00 H 13317 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 790.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 308 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 321 through 324 removed outlier: 6.723A pdb=" N SER A 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER C 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER E 324 " --> pdb=" O GLY G 323 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER G 324 " --> pdb=" O GLY I 323 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER I 324 " --> pdb=" O GLY K 323 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER K 324 " --> pdb=" O GLY M 323 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER M 324 " --> pdb=" O GLY O 323 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER O 324 " --> pdb=" O GLY Q 323 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER Q 324 " --> pdb=" O GLY S 323 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER S 324 " --> pdb=" O GLY U 323 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER U 324 " --> pdb=" O GLY W 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.377A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE E 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE G 328 " --> pdb=" O HIS I 329 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE I 328 " --> pdb=" O HIS K 329 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE K 328 " --> pdb=" O HIS M 329 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE M 328 " --> pdb=" O HIS O 329 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE O 328 " --> pdb=" O HIS Q 329 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE Q 328 " --> pdb=" O HIS S 329 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE S 328 " --> pdb=" O HIS U 329 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE U 328 " --> pdb=" O HIS W 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 356 removed outlier: 6.728A pdb=" N SER A 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER C 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER E 356 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER G 356 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER I 356 " --> pdb=" O GLY K 355 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER K 356 " --> pdb=" O GLY M 355 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER M 356 " --> pdb=" O GLY O 355 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER O 356 " --> pdb=" O GLY Q 355 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER Q 356 " --> pdb=" O GLY S 355 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER S 356 " --> pdb=" O GLY U 355 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER U 356 " --> pdb=" O GLY W 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.460A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN E 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN G 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN I 359 " --> pdb=" O ILE K 360 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN K 359 " --> pdb=" O ILE M 360 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN M 359 " --> pdb=" O ILE O 360 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN O 359 " --> pdb=" O ILE Q 360 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN Q 359 " --> pdb=" O ILE S 360 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN S 359 " --> pdb=" O ILE U 360 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN U 359 " --> pdb=" O ILE W 360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 365 through 374 removed outlier: 5.585A pdb=" N GLY A 366 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LYS C 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN A 368 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE C 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLY C 366 " --> pdb=" O GLY E 367 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LYS E 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN C 368 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE E 371 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS C 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR E 373 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU C 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLY E 366 " --> pdb=" O GLY G 367 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LYS G 369 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN E 368 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE G 371 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS E 370 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N THR G 373 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU E 372 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLY G 366 " --> pdb=" O GLY I 367 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LYS I 369 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN G 368 " --> pdb=" O LYS I 369 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE I 371 " --> pdb=" O ASN G 368 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS G 370 " --> pdb=" O ILE I 371 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N THR I 373 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLU G 372 " --> pdb=" O THR I 373 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLY I 366 " --> pdb=" O GLY K 367 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LYS K 369 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN I 368 " --> pdb=" O LYS K 369 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE K 371 " --> pdb=" O ASN I 368 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS I 370 " --> pdb=" O ILE K 371 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR K 373 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU I 372 " --> pdb=" O THR K 373 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLY K 366 " --> pdb=" O GLY M 367 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LYS M 369 " --> pdb=" O GLY K 366 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN K 368 " --> pdb=" O LYS M 369 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE M 371 " --> pdb=" O ASN K 368 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS K 370 " --> pdb=" O ILE M 371 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR M 373 " --> pdb=" O LYS K 370 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU K 372 " --> pdb=" O THR M 373 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLY M 366 " --> pdb=" O GLY O 367 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LYS O 369 " --> pdb=" O GLY M 366 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN M 368 " --> pdb=" O LYS O 369 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE O 371 " --> pdb=" O ASN M 368 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS M 370 " --> pdb=" O ILE O 371 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR O 373 " --> pdb=" O LYS M 370 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU M 372 " --> pdb=" O THR O 373 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLY O 366 " --> pdb=" O GLY Q 367 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LYS Q 369 " --> pdb=" O GLY O 366 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN O 368 " --> pdb=" O LYS Q 369 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE Q 371 " --> pdb=" O ASN O 368 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS O 370 " --> pdb=" O ILE Q 371 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR Q 373 " --> pdb=" O LYS O 370 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU O 372 " --> pdb=" O THR Q 373 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLY Q 366 " --> pdb=" O GLY S 367 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LYS S 369 " --> pdb=" O GLY Q 366 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN Q 368 " --> pdb=" O LYS S 369 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE S 371 " --> pdb=" O ASN Q 368 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS Q 370 " --> pdb=" O ILE S 371 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR S 373 " --> pdb=" O LYS Q 370 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU Q 372 " --> pdb=" O THR S 373 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLY S 366 " --> pdb=" O GLY U 367 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LYS U 369 " --> pdb=" O GLY S 366 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN S 368 " --> pdb=" O LYS U 369 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE U 371 " --> pdb=" O ASN S 368 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS S 370 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N THR U 373 " --> pdb=" O LYS S 370 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLU S 372 " --> pdb=" O THR U 373 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLY U 366 " --> pdb=" O GLY W 367 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LYS W 369 " --> pdb=" O GLY U 366 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN U 368 " --> pdb=" O LYS W 369 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE W 371 " --> pdb=" O ASN U 368 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS U 370 " --> pdb=" O ILE W 371 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N THR W 373 " --> pdb=" O LYS U 370 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU U 372 " --> pdb=" O THR W 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB3, first strand: chain 'B' and resid 321 through 324 removed outlier: 6.723A pdb=" N SER B 324 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER