Starting phenix.real_space_refine on Mon Jun 23 02:42:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fug_29458/06_2025/8fug_29458_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fug_29458/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fug_29458/06_2025/8fug_29458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fug_29458/06_2025/8fug_29458.map" model { file = "/net/cci-nas-00/data/ceres_data/8fug_29458/06_2025/8fug_29458_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fug_29458/06_2025/8fug_29458_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V Time building chain proxies: 5.76, per 1000 atoms: 0.22 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: 6.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 3.08 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: 10.10 Time building geometry restraints manager: 7.93 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' } 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: 0.960 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: 0.460 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 48.680 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.190 ------------------------------------------------------------------------------- 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 : 7.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (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 HIS 0.002 0.001 HIS P 330 PHE 0.004 0.001 PHE S 346 TYR 0.004 0.001 TYR J 310 ARG 0.002 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.17606 ( 328) hydrogen bonds : angle 7.66000 ( 984) covalent geometry : bond 0.00495 (13593) covalent geometry : angle 0.56423 (18239) *********************** 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 : 2.065 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: 0.7749 (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: 0.8155 (p) outliers start: 46 outliers final: 22 residues processed: 440 average time/residue: 2.8734 time to fit residues: 1372.3329 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 : 2.090 ------------------------------------------------------------------------------- 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 135 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 0.2980 chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 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: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.203517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.165756 restraints weight = 41051.721| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.24 r_work: 0.4020 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13593 Z= 0.136 Angle : 0.593 5.042 18239 Z= 0.294 Chirality : 0.049 0.132 2001 Planarity : 0.004 0.028 2231 Dihedral : 6.542 59.787 2130 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 4.69 % Allowed : 15.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (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 HIS 0.002 0.001 HIS W 329 PHE 0.005 0.001 PHE P 346 TYR 0.009 0.002 TYR Q 310 ARG 0.001 0.000 ARG V 349 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 328) hydrogen bonds : angle 4.38062 ( 984) covalent geometry : bond 0.00312 (13593) covalent geometry : angle 0.59331 (18239) *********************** 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 393 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 324 time to evaluate : 2.180 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 342 GLU cc_start: 0.6913 (tm-30) cc_final: 0.6673 (tm-30) REVERT: A 350 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7670 (p) REVERT: A 370 LYS cc_start: 0.7594 (tttm) cc_final: 0.7308 (tttm) REVERT: B 320 SER cc_start: 0.8185 (m) cc_final: 0.7957 (t) REVERT: B 370 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8043 (tttp) REVERT: D 321 LYS cc_start: 0.8571 (mtpt) cc_final: 0.8116 (mttt) REVERT: E 321 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7891 (mttp) REVERT: E 370 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7596 (ttpp) REVERT: F 321 LYS cc_start: 0.8396 (mtpt) cc_final: 0.8078 (mttp) REVERT: H 377 THR cc_start: 0.8037 (m) cc_final: 0.7504 (p) REVERT: I 340 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7997 (mtpt) REVERT: J 369 LYS cc_start: 0.8147 (ptpt) cc_final: 0.7699 (ptmt) REVERT: J 370 LYS cc_start: 0.8140 (tttm) cc_final: 0.7678 (ttpt) REVERT: J 377 THR cc_start: 0.8218 (m) cc_final: 0.7783 (p) REVERT: K 331 LYS