D 324 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER F 324 " --> pdb=" O GLY H 323 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER H 324 " --> pdb=" O GLY J 323 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER J 324 " --> pdb=" O GLY L 323 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER L 324 " --> pdb=" O GLY N 323 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER N 324 " --> pdb=" O GLY P 323 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N CYS P 322 " --> pdb=" O GLY R 323 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER R 324 " --> pdb=" O GLY T 323 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER T 324 " --> pdb=" O GLY V 323 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.383A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE F 328 " --> pdb=" O HIS H 329 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE H 328 " --> pdb=" O HIS J 329 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE J 328 " --> pdb=" O HIS L 329 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE L 328 " --> pdb=" O HIS N 329 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE N 328 " --> pdb=" O HIS P 329 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE P 328 " --> pdb=" O HIS R 329 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE R 328 " --> pdb=" O HIS T 329 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE T 328 " --> pdb=" O HIS V 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 336 through 340 Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AB7, first strand: chain 'B' and resid 350 through 356 removed outlier: 6.722A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER D 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER F 356 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER H 356 " --> pdb=" O GLY J 355 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER J 356 " --> pdb=" O GLY L 355 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER L 356 " --> pdb=" O GLY N 355 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER N 356 " --> pdb=" O GLY P 355 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL P 350 " --> pdb=" O GLN R 351 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LYS R 353 " --> pdb=" O VAL P 350 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER P 352 " --> pdb=" O LYS R 353 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY R 355 " --> pdb=" O SER P 352 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE P 354 " --> pdb=" O GLY R 355 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER R 356 " --> pdb=" O GLY T 355 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER T 356 " --> pdb=" O GLY V 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.450A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN F 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASN H 359 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN J 359 " --> pdb=" O ILE L 360 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN L 359 " --> pdb=" O ILE N 360 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASN N 359 " --> pdb=" O ILE P 360 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN P 359 " --> pdb=" O ILE R 360 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN R 359 " --> pdb=" O ILE T 360 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN T 359 " --> pdb=" O ILE V 360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 365 through 374 removed outlier: 5.542A pdb=" N GLY B 366 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS D 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 368 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE D 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR D 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLU B 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY D 366 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS F 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN D 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE F 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR F 373 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU D 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLY F 366 " --> pdb=" O GLY H 367 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS H 369 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN F 368 " --> pdb=" O LYS H 369 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE H 371 " --> pdb=" O ASN F 368 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LYS F 370 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR H 373 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU F 372 " --> pdb=" O THR H 373 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLY H 366 " --> pdb=" O GLY J 367 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS J 369 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN H 368 " --> pdb=" O LYS J 369 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE J 371 " --> pdb=" O ASN H 368 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS H 370 " --> pdb=" O ILE J 371 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR J 373 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU H 372 " --> pdb=" O THR J 373 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY J 366 " --> pdb=" O GLY L 367 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS L 369 " --> pdb=" O GLY J 366 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN J 368 " --> pdb=" O LYS L 369 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE L 371 " --> pdb=" O ASN J 368 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS J 370 " --> pdb=" O ILE L 371 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR L 373 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLU J 372 " --> pdb=" O THR L 373 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLY L 366 " --> pdb=" O GLY N 367 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS N 369 " --> pdb=" O GLY L 366 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN L 368 " --> pdb=" O LYS N 369 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE N 371 " --> pdb=" O ASN L 368 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS L 370 " --> pdb=" O ILE N 371 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR N 373 " --> pdb=" O LYS L 370 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU L 372 " --> pdb=" O THR N 373 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY N 366 " --> pdb=" O GLY P 367 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS P 369 " --> pdb=" O GLY N 366 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN N 368 " --> pdb=" O LYS P 369 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE P 371 " --> pdb=" O ASN N 368 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS N 370 " --> pdb=" O ILE P 371 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR P 373 " --> pdb=" O LYS N 370 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLU N 372 " --> pdb=" O THR P 373 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLY P 366 " --> pdb=" O GLY R 367 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LYS R 369 " --> pdb=" O GLY P 366 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN P 368 " --> pdb=" O LYS R 369 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE R 371 " --> pdb=" O ASN P 368 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS P 370 " --> pdb=" O ILE R 371 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR R 373 " --> pdb=" O LYS P 370 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLU P 372 " --> pdb=" O THR R 373 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY R 366 " --> pdb=" O GLY T 367 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS T 369 " --> pdb=" O GLY R 366 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN R 368 " --> pdb=" O LYS T 369 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE T 371 " --> pdb=" O ASN R 368 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS R 370 " --> pdb=" O ILE T 371 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR T 373 " --> pdb=" O LYS R 370 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU R 372 " --> pdb=" O THR T 373 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLY T 366 " --> pdb=" O GLY V 367 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS V 369 " --> pdb=" O GLY T 366 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN T 368 " --> pdb=" O LYS V 369 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE V 371 " --> pdb=" O ASN T 368 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS T 370 " --> pdb=" O ILE V 371 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR V 373 " --> pdb=" O LYS T 370 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU T 372 " --> pdb=" O THR V 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'Q' and resid 307 through 308 328 hydrogen bonds defined for protein. 984 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: 7.15 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13294 1.03 - 1.22: 23 1.22 - 1.42: 5428 1.42 - 1.61: 8142 1.61 - 1.81: 23 Bond restraints: 26910 Sorted by residual: bond pdb=" C16 Y9H F 401 " pdb=" C7 Y9H F 401 " ideal model delta sigma weight residual 1.445 1.396 0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" C15 Y9H P 401 " pdb=" C16 Y9H P 401 " ideal model delta sigma weight residual 1.351 1.400 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" C15 Y9H E 401 " pdb=" C16 Y9H E 401 " ideal model delta sigma weight residual 1.351 1.400 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C16 Y9H S 401 " pdb=" C7 Y9H S 401 " ideal model delta sigma weight residual 1.445 1.396 0.049 2.00e-02 2.50e+03 5.93e+00 bond pdb=" C16 Y9H P 401 " pdb=" C7 Y9H P 401 " ideal model delta sigma weight residual 1.445 1.396 0.049 2.00e-02 2.50e+03 5.92e+00 ... (remaining 26905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 44427 0.78 - 1.56: 3873 1.56 - 2.34: 371 2.34 - 3.12: 112 3.12 - 3.90: 92 Bond angle restraints: 48875 Sorted by residual: angle pdb=" N GLY P 365 " pdb=" CA GLY P 365 " pdb=" C GLY P 365 " ideal model delta sigma weight residual 113.18 109.28 3.90 2.37e+00 1.78e-01 2.71e+00 angle pdb=" N GLY H 365 " pdb=" CA GLY H 365 " pdb=" C GLY H 365 " ideal model delta sigma weight residual 113.18 109.33 3.85 2.37e+00 1.78e-01 2.64e+00 angle pdb=" N GLY U 365 " pdb=" CA GLY U 365 " pdb=" C GLY U 365 " ideal model delta sigma weight residual 113.18 109.35 3.83 2.37e+00 1.78e-01 2.61e+00 angle pdb=" N GLY D 365 " pdb=" CA GLY D 365 " pdb=" C GLY D 365 " ideal model delta sigma weight residual 113.18 109.36 3.82 2.37e+00 1.78e-01 2.60e+00 angle pdb=" N GLY I 365 " pdb=" CA GLY I 365 " pdb=" C GLY I 365 " ideal model delta sigma weight residual 113.18 109.37 3.81 2.37e+00 1.78e-01 2.59e+00 ... (remaining 48870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.70: 10858 11.70 - 23.40: 1171 23.40 - 35.10: 253 35.10 - 46.81: 69 46.81 - 58.51: 161 Dihedral angle restraints: 12512 sinusoidal: 7291 harmonic: 5221 Sorted by residual: dihedral pdb=" CA LYS L 347 " pdb=" C LYS L 347 " pdb=" N ASP L 348 " pdb=" CA ASP L 348 " ideal model delta harmonic sigma weight residual 180.00 162.85 17.15 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA LYS H 347 " pdb=" C LYS H 347 " pdb=" N ASP H 348 " pdb=" CA ASP H 348 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA LYS N 347 " pdb=" C LYS N 347 " pdb=" N ASP N 348 " pdb=" CA ASP N 348 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 12509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1022 0.026 - 0.052: 536 0.052 - 0.078: 167 0.078 - 0.103: 210 0.103 - 0.129: 66 Chirality restraints: 2001 Sorted by residual: chirality pdb=" CA ILE S 308 " pdb=" N ILE S 308 " pdb=" C ILE S 308 " pdb=" CB ILE S 308 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE U 308 " pdb=" N ILE U 308 " pdb=" C ILE U 308 " pdb=" CB ILE U 308 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE A 308 " pdb=" N ILE A 308 " pdb=" C ILE A 308 " pdb=" CB ILE A 308 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1998 not shown) Planarity restraints: 3818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 331 " 0.016 5.00e-02 4.00e+02 2.34e-02 8.80e-01 pdb=" N PRO L 332 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO L 332 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 332 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 331 " 0.015 5.00e-02 4.00e+02 2.34e-02 8.78e-01 pdb=" N PRO I 332 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO I 332 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO I 332 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS T 331 " 0.015 5.00e-02 4.00e+02 2.34e-02 8.76e-01 pdb=" N PRO T 332 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO T 332 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO T 332 " 0.013 5.00e-02 4.00e+02 ... (remaining 3815 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 10911 2.35 - 2.91: 62882 2.91 - 3.48: 65804 3.48 - 4.04: 103935 4.04 - 4.60: 143182 Nonbonded interactions: 386714 Sorted by model distance: nonbonded pdb=" OG SER U 320 " pdb="HD22 ASN U 368 " model vdw 1.790 2.450 nonbonded pdb=" OG SER E 320 " pdb="HD22 ASN E 368 " model vdw 1.790 2.450 nonbonded pdb=" OG SER W 320 " pdb="HD22 ASN W 368 " model vdw 1.791 2.450 nonbonded pdb=" OG SER M 320 " pdb="HD22 ASN M 368 " model vdw 1.791 2.450 nonbonded pdb=" OG SER A 320 " pdb="HD22 ASN A 368 " model vdw 1.791 2.450 ... (remaining 386709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.170 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.790 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.005 0.049 13593 Z= 0.246 Angle : 0.564 3.902 18239 Z= 0.278 Chirality : 0.046 0.129 2001 Planarity : 0.003 0.023 2231 Dihedral : 9.780 58.507 5359 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.12 % Allowed : 3.12 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.91 (0.16), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.12), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 349 TYR 0.004 0.001 TYR J 310 PHE 0.004 0.001 PHE S 346 HIS 0.002 0.001 HIS P 330 Details of bonding type rmsd covalent geometry : bond 0.00495 (13593) covalent geometry : angle 0.56423 (18239) hydrogen bonds : bond 0.17606 ( 328) hydrogen bonds : angle 7.66000 ( 984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 407 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 SER cc_start: 0.8214 (m) cc_final: 0.7825 (t) REVERT: D 321 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8079 (mtmt) REVERT: E 321 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7833 (mttp) REVERT: F 321 LYS cc_start: 0.8253 (mtpt) cc_final: 0.8019 (mttp) REVERT: I 340 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7956 (mtpt) REVERT: I 369 LYS cc_start: 0.8095 (ptpt) cc_final: 0.7870 (ptpt) REVERT: J 369 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7669 (ptmt) REVERT: J 370 LYS cc_start: 0.7875 (tttm) cc_final: 0.7601 (ttpt) REVERT: J 377 THR cc_start: 0.8034 (m) cc_final: 0.7632 (p) REVERT: K 331 LYS cc_start: 0.8696 (mttp) cc_final: 0.8474 (mtpm) REVERT: K 369 LYS cc_start: 0.8037 (ptpt) cc_final: 0.7748 (ptpt) REVERT: L 331 LYS cc_start: 0.8697 (mttp) cc_final: 0.8435 (mtpm) REVERT: L 340 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7702 (mttt) REVERT: L 350 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7341 (p) REVERT: L 369 LYS cc_start: 0.8201 (ptpt) cc_final: 0.7800 (ptmt) REVERT: L 370 LYS cc_start: 0.7965 (tttm) cc_final: 0.7646 (ttpt) REVERT: L 378 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: M 319 THR cc_start: 0.7741 (m) cc_final: 0.7348 (p) REVERT: M 331 LYS cc_start: 0.8767 (mttp) cc_final: 0.8470 (mtmt) REVERT: M 340 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7859 (mtmm) REVERT: M 350 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7335 (p) REVERT: M 369 LYS cc_start: 0.8067 (ptpt) cc_final: 0.7716 (ptmt) REVERT: N 321 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7642 (mttp) REVERT: N 331 LYS cc_start: 0.8777 (mttp) cc_final: 0.8439 (mtpm) REVERT: N 340 LYS cc_start: 0.8297 (ttmm) cc_final: 0.8018 (mtmm) REVERT: N 369 LYS cc_start: 0.8231 (ptpt) cc_final: 0.7728 (ptmt) REVERT: N 377 THR cc_start: 0.7979 (m) cc_final: 0.7765 (p) REVERT: N 378 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6038 (m-80) REVERT: O 331 LYS cc_start: 0.8807 (mttp) cc_final: 0.8411 (mtpm) REVERT: O 340 LYS cc_start: 0.8303 (ttmm) cc_final: 0.8033 (mtmm) REVERT: P 370 LYS cc_start: 0.8116 (tttm) cc_final: 0.7884 (ttpt) REVERT: Q 317 LYS cc_start: 0.6377 (ptmt) cc_final: 0.6097 (ptmt) REVERT: Q 319 THR cc_start: 0.8051 (m) cc_final: 0.7671 (p) REVERT: Q 321 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7650 (tttp) REVERT: Q 373 THR cc_start: 0.8606 (m) cc_final: 0.8137 (p) REVERT: R 331 LYS cc_start: 0.8783 (mttp) cc_final: 0.8490 (mtmt) REVERT: R 378 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5941 (m-80) REVERT: S 319 THR cc_start: 0.7742 (m) cc_final: 0.7509 (p) REVERT: S 331 LYS cc_start: 0.8681 (mttp) cc_final: 0.8415 (mtmt) REVERT: S 345 ASP cc_start: 0.7965 (m-30) cc_final: 0.7586 (t0) REVERT: S 373 THR cc_start: 0.8494 (m) cc_final: 0.8058 (p) REVERT: S 375 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7801 (ttpp) REVERT: S 378 PHE cc_start: 0.6479 (OUTLIER) cc_final: 0.6043 (m-80) REVERT: T 331 LYS cc_start: 0.8632 (mttp) cc_final: 0.8423 (mtmt) REVERT: U 319 THR cc_start: 0.7743 (m) cc_final: 0.7337 (p) REVERT: U 331 LYS cc_start: 0.8761 (mttp) cc_final: 0.8402 (mtpt) REVERT: U 373 THR cc_start: 0.8636 (m) cc_final: 0.8245 (p) REVERT: U 378 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: V 331 LYS cc_start: 0.8760 (mttp) cc_final: 0.8450 (mtpt) REVERT: V 378 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.5677 (p90) REVERT: W 338 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7354 (tm-30) REVERT: W 373 THR cc_start: 0.8653 (m) cc_final: 0.8156 (p) outliers start: 46 outliers final: 22 residues processed: 440 average time/residue: 1.3285 time to fit residues: 633.5172 Evaluate side-chains 323 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 378 PHE Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 378 PHE Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN A 368 ASN B 359 ASN B 368 ASN C 359 ASN C 368 ASN D 359 ASN D 368 ASN E 359 ASN E 362 HIS E 368 ASN F 359 ASN F 368 ASN G 359 ASN G 368 ASN H 359 ASN H 368 ASN I 359 ASN I 368 ASN J 359 ASN J 368 ASN K 359 ASN K 368 ASN L 359 ASN L 368 ASN M 359 ASN M 368 ASN N 359 ASN N 368 ASN O 359 ASN O 368 ASN P 359 ASN P 362 HIS P 368 ASN Q 359 ASN Q 368 ASN R 359 ASN R 368 ASN S 359 ASN S 368 ASN T 359 ASN T 368 ASN U 359 ASN U 368 ASN V 359 ASN V 368 ASN W 359 ASN W 368 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.163758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.130875 restraints weight = 41095.335| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.75 r_work: 0.4008 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13593 Z= 0.112 Angle : 0.567 4.798 18239 Z= 0.281 Chirality : 0.049 0.133 2001 Planarity : 0.003 0.027 2231 