cc_start: 0.8635 (mttp) cc_final: 0.8434 (mtpm) REVERT: K 369 LYS cc_start: 0.8150 (ptpt) cc_final: 0.7860 (ptpt) REVERT: L 320 SER cc_start: 0.8203 (m) cc_final: 0.7961 (t) REVERT: L 340 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7713 (mttt) REVERT: L 369 LYS cc_start: 0.8138 (ptpt) cc_final: 0.7791 (ptmt) REVERT: L 370 LYS cc_start: 0.8119 (tttm) cc_final: 0.7751 (ttpt) REVERT: L 378 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: M 331 LYS cc_start: 0.8740 (mttp) cc_final: 0.8508 (mtmt) REVERT: M 340 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7931 (mtmm) REVERT: M 350 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7750 (p) REVERT: M 369 LYS cc_start: 0.8133 (ptpt) cc_final: 0.7911 (ptmt) REVERT: M 370 LYS cc_start: 0.8079 (tttm) cc_final: 0.7749 (ttpt) REVERT: N 311 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8254 (tmtt) REVERT: N 321 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7968 (mttp) REVERT: N 340 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8072 (mtmm) REVERT: N 369 LYS cc_start: 0.8239 (ptpt) cc_final: 0.7934 (ptmt) REVERT: N 378 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6093 (m-80) REVERT: O 331 LYS cc_start: 0.8788 (mttp) cc_final: 0.8524 (mtmt) REVERT: O 340 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8069 (mtmm) REVERT: O 378 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6018 (m-80) REVERT: P 370 LYS cc_start: 0.8286 (tttm) cc_final: 0.7950 (ttpt) REVERT: Q 317 LYS cc_start: 0.6373 (ptmt) cc_final: 0.6070 (ptmt) REVERT: Q 345 ASP cc_start: 0.7802 (t0) cc_final: 0.7522 (t70) REVERT: Q 350 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7732 (m) REVERT: Q 378 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6039 (m-80) REVERT: R 331 LYS cc_start: 0.8810 (mttp) cc_final: 0.8569 (mtmt) REVERT: R 378 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.5946 (m-80) REVERT: S 319 THR cc_start: 0.7794 (m) cc_final: 0.7578 (p) REVERT: S 331 LYS cc_start: 0.8700 (mttp) cc_final: 0.8473 (mtmt) REVERT: S 345 ASP cc_start: 0.7834 (m-30) cc_final: 0.7418 (t0) REVERT: S 373 THR cc_start: 0.8547 (m) cc_final: 0.8001 (p) REVERT: S 375 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7680 (ttpp) REVERT: S 378 PHE cc_start: 0.6591 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: U 319 THR cc_start: 0.7754 (m) cc_final: 0.7410 (p) REVERT: U 378 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.5958 (m-80) REVERT: V 331 LYS cc_start: 0.8799 (mttp) cc_final: 0.8456 (mtpt) REVERT: V 378 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.5662 (p90) REVERT: W 338 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7682 (tm-30) outliers start: 69 outliers final: 40 residues processed: 366 average time/residue: 2.8224 time to fit residues: 1126.0178 Evaluate side-chains 354 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 300 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 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 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 338 GLU 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 35 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS J 368 ASN ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 ASN ** M 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 368 ASN P 368 ASN ** Q 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 362 HIS ** U 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 368 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.196538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.154172 restraints weight = 41458.153| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.31 r_work: 0.3863 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 13593 Z= 0.285 Angle : 0.732 5.101 18239 Z= 0.364 Chirality : 0.051 0.149 2001 Planarity : 0.004 0.029 2231 Dihedral : 8.810 59.007 2130 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % Rotamer: Outliers : 6.86 % Allowed : 14.27 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 330 PHE 0.009 0.001 PHE T 378 TYR 0.027 0.004 TYR L 310 ARG 0.002 0.000 ARG N 349 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 328) hydrogen bonds : angle 4.40938 ( 984) covalent geometry : bond 0.00651 (13593) covalent geometry : angle 0.73161 (18239) *********************** 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 439 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 338 time to evaluate : 4.177 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: A 320 SER cc_start: 0.7517 (m) cc_final: 0.7276 (t) REVERT: A 370 LYS cc_start: 0.7553 (tttm) cc_final: 0.7267 (tttm) REVERT: B 338 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8027 (tm-30) REVERT: D 321 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8123 (mttt) REVERT: E 321 LYS cc_start: 0.8429 (mtpt) cc_final: 0.7921 (mttp) REVERT: F 321 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8145 (mttp) REVERT: I 340 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7969 (mtpt) REVERT: I 369 LYS cc_start: 0.8624 (ptpt) cc_final: 0.8047 (ptmt) REVERT: J 331 LYS cc_start: 0.8790 (mttp) cc_final: 0.8549 (mtpm) REVERT: J 369 LYS cc_start: 0.8446 (ptpt) cc_final: 0.7875 (ptmt) REVERT: J 370 LYS cc_start: 0.8525 (tttm) cc_final: 0.8045 (ttpt) REVERT: K 369 LYS cc_start: 0.8398 (ptpt) cc_final: 0.8083 (ptpt) REVERT: K 370 LYS cc_start: 0.8524 (tttm) cc_final: 0.8233 (ttpt) REVERT: L 369 LYS cc_start: 0.8309 (ptpt) cc_final: 0.7970 (ptmt) REVERT: L 370 LYS cc_start: 0.8475 (tttm) cc_final: 0.8086 (ttpt) REVERT: M 331 LYS cc_start: 0.8843 (mttp) cc_final: 0.8630 (mtmt) REVERT: M 340 LYS cc_start: 0.8430 (ttmm) cc_final: 0.7994 (mtmm) REVERT: M 369 LYS cc_start: 0.8408 (ptpt) cc_final: 0.8094 (ptmt) REVERT: M 370 LYS cc_start: 0.8425 (tttm) cc_final: 0.8081 (ttpt) REVERT: M 378 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6441 (m-80) REVERT: N 321 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8186 (mttp) REVERT: N 340 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8077 (mtmm) REVERT: N 369 LYS cc_start: 0.8431 (ptpt) cc_final: 0.8018 (ptmt) REVERT: N 370 LYS cc_start: 0.8550 (tttm) cc_final: 0.8210 (ttpt) REVERT: O 317 LYS cc_start: 0.6706 (ptmt) cc_final: 0.6443 (ptmt) REVERT: O 321 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8089 (mttp) REVERT: O 331 LYS cc_start: 0.8842 (mttp) cc_final: 0.8626 (mtpt) REVERT: O 340 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8103 (mttt) REVERT: O 378 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6109 (m-80) REVERT: P 317 LYS cc_start: 0.6708 (ptmt) cc_final: 0.6457 (ptmt) REVERT: P 340 LYS cc_start: 0.8342 (ttmm) cc_final: 0.8136 (mtmm) REVERT: P 370 LYS cc_start: 0.8601 (tttm) cc_final: 0.8203 (ttpt) REVERT: Q 370 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8452 (ttmp) REVERT: Q 378 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6318 (m-80) REVERT: R 331 LYS cc_start: 0.8926 (mttp) cc_final: 0.8725 (mtmt) REVERT: R 338 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: R 345 ASP cc_start: 0.8170 (m-30) cc_final: 0.7696 (t0) REVERT: S 317 LYS cc_start: 0.6836 (ptmt) cc_final: 0.6501 (ptmm) REVERT: S 319 THR cc_start: 0.8173 (m) cc_final: 0.7912 (p) REVERT: S 345 ASP cc_start: 0.8139 (m-30) cc_final: 0.7586 (t0) REVERT: S 375 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7764 (ttpp) REVERT: S 378 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6234 (m-80) REVERT: T 345 ASP cc_start: 0.7950 (m-30) cc_final: 0.7621 (t0) REVERT: U 345 ASP cc_start: 0.7746 (m-30) cc_final: 0.7226 (t0) REVERT: U 348 ASP cc_start: 0.7621 (t0) cc_final: 0.7353 (m-30) REVERT: U 378 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6116 (m-80) REVERT: V 331 LYS cc_start: 0.8939 (mttp) cc_final: 0.8531 (mtpt) REVERT: V 345 ASP cc_start: 0.7775 (m-30) cc_final: 0.7266 (t0) REVERT: V 378 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.5764 (p90) REVERT: W 343 LYS cc_start: 0.7511 (mttt) cc_final: 0.7161 (mptt) outliers start: 101 outliers final: 54 residues processed: 392 average time/residue: 3.1734 time to fit residues: 1370.6521 Evaluate side-chains 368 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 305 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 320 SER 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 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 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 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 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 369 LYS 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 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 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 48 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.0170 chunk 156 optimal weight: 0.0870 chunk 119 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN B 368 ASN G 368 ASN I 368 ASN K 368 ASN L 368 ASN N 368 ASN ** Q 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 