Dihedral : 6.293 59.682 2130 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 4.55 % Allowed : 15.35 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.52 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 349 TYR 0.007 0.002 TYR Q 310 PHE 0.005 0.001 PHE P 346 HIS 0.002 0.001 HIS W 329 Details of bonding type rmsd covalent geometry : bond 0.00259 (13593) covalent geometry : angle 0.56686 (18239) hydrogen bonds : bond 0.04213 ( 328) hydrogen bonds : angle 4.39136 ( 984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 319 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8562 (mttp) cc_final: 0.8358 (mtmt) REVERT: A 350 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7632 (p) REVERT: A 370 LYS cc_start: 0.7624 (tttm) cc_final: 0.7347 (tttm) REVERT: B 320 SER cc_start: 0.8143 (m) cc_final: 0.7888 (t) REVERT: B 370 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8077 (tttp) REVERT: C 311 LYS cc_start: 0.8064 (tttm) cc_final: 0.7841 (tttp) REVERT: D 321 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8094 (mttt) REVERT: E 321 LYS cc_start: 0.8343 (mtpt) cc_final: 0.7899 (mttp) REVERT: E 370 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7609 (ttpp) REVERT: F 321 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8124 (mttp) REVERT: H 377 THR cc_start: 0.8025 (m) cc_final: 0.7491 (p) REVERT: I 340 LYS cc_start: 0.8311 (ttmm) cc_final: 0.8047 (mtpt) REVERT: J 321 LYS cc_start: 0.8717 (mtpm) cc_final: 0.8155 (mtmt) REVERT: J 369 LYS cc_start: 0.8123 (ptpt) cc_final: 0.7726 (ptmt) REVERT: J 377 THR cc_start: 0.8138 (m) cc_final: 0.7751 (p) REVERT: K 331 LYS cc_start: 0.8713 (mttp) cc_final: 0.8468 (mtpm) REVERT: K 369 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7837 (ptpt) REVERT: L 320 SER cc_start: 0.8135 (m) cc_final: 0.7819 (t) REVERT: L 331 LYS cc_start: 0.8725 (mttp) cc_final: 0.8487 (mtpm) REVERT: L 340 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7731 (mttt) REVERT: L 369 LYS cc_start: 0.8093 (ptpt) cc_final: 0.7742 (ptmt) REVERT: L 378 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: M 331 LYS cc_start: 0.8801 (mttp) cc_final: 0.8526 (mtmt) REVERT: M 340 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7935 (mtmm) REVERT: M 350 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7738 (p) REVERT: M 369 LYS cc_start: 0.8093 (ptpt) cc_final: 0.7889 (ptmt) REVERT: N 311 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8268 (tmtt) REVERT: N 321 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7930 (mttp) REVERT: N 331 LYS cc_start: 0.8824 (mttp) cc_final: 0.8515 (mttt) REVERT: N 340 LYS cc_start: 0.8437 (ttmm) cc_final: 0.8073 (mtmm) REVERT: N 369 LYS cc_start: 0.8224 (ptpt) cc_final: 0.7840 (ptmt) REVERT: N 378 PHE cc_start: 0.6784 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: O 331 LYS cc_start: 0.8830 (mttp) cc_final: 0.8571 (mtpm) REVERT: O 340 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8108 (mtmm) REVERT: O 378 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6054 (m-80) REVERT: P 370 LYS cc_start: 0.8263 (tttm) cc_final: 0.7962 (ttpt) REVERT: Q 317 LYS cc_start: 0.6259 (ptmt) cc_final: 0.5976 (ptmt) REVERT: Q 321 LYS cc_start: 0.8303 (mtpt) cc_final: 0.8083 (mttp) REVERT: Q 345 ASP cc_start: 0.7840 (t0) cc_final: 0.7571 (t70) REVERT: Q 350 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7701 (m) REVERT: Q 378 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6029 (m-80) REVERT: R 378 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6008 (m-80) REVERT: S 319 THR cc_start: 0.7762 (m) cc_final: 0.7547 (p) REVERT: S 331 LYS cc_start: 0.8760 (mttp) cc_final: 0.8515 (mtmt) REVERT: S 345 ASP cc_start: 0.7885 (m-30) cc_final: 0.7409 (t0) REVERT: S 373 THR cc_start: 0.8533 (m) cc_final: 0.8028 (p) REVERT: S 375 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7638 (tttt) REVERT: S 378 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.6126 (m-80) REVERT: T 331 LYS cc_start: 0.8679 (mttp) cc_final: 0.8434 (mtmt) REVERT: U 319 THR cc_start: 0.7747 (m) cc_final: 0.7383 (p) REVERT: U 378 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.5936 (m-80) REVERT: V 331 LYS cc_start: 0.8782 (mttp) cc_final: 0.8442 (mtpt) REVERT: V 350 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7189 (p) REVERT: V 378 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.5709 (p90) REVERT: W 338 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7811 (tm-30) outliers start: 67 outliers final: 36 residues processed: 358 average time/residue: 1.2791 time to fit residues: 497.8492 Evaluate side-chains 344 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 293 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 378 PHE Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain N residue 311 LYS Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 378 PHE Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 352 SER Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN F 368 ASN G 368 ASN H 368 ASN I 368 ASN J 368 ASN K 368 ASN L 368 ASN M 368 ASN N 368 ASN P 368 ASN R 368 ASN U 368 ASN V 368 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.198691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.157750 restraints weight = 41384.240| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.32 r_work: 0.3915 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13593 Z= 0.213 Angle : 0.651 4.983 18239 Z= 0.322 Chirality : 0.049 0.138 2001 Planarity : 0.004 0.028 2231 Dihedral : 7.832 59.726 2130 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.96 % Favored : 86.04 % Rotamer: Outliers : 5.98 % Allowed : 14.67 % Favored : 79.35 % 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: -3.35 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 349 TYR 0.023 0.003 TYR L 310 PHE 0.007 0.001 PHE U 346 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00486 (13593) covalent geometry : angle 0.65116 (18239) hydrogen bonds : bond 0.03226 ( 328) hydrogen bonds : angle 4.22266 ( 984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 348 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7542 (m) cc_final: 0.7264 (t) REVERT: A 350 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7754 (p) REVERT: A 368 ASN cc_start: 0.7654 (m110) cc_final: 0.7368 (m110) REVERT: A 370 LYS cc_start: 0.7544 (tttm) cc_final: 0.7302 (tttm) REVERT: D 321 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8116 (mttt) REVERT: E 321 LYS cc_start: 0.8408 (mtpt) cc_final: 0.7926 (mttp) REVERT: E 370 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7725 (ttpp) REVERT: F 317 LYS cc_start: 0.7429 (ptmt) cc_final: 0.7219 (ptmt) REVERT: F 321 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8159 (mttp) REVERT: F 377 THR cc_start: 0.8343 (m) cc_final: 0.8141 (m) REVERT: H 377 THR cc_start: 0.8149 (m) cc_final: 0.7707 (p) REVERT: I 340 LYS cc_start: 0.8309 (ttmm) cc_final: 0.7996 (mtpt) REVERT: J 350 VAL cc_start: 0.8084 (OUTLIER) cc_final: 0.7674 (p) REVERT: J 369 LYS cc_start: 0.8426 (ptpt) cc_final: 0.7835 (ptmt) REVERT: J 370 LYS cc_start: 0.8395 (tttm) cc_final: 0.7965 (ttpt) REVERT: K 331 LYS cc_start: 0.8769 (mttp) cc_final: 0.8564 (mtpm) REVERT: K 369 LYS cc_start: 0.8333 (ptpt) cc_final: 0.8031 (ptpt) REVERT: K 370 LYS cc_start: 0.8430 (tttm) cc_final: 0.8153 (ttpt) REVERT: L 369 LYS cc_start: 0.8247 (ptpt) cc_final: 0.7964 (ptmt) REVERT: L 370 LYS cc_start: 0.8410 (tttm) cc_final: 0.8015 (ttpt) REVERT: M 331 LYS cc_start: 0.8799 (mttp) cc_final: 0.8595 (mtmt) REVERT: M 340 LYS cc_start: 0.8378 (ttmm) cc_final: 0.7958 (mtmm) REVERT: M 350 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7756 (p) REVERT: M 369 LYS cc_start: 0.8335 (ptpt) cc_final: 0.8057 (ptmt) REVERT: M 370 LYS cc_start: 0.8375 (tttm) cc_final: 0.8044 (ttpt) REVERT: M 378 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6476 (m-80) REVERT: N 321 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8192 (mttp) REVERT: N 331 LYS cc_start: 0.8880 (mttp) cc_final: 0.8674 (mttt) REVERT: N 340 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8127 (mtmm) REVERT: N 351 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: N 369 LYS cc_start: 0.8372 (ptpt) cc_final: 0.8008 (ptmt) REVERT: N 370 LYS cc_start: 0.8465 (tttm) cc_final: 0.8103 (ttpt) REVERT: N 378 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: O 317 LYS cc_start: 0.6700 (ptmt) cc_final: 0.6442 (ptmt) REVERT: O 340 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8110 (mttt) REVERT: O 378 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: P 317 LYS cc_start: 0.6672 (ptmt) cc_final: 0.6417 (ptmt) REVERT: P 370 LYS cc_start: 0.8560 (tttm) cc_final: 0.8206 (ttpt) REVERT: P 378 PHE cc_start: 0.6599 (OUTLIER) cc_final: 0.6210 (m-80) REVERT: Q 317 LYS cc_start: 0.6634 (ptmt) cc_final: 0.6273 (ptmt) REVERT: Q 370 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8361 (ttmp) REVERT: Q 378 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: R 338 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: R 340 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8461 (mtmm) REVERT: R 345 ASP cc_start: 0.8254 (m-30) cc_final: 0.7689 (t0) REVERT: R 370 LYS cc_start: 0.8556 (tttm) cc_final: 0.8298 (tttp) REVERT: R 378 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: S 319 THR cc_start: 0.8064 (m) cc_final: 0.7791 (p) REVERT: S 331 LYS cc_start: 0.8808 (mttp) cc_final: 0.8557 (mtmt) REVERT: S 345 ASP cc_start: 0.8044 (m-30) cc_final: 0.7533 (t0) REVERT: S 370 LYS cc_start: 0.8596 (tttm) cc_final: 0.8356 (tttp) REVERT: S 375 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7729 (ttpp) REVERT: S 378 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.6195 (m-80) REVERT: T 345 ASP cc_start: 0.7918 (m-30) cc_final: 0.7526 (t0) REVERT: U 345 ASP cc_start: 0.7655 (m-30) cc_final: 0.7080 (t0) REVERT: U 378 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.6035 (m-80) REVERT: V 331 LYS cc_start: 0.8938 (mttp) cc_final: 0.8564 (mtpt) REVERT: V 345 ASP cc_start: 0.7739 (m-30) cc_final: 0.7149 (t0) REVERT: V 378 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5648 (p90) REVERT: W 343 LYS cc_start: 0.7462 (mttt) cc_final: 0.7120 (mptt) outliers start: 88 outliers final: 45 residues processed: 396 average time/residue: 1.4135 time to fit residues: 608.0135 Evaluate side-chains 376 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 314 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 352 SER Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 351 GLN Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 378 PHE Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 351 GLN Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 377 THR Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain P residue 378 PHE Chi-restraints excluded: chain Q residue 319 THR Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 370 LYS Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 338 GLU Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 352 SER Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN E 351 GLN L 368 ASN N 362 HIS N 368 ASN O 368 ASN R 368 ASN W 368 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.200560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.159271 restraints weight = 41246.053| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.33 r_work: 0.3928 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13593 Z= 0.170 Angle : 0.621 4.959 18239 Z= 0.303 Chirality : 0.048 0.137 2001 Planarity : 0.003 0.030 2231 Dihedral : 7.597 58.672 2126 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 5.43 % Allowed : 16.71 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.44 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 349 TYR 0.012 0.002 TYR T 310 PHE 0.004 0.001 PHE U 346 HIS 0.003 0.001 HIS V 362 Details of bonding type rmsd covalent geometry : bond 0.00384 (13593) covalent geometry : angle 0.62106 (18239) hydrogen bonds : bond 0.02676 ( 328) hydrogen bonds : angle 4.13681 ( 984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 310 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7512 (m) cc_final: 0.7293 (t) REVERT: A 350 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7682 (p) REVERT: A 368 ASN cc_start: 0.7422 (m110) cc_final: 0.7114 (m110) REVERT: A 370 LYS cc_start: 0.7607 (tttm) cc_final: 0.7347 (tttm) REVERT: B 338 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7975 (tm-30) REVERT: D 321 LYS cc_start: 0.8585 (mtpt) cc_final: 0.8103 (mttt) REVERT: E 321 LYS cc_start: 0.8432 (mtpt) cc_final: 0.7945 (mttp) REVERT: F 317 LYS cc_start: 0.7450 (ptmt) cc_final: 0.7193 (ptmt) REVERT: F 321 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8108 (mttp) REVERT: H 377 THR cc_start: 0.8148 (m) cc_final: 0.7757 (p) REVERT: I 340 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7958 (mtpt) REVERT: J 350 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7672 (p) REVERT: J 369 LYS cc_start: 0.8458 (ptpt) cc_final: 0.7866 (ptmt) REVERT: J 370 LYS cc_start: 0.8327 (tttm) cc_final: 0.7868 (ttpt) REVERT: K 331 LYS cc_start: 0.8719 (mttp) cc_final: 0.8500 (mtpm) REVERT: K 369 LYS cc_start: 0.8107 (ptpt) cc_final: 0.7850 (ptpt) REVERT: K 370 LYS cc_start: 0.8266 (tttm) cc_final: 0.7929 (ttpt) REVERT: L 352 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8437 (m) REVERT: L 369 LYS cc_start: 0.8275 (ptpt) cc_final: 0.7860 (ptmt) REVERT: L 370 LYS cc_start: 0.8316 (tttm) cc_final: 0.7954 (ttpt) REVERT: M 331 LYS cc_start: 0.8815 (mttp) cc_final: 0.8580 (mtmt) REVERT: M 340 LYS cc_start: 0.8396 (ttmm) cc_final: 0.7989 (mtmm) REVERT: M 350 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7826 (p) REVERT: M 369 LYS cc_start: 0.8337 (ptpt) cc_final: 0.8010 (ptmt) REVERT: M 370 LYS cc_start: 0.8305 (tttm) cc_final: 0.7923 (ttpt) REVERT: M 378 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6420 (m-80) REVERT: N 311 LYS cc_start: 0.8481 (tmtt) cc_final: 0.8221 (tptt) REVERT: N 321 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8162 (mttp) REVERT: N 331 LYS cc_start: 0.8819 (mttp) cc_final: 0.8518 (mtpm) REVERT: N 340 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8048 (mtmm) REVERT: N 350 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7764 (p) REVERT: N 369 LYS cc_start: 0.8358 (ptpt) cc_final: 0.7985 (ptmt) REVERT: N 370 LYS cc_start: 0.8395 (tttm) cc_final: 0.8052 (ttpt) REVERT: O 340 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8110 (mttt) REVERT: O 370 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8140 (tttp) REVERT: O 378 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6130 (m-80) REVERT: P 317 LYS cc_start: 0.6685 (ptmt) cc_final: 0.6451 (ptmt) REVERT: P 370 LYS cc_start: 0.8477 (tttm) cc_final: 0.8120 (ttpt) REVERT: Q 378 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: R 345 ASP cc_start: 0.8225 (m-30) cc_final: 0.7705 (t0) REVERT: R 370 LYS cc_start: 0.8466 (tttm) cc_final: 0.8196 (tttp) REVERT: S 319 THR cc_start: 0.8023 (m) cc_final: 0.7745 (p) REVERT: S 331 LYS cc_start: 0.8787 (mttp) cc_final: 0.8537 (mtmt) REVERT: S 345 ASP cc_start: 0.8104 (m-30) cc_final: 0.7578 (t0) REVERT: S 370 LYS cc_start: 0.8506 (tttm) cc_final: 0.8263 (tttp) REVERT: S 375 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7685 (ttpp) REVERT: S 378 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.6265 (m-80) REVERT: T 345 ASP cc_start: 0.7872 (m-30) cc_final: 0.7565 (t0) REVERT: U 345 ASP cc_start: 0.7672 (m-30) cc_final: 0.7169 (t0) REVERT: U 378 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6125 (m-80) REVERT: V 331 LYS cc_start: 0.8914 (mttp) cc_final: 0.8554 (mtpt) REVERT: V 345 ASP cc_start: 0.7751 (m-30) cc_final: 0.7170 (t0) REVERT: V 378 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.5644 (p90) REVERT: W 343 LYS cc_start: 0.7456 (mttt) cc_final: 0.7171 (mptt) outliers start: 80 outliers final: 47 residues processed: 355 average time/residue: 1.3199 time to fit residues: 510.2430 Evaluate side-chains 364 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 305 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 352 SER Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 370 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 369 LYS Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 352 SER Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 356 SER Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 134 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN F 368 ASN H 368 ASN J 362 HIS L 368 ASN N 368 ASN R 362 HIS T 362 HIS U 362 HIS W 368 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.195214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.152460 restraints weight = 41213.555| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.28 r_work: 0.3828 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 13593 Z= 0.314 Angle : 0.745 5.413 18239 Z= 0.371 Chirality : 0.050 0.136 2001 Planarity : 0.004 0.035 2231 Dihedral : 8.893 59.547 2122 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.90 % Favored : 86.10 % Rotamer: Outliers : 6.59 % Allowed : 16.30 % Favored : 77.11 % 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: -3.42 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 349 TYR 0.022 0.004 TYR V 310 PHE 0.008 0.001 PHE U 346 HIS 0.004 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00706 (13593) covalent geometry : angle 0.74550 (18239) hydrogen bonds : bond 0.02820 ( 328) hydrogen bonds : angle 4.29963 ( 984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 340 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 369 LYS cc_start: 0.8736 (ptpt) cc_final: 0.8419 (mttm) REVERT: D 321 LYS cc_start: 0.8599 (mtpt) cc_final: 0.8108 (mttt) REVERT: D 342 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: E 321 LYS cc_start: 0.8464 (mtpt) cc_final: 0.7959 (mttp) REVERT: F 321 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8128 (mttp) REVERT: H 369 LYS cc_start: 0.8466 (ptpt) cc_final: 0.8174 (ptpp) REVERT: I 343 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7865 (mppt) REVERT: J 369 LYS cc_start: 0.8535 (ptpt) cc_final: 0.7961 (ptmt) REVERT: J 370 LYS cc_start: 0.8531 (tttm) cc_final: 0.8030 (ttpt) REVERT: K 343 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7950 (mtpm) REVERT: K 369 LYS cc_start: 0.8324 (ptpt) cc_final: 0.8007 (ptpt) REVERT: K 370 LYS cc_start: 0.8474 (tttm) cc_final: 0.8226 (ttpt) REVERT: L 352 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8427 (m) REVERT: L 369 LYS cc_start: 0.8337 (ptpt) cc_final: 0.7999 (ptmt) REVERT: L 370 LYS cc_start: 0.8441 (tttm) cc_final: 0.8154 (ttpt) REVERT: M 331 LYS cc_start: 0.8878 (mttp) cc_final: 0.8641 (mtmt) REVERT: M 340 LYS cc_start: 0.8453 (ttmm) cc_final: 0.7997 (mtmm) REVERT: M 369 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8047 (ptmt) REVERT: M 370 LYS cc_start: 0.8403 (tttm) cc_final: 0.8066 (ttpt) REVERT: M 378 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6403 (m-80) REVERT: N 321 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8164 (mttp) REVERT: N 331 LYS cc_start: 0.8880 (mttp) cc_final: 0.8673 (mttt) REVERT: N 340 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8052 (mtmm) REVERT: N 369 LYS cc_start: 0.8545 (ptpt) cc_final: 0.8038 (ptmt) REVERT: N 370 LYS cc_start: 0.8498 (tttm) cc_final: 0.8175 (ttpt) REVERT: O 321 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8053 (mttp) REVERT: O 340 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8076 (mttt) REVERT: O 370 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8143 (tttp) REVERT: O 378 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.6109 (m-80) REVERT: P 370 LYS cc_start: 0.8599 (tttm) cc_final: 0.8162 (ttpt) REVERT: Q 378 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: R 317 LYS cc_start: 0.6846 (ptmt) cc_final: 0.6442 (ptmt) REVERT: R 345 ASP cc_start: 0.8090 (m-30) cc_final: 0.7719 (t0) REVERT: R 370 LYS cc_start: 0.8611 (tttm) cc_final: 0.8356 (tttp) REVERT: R 372 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8082 (mm-30) REVERT: S 317 LYS cc_start: 0.7087 (ptmt) cc_final: 0.6691 (ptmt) REVERT: S 319 THR cc_start: 0.8225 (m) cc_final: 0.7924 (p) REVERT: S 331 LYS cc_start: 0.8849 (mttp) cc_final: 0.8628 (mtmt) REVERT: S 345 ASP cc_start: 0.8138 (m-30) cc_final: 0.7626 (t0) REVERT: S 370 LYS cc_start: 0.8653 (tttm) cc_final: 0.8371 (tttp) REVERT: S 375 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7745 (ttpp) REVERT: S 378 PHE cc_start: 0.6635 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: T 345 ASP cc_start: 0.7946 (m-30) cc_final: 0.7632 (t0) REVERT: U 345 ASP cc_start: 0.7790 (m-30) cc_final: 0.7257 (t0) REVERT: U 378 PHE cc_start: 0.6712 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: V 315 LEU cc_start: 0.7994 (tt) cc_final: 0.7534 (mp) REVERT: V 331 LYS cc_start: 0.8980 (mttp) cc_final: 0.8550 (mtpt) REVERT: V 345 ASP cc_start: 0.7740 (m-30) cc_final: 0.7202 (t0) REVERT: V 378 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.5709 (p90) REVERT: W 343 LYS cc_start: 0.7464 (mttt) cc_final: 0.7093 (mptt) outliers start: 97 outliers final: 67 residues processed: 388 average time/residue: 1.3417 time to fit residues: 565.5732 Evaluate side-chains 395 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 316 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 343 LYS Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 343 LYS Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 343 LYS Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 352 SER Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 370 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 319 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 319 THR Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 369 LYS Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 319 THR Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 352 SER Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 319 THR Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 356 SER Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 106 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 155 optimal weight: 0.4980 chunk 119 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 149 optimal weight: 0.0060 chunk 7 optimal weight: 8.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN L 368 ASN N 368 ASN P 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.201253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.158546 restraints weight = 41407.034| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.34 r_work: 0.3889 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13593 Z= 0.117 Angle : 0.606 5.261 18239 Z= 0.296 Chirality : 0.049 0.133 2001 Planarity : 0.003 0.035 2231 Dihedral : 7.548 57.504 2122 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 4.21 % Allowed : 20.11 % Favored : 75.68 % 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: -3.51 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.011 0.002 TYR L 310 PHE 0.005 0.001 PHE I 346 HIS 0.002 0.000 HIS V 362 Details of bonding type rmsd covalent geometry : bond 0.00271 (13593) covalent geometry : angle 0.60644 (18239) hydrogen bonds : bond 0.02378 ( 328) hydrogen bonds : angle 4.08766 ( 984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 316 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7481 (m) cc_final: 0.7229 (t) REVERT: A 350 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7621 (p) REVERT: A 370 LYS cc_start: 0.7607 (tttm) cc_final: 0.7381 (ttpp) REVERT: D 321 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8123 (mttt) REVERT: E 321 LYS cc_start: 0.8494 (mtpt) cc_final: 0.7994 (mttp) REVERT: F 321 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8122 (mttp) REVERT: H 352 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8318 (m) REVERT: J 350 VAL cc_start: 0.8168 (OUTLIER) cc_final: 0.7773 (p) REVERT: J 369 LYS cc_start: 0.8447 (ptpt) cc_final: 0.7865 (ptmt) REVERT: J 370 LYS cc_start: 0.8332 (tttm) cc_final: 0.7883 (ttpt) REVERT: K 343 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7897 (mtpm) REVERT: K 369 LYS cc_start: 0.8087 (ptpt) cc_final: 0.7859 (ptpp) REVERT: K 370 LYS cc_start: 0.8251 (tttm) cc_final: 0.7955 (ttpt) REVERT: L 369 LYS cc_start: 0.8212 (ptpt) cc_final: 0.7812 (ptmt) REVERT: L 370 LYS cc_start: 0.8295 (tttm) cc_final: 0.8020 (ttpt) REVERT: M 331 LYS cc_start: 0.8785 (mttp) cc_final: 0.8571 (mtmt) REVERT: M 340 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8001 (mtmm) REVERT: M 350 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7929 (p) REVERT: M 369 LYS cc_start: 0.8432 (ptpt) cc_final: 0.8039 (ptmt) REVERT: M 370 LYS cc_start: 0.8298 (tttm) cc_final: 0.7885 (ttpt) REVERT: M 378 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6328 (m-80) REVERT: N 311 LYS cc_start: 0.8505 (tmtt) cc_final: 0.8265 (tptt) REVERT: N 321 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8200 (mttp) REVERT: N 331 LYS cc_start: 0.8837 (mttp) cc_final: 0.8562 (mtpm) REVERT: N 340 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8026 (mtmm) REVERT: N 350 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7856 (p) REVERT: N 352 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8265 (m) REVERT: N 369 LYS cc_start: 0.8434 (ptpt) cc_final: 0.7954 (ptmt) REVERT: N 370 LYS cc_start: 0.8306 (tttm) cc_final: 0.7991 (ttpt) REVERT: O 321 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8036 (mttp) REVERT: O 340 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8104 (mttt) REVERT: O 378 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6132 (m-80) REVERT: P 345 ASP cc_start: 0.8130 (t0) cc_final: 0.7823 (t0) REVERT: P 370 LYS cc_start: 0.8450 (tttm) cc_final: 0.8084 (ttpt) REVERT: Q 378 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.6146 (m-80) REVERT: R 317 LYS cc_start: 0.6770 (ptmt) cc_final: 0.6395 (ptmt) REVERT: R 345 ASP cc_start: 0.8052 (m-30) cc_final: 0.7652 (t0) REVERT: R 370 LYS cc_start: 0.8457 (tttm) cc_final: 0.8227 (tttp) REVERT: S 319 THR cc_start: 0.7978 (m) cc_final: 0.7704 (p) REVERT: S 340 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8108 (ttmm) REVERT: S 345 ASP cc_start: 0.8111 (m-30) cc_final: 0.7605 (t0) REVERT: S 370 LYS cc_start: 0.8416 (tttm) cc_final: 0.8106 (tttp) REVERT: S 375 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7709 (ttpp) REVERT: T 345 ASP cc_start: 0.7939 (m-30) cc_final: 0.7632 (t0) REVERT: U 345 ASP cc_start: 0.7714 (m-30) cc_final: 0.7240 (t0) REVERT: U 378 PHE cc_start: 0.6692 (OUTLIER) cc_final: 0.6091 (m-80) REVERT: V 331 LYS cc_start: 0.8954 (mttp) cc_final: 0.8553 (mtpt) REVERT: V 345 ASP cc_start: 0.7745 (m-30) cc_final: 0.7180 (t0) REVERT: V 378 PHE cc_start: 0.6571 (OUTLIER) cc_final: 0.5649 (p90) REVERT: W 343 LYS cc_start: 0.7407 (mttt) cc_final: 0.7093 (mptt) outliers start: 62 outliers final: 36 residues processed: 350 average time/residue: 1.4474 time to fit residues: 552.1811 Evaluate side-chains 352 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 343 LYS Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain O residue 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 63 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 ASN N 368 ASN P 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.199632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.155843 restraints weight = 41222.636| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.34 r_work: 0.3843 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13593 Z= 0.177 Angle : 0.620 5.337 18239 Z= 0.304 Chirality : 0.048 0.129 2001 Planarity : 0.004 0.034 2231 Dihedral : 7.667 57.729 2120 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 4.28 % Allowed : 19.63 % Favored : 76.09 % 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: -3.49 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.012 0.002 TYR V 310 PHE 0.004 0.001 PHE T 378 HIS 0.002 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00401 (13593) covalent geometry : angle 0.62045 (18239) hydrogen bonds : bond 0.02269 ( 328) hydrogen bonds : angle 4.08005 ( 984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 313 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7696 (p) REVERT: A 351 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: A 370 LYS cc_start: 0.7627 (tttm) cc_final: 0.7354 (tttm) REVERT: C 317 LYS cc_start: 0.7112 (ptmt) cc_final: 0.6604 (ptpp) REVERT: D 321 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8175 (mttt) REVERT: E 321 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8039 (mttp) REVERT: F 321 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8180 (mttp) REVERT: H 369 LYS cc_start: 0.8429 (ptpt) cc_final: 0.8134 (ptpp) REVERT: I 340 LYS cc_start: 0.8259 (mtpm) cc_final: 0.7936 (mtpt) REVERT: J 350 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.7851 (p) REVERT: J 369 LYS cc_start: 0.8490 (ptpt) cc_final: 0.7918 (ptmt) REVERT: K 343 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7914 (mtpm) REVERT: K 369 LYS cc_start: 0.8300 (ptpt) cc_final: 0.8016 (ptpt) REVERT: K 370 LYS cc_start: 0.8343 (tttm) cc_final: 0.8072 (ttpt) REVERT: L 369 LYS cc_start: 0.8276 (ptpt) cc_final: 0.7855 (ptmt) REVERT: M 340 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8029 (mtmm) REVERT: M 350 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.7987 (p) REVERT: M 369 LYS cc_start: 0.8506 (ptpt) cc_final: 0.8132 (ptmt) REVERT: M 370 LYS cc_start: 0.8345 (tttm) cc_final: 0.7926 (ttpt) REVERT: M 378 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6350 (m-80) REVERT: N 321 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8244 (mttp) REVERT: N 331 LYS cc_start: 0.8843 (mttp) cc_final: 0.8606 (mtpm) REVERT: N 340 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8101 (mtmm) REVERT: N 350 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7903 (p) REVERT: N 352 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8269 (m) REVERT: N 369 LYS cc_start: 0.8543 (ptpt) cc_final: 0.8057 (ptmt) REVERT: N 370 LYS cc_start: 0.8354 (tttm) cc_final: 0.8057 (ttpt) REVERT: O 321 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8098 (mttp) REVERT: O 340 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8173 (mttt) REVERT: O 378 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6129 (m-80) REVERT: P 370 LYS cc_start: 0.8537 (tttm) cc_final: 0.8193 (ttpt) REVERT: Q 378 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6277 (m-80) REVERT: R 317 LYS cc_start: 0.6842 (ptmt) cc_final: 0.6473 (ptmt) REVERT: R 345 ASP cc_start: 0.8084 (m-30) cc_final: 0.7730 (t0) REVERT: R 370 LYS cc_start: 0.8529 (tttm) cc_final: 0.8281 (tttp) REVERT: S 317 LYS cc_start: 0.7066 (ptmt) cc_final: 0.6668 (ptmt) REVERT: S 319 THR cc_start: 0.8072 (m) cc_final: 0.7827 (p) REVERT: S 345 ASP cc_start: 0.8138 (m-30) cc_final: 0.7663 (t0) REVERT: S 370 LYS cc_start: 0.8494 (tttm) cc_final: 0.8192 (tttp) REVERT: S 375 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7746 (ttpp) REVERT: T 345 ASP cc_start: 0.7958 (m-30) cc_final: 0.7653 (t0) REVERT: U 345 ASP cc_start: 0.7750 (m-30) cc_final: 0.7309 (t0) REVERT: U 378 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.6137 (m-80) REVERT: V 331 LYS cc_start: 0.8957 (mttp) cc_final: 0.8565 (mtpt) REVERT: V 345 ASP cc_start: 0.7723 (m-30) cc_final: 0.7192 (t0) REVERT: V 378 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.5677 (p90) REVERT: W 343 LYS cc_start: 0.7374 (mttt) cc_final: 0.7074 (mptt) outliers start: 63 outliers final: 47 residues processed: 348 average time/residue: 1.4190 time to fit residues: 538.7432 Evaluate side-chains 364 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 304 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 343 LYS Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain O residue 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 369 LYS Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 360 ILE Chi-restraints excluded: chain V residue 376 LEU Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 61 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 52 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.187654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.156259 restraints weight = 40151.767| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.30 r_work: 0.3842 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13593 Z= 0.192 Angle : 0.647 5.643 18239 Z= 0.318 Chirality : 0.049 0.129 2001 Planarity : 0.004 0.033 2231 Dihedral : 7.810 57.114 2120 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 4.89 % Allowed : 19.43 % Favored : 75.68 % 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: -3.50 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 349 TYR 0.014 0.003 TYR V 310 PHE 0.005 0.001 PHE I 346 HIS 0.002 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00432 (13593) covalent geometry : angle 0.64715 (18239) hydrogen bonds : bond 0.02376 ( 328) hydrogen bonds : angle 4.06645 ( 984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 309 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: A 370 LYS cc_start: 0.7589 (tttm) cc_final: 0.7306 (tttm) REVERT: C 317 LYS cc_start: 0.7058 (ptmt) cc_final: 0.6535 (ptpp) REVERT: D 321 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8123 (mttt) REVERT: E 321 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8000 (mttp) REVERT: F 321 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8151 (mttp) REVERT: I 340 LYS cc_start: 0.8265 (mtpm) cc_final: 0.7900 (mtpt) REVERT: I 378 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6386 (m-80) REVERT: J 369 LYS cc_start: 0.8526 (ptpt) cc_final: 0.7943 (ptmt) REVERT: K 343 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7892 (mtpm) REVERT: K 369 LYS cc_start: 0.8296 (ptpt) cc_final: 0.7997 (ptpt) REVERT: K 370 LYS cc_start: 0.8365 (tttm) cc_final: 0.8082 (ttpt) REVERT: L 369 LYS cc_start: 0.8289 (ptpt) cc_final: 0.7847 (ptmt) REVERT: L 370 LYS cc_start: 0.8388 (tttm) cc_final: 0.8122 (ttpt) REVERT: M 350 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.7994 (p) REVERT: M 370 LYS cc_start: 0.8343 (tttm) cc_final: 0.7981 (ttpt) REVERT: M 378 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6296 (m-80) REVERT: N 321 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8222 (mttp) REVERT: N 331 LYS cc_start: 0.8843 (mttp) cc_final: 0.8595 (mtpm) REVERT: N 340 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8076 (mtmm) REVERT: N 350 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.7916 (p) REVERT: N 352 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8250 (m) REVERT: N 369 LYS cc_start: 0.8560 (ptpt) cc_final: 0.8043 (ptmt) REVERT: N 370 LYS cc_start: 0.8355 (tttm) cc_final: 0.8049 (ttpt) REVERT: O 321 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8088 (mttp) REVERT: O 340 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8152 (mttt) REVERT: O 378 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: P 370 LYS cc_start: 0.8553 (tttm) cc_final: 0.8189 (ttpt) REVERT: Q 378 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6252 (m-80) REVERT: R 317 LYS cc_start: 0.6940 (ptmt) cc_final: 0.6740 (ptmt) REVERT: R 345 ASP cc_start: 0.8057 (m-30) cc_final: 0.7709 (t0) REVERT: R 370 LYS cc_start: 0.8538 (tttm) cc_final: 0.8275 (tttp) REVERT: S 317 LYS cc_start: 0.7061 (ptmt) cc_final: 0.6647 (ptmt) REVERT: S 319 THR cc_start: 0.8108 (m) cc_final: 0.7855 (p) REVERT: S 345 ASP cc_start: 0.8105 (m-30) cc_final: 0.7631 (t0) REVERT: S 370 LYS cc_start: 0.8506 (tttm) cc_final: 0.8200 (tttp) REVERT: S 375 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7747 (ttpp) REVERT: T 345 ASP cc_start: 0.7925 (m-30) cc_final: 0.7623 (t0) REVERT: U 331 LYS cc_start: 0.8891 (mttp) cc_final: 0.8448 (mtmt) REVERT: U 345 ASP cc_start: 0.7732 (m-30) cc_final: 0.7265 (t0) REVERT: U 370 LYS cc_start: 0.8414 (tttm) cc_final: 0.8106 (tttp) REVERT: U 378 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: V 331 LYS cc_start: 0.8949 (mttp) cc_final: 0.8536 (mtpt) REVERT: V 345 ASP cc_start: 0.7676 (m-30) cc_final: 0.7141 (t0) REVERT: V 378 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.5678 (p90) REVERT: W 343 LYS cc_start: 0.7365 (mttt) cc_final: 0.7034 (mptt) REVERT: W 378 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6506 (m-80) outliers start: 72 outliers final: 51 residues processed: 346 average time/residue: 1.4350 time to fit residues: 541.2314 Evaluate side-chains 368 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 304 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 369 LYS Chi-restraints excluded: chain I residue 378 PHE Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 343 LYS Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 369 LYS Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 376 LEU Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 369 LYS Chi-restraints excluded: chain W residue 378 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 55 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN P 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.146304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.112329 restraints weight = 41779.535| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.77 r_work: 0.3804 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13593 Z= 0.160 Angle : 0.622 5.668 18239 Z= 0.305 Chirality : 0.048 0.126 2001 Planarity : 0.004 0.042 2231 Dihedral : 7.550 57.390 2120 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 4.42 % Allowed : 20.11 % Favored : 75.48 % 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: -3.52 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 349 TYR 0.011 0.002 TYR T 310 PHE 0.003 0.001 PHE L 346 HIS 0.002 0.000 HIS M 362 Details of bonding type rmsd covalent geometry : bond 0.00361 (13593) covalent geometry : angle 0.62234 (18239) hydrogen bonds : bond 0.02221 ( 328) hydrogen bonds : angle 4.00452 ( 984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 312 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: A 370 LYS cc_start: 0.7587 (tttm) cc_final: 0.7307 (tttm) REVERT: C 317 LYS cc_start: 0.6952 (ptmt) cc_final: 0.6437 (ptpp) REVERT: D 321 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8091 (mttt) REVERT: D 342 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: E 321 LYS cc_start: 0.8513 (mtpt) cc_final: 0.7999 (mttp) REVERT: F 321 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8158 (mttp) REVERT: H 352 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8339 (m) REVERT: I 340 LYS cc_start: 0.8295 (mtpm) cc_final: 0.7939 (mtpt) REVERT: I 378 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6380 (m-80) REVERT: J 350 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.7811 (p) REVERT: J 369 LYS cc_start: 0.8531 (ptpt) cc_final: 0.7927 (ptmt) REVERT: K 331 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8687 (mtpm) REVERT: K 343 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7890 (mtpm) REVERT: K 369 LYS cc_start: 0.8292 (ptpt) cc_final: 0.8003 (ptpt) REVERT: K 370 LYS cc_start: 0.8408 (tttm) cc_final: 0.8113 (ttpt) REVERT: L 350 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.7910 (p) REVERT: L 369 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7864 (ptmt) REVERT: M 350 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8074 (p) REVERT: M 352 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8314 (m) REVERT: M 370 LYS cc_start: 0.8365 (tttm) cc_final: 0.7995 (ttpt) REVERT: M 378 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6252 (m-80) REVERT: N 321 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8254 (mttp) REVERT: N 331 LYS cc_start: 0.8886 (mttp) cc_final: 0.8662 (mtpm) REVERT: N 340 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8073 (mtmm) REVERT: N 350 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.7930 (p) REVERT: N 352 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8267 (m) REVERT: N 369 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8025 (ptmt) REVERT: N 370 LYS cc_start: 0.8398 (tttm) cc_final: 0.8084 (ttpt) REVERT: O 321 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8072 (mttp) REVERT: O 340 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8154 (mttt) REVERT: O 378 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6115 (m-80) REVERT: P 370 LYS cc_start: 0.8627 (tttm) cc_final: 0.8240 (ttpt) REVERT: Q 378 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6254 (m-80) REVERT: R 317 LYS cc_start: 0.6889 (ptmt) cc_final: 0.6595 (ptmt) REVERT: R 345 ASP cc_start: 0.8128 (m-30) cc_final: 0.7702 (t0) REVERT: R 370 LYS cc_start: 0.8535 (tttm) cc_final: 0.8291 (tttp) REVERT: S 317 LYS cc_start: 0.6940 (ptmt) cc_final: 0.6506 (ptmt) REVERT: S 319 THR cc_start: 0.8146 (m) cc_final: 0.7907 (p) REVERT: S 345 ASP cc_start: 0.8152 (m-30) cc_final: 0.7625 (t0) REVERT: S 370 LYS cc_start: 0.8506 (tttm) cc_final: 0.8199 (tttp) REVERT: S 375 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7719 (ttpp) REVERT: T 345 ASP cc_start: 0.7982 (m-30) cc_final: 0.7596 (t0) REVERT: U 331 LYS cc_start: 0.8922 (mttp) cc_final: 0.8462 (mtmt) REVERT: U 345 ASP cc_start: 0.7765 (m-30) cc_final: 0.7217 (t0) REVERT: U 370 LYS cc_start: 0.8420 (tttm) cc_final: 0.8106 (tttp) REVERT: U 378 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.6007 (m-80) REVERT: V 331 LYS cc_start: 0.9009 (mttp) cc_final: 0.8578 (mtpt) REVERT: V 345 ASP cc_start: 0.7692 (m-30) cc_final: 0.7071 (t0) REVERT: V 378 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.5685 (p90) REVERT: W 343 LYS cc_start: 0.7324 (mttt) cc_final: 0.6908 (mptt) outliers start: 65 outliers final: 43 residues processed: 346 average time/residue: 1.4021 time to fit residues: 529.0221 Evaluate side-chains 364 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 303 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 378 PHE Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 343 LYS Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 369 LYS Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 141 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 128 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN L 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.144920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.110730 restraints weight = 41690.814| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.76 r_work: 0.3781 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13593 Z= 0.196 Angle : 0.654 5.999 18239 Z= 0.321 Chirality : 0.049 0.127 2001 Planarity : 0.004 0.044 2231 Dihedral : 7.792 57.163 2120 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 4.42 % Allowed : 20.58 % Favored : 75.00 % 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: -3.52 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 349 TYR 0.014 0.003 TYR V 310 PHE 0.004 0.001 PHE T 378 HIS 0.002 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00441 (13593) covalent geometry : angle 0.65379 (18239) hydrogen bonds : bond 0.02319 ( 328) hydrogen bonds : angle 4.01095 ( 984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 311 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.7575 (tttm) cc_final: 0.7290 (tttm) REVERT: C 317 LYS cc_start: 0.6963 (ptmt) cc_final: 0.6452 (ptpp) REVERT: C 349 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7385 (mtp-110) REVERT: D 321 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8092 (mttt) REVERT: D 342 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: E 321 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8018 (mttp) REVERT: F 321 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8172 (mttp) REVERT: I 340 LYS cc_start: 0.8306 (mtpm) cc_final: 0.7774 (mtmt) REVERT: I 378 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: J 369 LYS cc_start: 0.8562 (ptpt) cc_final: 0.7976 (ptmt) REVERT: K 343 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7893 (mtpm) REVERT: K 369 LYS cc_start: 0.8343 (ptpt) cc_final: 0.8049 (ptpt) REVERT: K 370 LYS cc_start: 0.8446 (tttm) cc_final: 0.8152 (ttpt) REVERT: L 369 LYS cc_start: 0.8298 (ptpt) cc_final: 0.7850 (ptmt) REVERT: M 350 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8038 (p) REVERT: M 370 LYS cc_start: 0.8392 (tttm) cc_final: 0.8024 (ttpt) REVERT: M 378 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6290 (m-80) REVERT: N 321 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8269 (mttp) REVERT: N 331 LYS cc_start: 0.8899 (mttp) cc_final: 0.8651 (mtpm) REVERT: N 340 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8081 (mtmm) REVERT: N 350 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.7989 (p) REVERT: N 352 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8274 (m) REVERT: N 369 LYS cc_start: 0.8609 (ptpt) cc_final: 0.8095 (ptmt) REVERT: N 370 LYS cc_start: 0.8407 (tttm) cc_final: 0.8086 (ttpt) REVERT: O 321 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8093 (mttp) REVERT: O 340 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8161 (mttt) REVERT: O 378 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6088 (m-80) REVERT: P 370 LYS cc_start: 0.8649 (tttm) cc_final: 0.8262 (ttpt) REVERT: Q 378 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: R 317 LYS cc_start: 0.7057 (ptmt) cc_final: 0.6763 (ptmt) REVERT: R 345 ASP cc_start: 0.8112 (m-30) cc_final: 0.7698 (t0) REVERT: R 370 LYS cc_start: 0.8583 (tttm) cc_final: 0.8305 (tttp) REVERT: S 317 LYS cc_start: 0.7028 (ptmt) cc_final: 0.6582 (ptmt) REVERT: S 319 THR cc_start: 0.8142 (m) cc_final: 0.7875 (p) REVERT: S 345 ASP cc_start: 0.8159 (m-30) cc_final: 0.7633 (t0) REVERT: S 370 LYS cc_start: 0.8534 (tttm) cc_final: 0.8223 (tttp) REVERT: S 375 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7731 (ttpp) REVERT: T 345 ASP cc_start: 0.7978 (m-30) cc_final: 0.7613 (t0) REVERT: U 331 LYS cc_start: 0.8924 (mttp) cc_final: 0.8465 (mtmt) REVERT: U 345 ASP cc_start: 0.7763 (m-30) cc_final: 0.7206 (t0) REVERT: U 370 LYS cc_start: 0.8479 (tttm) cc_final: 0.8175 (tttp) REVERT: U 378 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.6006 (m-80) REVERT: V 331 LYS cc_start: 0.9001 (mttp) cc_final: 0.8562 (mtpt) REVERT: V 345 ASP cc_start: 0.7699 (m-30) cc_final: 0.7066 (t0) REVERT: V 378 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.5700 (p90) REVERT: W 343 LYS cc_start: 0.7297 (mttt) cc_final: 0.6905 (mptt) outliers start: 65 outliers final: 49 residues processed: 347 average time/residue: 1.4532 time to fit residues: 548.7863 Evaluate side-chains 369 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 307 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 378 PHE Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 343 LYS Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 369 LYS Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 376 LEU Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 114 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN F 362 HIS L 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.146141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.112753 restraints weight = 41557.857| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.74 r_work: 0.3813 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13593 Z= 0.148 Angle : 0.622 6.090 18239 Z= 0.304 Chirality : 0.048 0.125 2001 Planarity : 0.004 0.045 2231 Dihedral : 7.428 57.221 2120 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 4.21 % Allowed : 20.72 % 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: -3.56 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 349 TYR 0.011 0.002 TYR V 310 PHE 0.003 0.001 PHE C 378 HIS 0.002 0.000 HIS V 362 Details of bonding type rmsd covalent geometry : bond 0.00337 (13593) covalent geometry : angle 0.62219 (18239) hydrogen bonds : bond 0.02227 ( 328) hydrogen bonds : angle 3.97536 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11752.80 seconds wall clock time: 200 minutes 32.23 seconds (12032.23 seconds total)