362 HIS ** U 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.199894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.158316 restraints weight = 41693.094| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.33 r_work: 0.3913 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13593 Z= 0.148 Angle : 0.623 5.198 18239 Z= 0.304 Chirality : 0.049 0.154 2001 Planarity : 0.003 0.029 2231 Dihedral : 7.655 58.258 2122 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 5.23 % Allowed : 17.87 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS V 362 PHE 0.004 0.001 PHE T 378 TYR 0.010 0.002 TYR N 310 ARG 0.001 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.02893 ( 328) hydrogen bonds : angle 4.23665 ( 984) covalent geometry : bond 0.00331 (13593) covalent geometry : angle 0.62304 (18239) *********************** 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 380 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 303 time to evaluate : 3.312 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: A 320 SER cc_start: 0.7472 (m) cc_final: 0.7258 (t) REVERT: A 350 VAL cc_start: 0.8033 (OUTLIER) cc_final: 0.7663 (p) REVERT: A 370 LYS cc_start: 0.7596 (tttm) cc_final: 0.7312 (tttm) REVERT: B 338 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7957 (tm-30) REVERT: D 321 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8093 (mttt) REVERT: E 321 LYS cc_start: 0.8433 (mtpt) cc_final: 0.7928 (mttp) REVERT: F 321 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8114 (mttp) REVERT: I 340 LYS cc_start: 0.8339 (ttmm) cc_final: 0.8002 (mtpt) REVERT: J 350 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7696 (p) REVERT: J 369 LYS cc_start: 0.8484 (ptpt) cc_final: 0.7884 (ptmt) REVERT: J 370 LYS cc_start: 0.8400 (tttm) cc_final: 0.7817 (ttpt) REVERT: K 369 LYS cc_start: 0.8271 (ptpt) cc_final: 0.7959 (ptpt) REVERT: K 370 LYS cc_start: 0.8312 (tttm) cc_final: 0.7963 (ttpt) REVERT: L 369 LYS cc_start: 0.8282 (ptpt) cc_final: 0.7860 (ptmt) REVERT: L 370 LYS cc_start: 0.8329 (tttm) cc_final: 0.7969 (ttpt) REVERT: M 340 LYS cc_start: 0.8415 (ttmm) cc_final: 0.7972 (mtmm) REVERT: M 350 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.7886 (p) REVERT: M 352 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8327 (m) REVERT: M 369 LYS cc_start: 0.8315 (ptpt) cc_final: 0.8077 (ptmt) REVERT: M 370 LYS cc_start: 0.8320 (tttm) cc_final: 0.7929 (ttpt) REVERT: M 378 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6395 (m-80) REVERT: N 311 LYS cc_start: 0.8485 (tmtt) cc_final: 0.8191 (tptt) REVERT: N 321 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8152 (mttp) REVERT: N 340 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8036 (mtmm) REVERT: N 350 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7798 (p) REVERT: N 369 LYS cc_start: 0.8433 (ptpt) cc_final: 0.7979 (ptmt) REVERT: N 370 LYS cc_start: 0.8377 (tttm) cc_final: 0.8046 (ttpt) REVERT: O 340 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8088 (mttt) REVERT: O 378 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6132 (m-80) REVERT: P 317 LYS cc_start: 0.6676 (ptmt) cc_final: 0.6459 (ptmt) REVERT: P 340 LYS cc_start: 0.8338 (ttmm) cc_final: 0.8118 (mtmm) REVERT: P 370 LYS cc_start: 0.8448 (tttm) cc_final: 0.8083 (ttpt) REVERT: P 378 PHE cc_start: 0.6378 (OUTLIER) cc_final: 0.5949 (m-80) REVERT: Q 378 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.6259 (m-80) REVERT: R 331 LYS cc_start: 0.8895 (mttp) cc_final: 0.8667 (mtmt) REVERT: R 345 ASP cc_start: 0.8169 (m-30) cc_final: 0.7689 (t0) REVERT: R 372 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7779 (mm-30) REVERT: S 319 THR cc_start: 0.8008 (m) cc_final: 0.7728 (p) REVERT: S 345 ASP cc_start: 0.8135 (m-30) cc_final: 0.7561 (t0) REVERT: S 375 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7665 (ttpp) REVERT: S 378 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: T 345 ASP cc_start: 0.7893 (m-30) cc_final: 0.7591 (t0) REVERT: T 348 ASP cc_start: 0.7765 (t0) cc_final: 0.7555 (m-30) REVERT: U 345 ASP cc_start: 0.7690 (m-30) cc_final: 0.7182 (t0) REVERT: U 348 ASP cc_start: 0.7557 (t0) cc_final: 0.7308 (m-30) REVERT: U 378 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.6152 (m-80) REVERT: V 331 LYS cc_start: 0.8942 (mttp) cc_final: 0.8540 (mtpt) REVERT: V 345 ASP cc_start: 0.7701 (m-30) cc_final: 0.7181 (t0) REVERT: V 378 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.5613 (p90) REVERT: W 343 LYS cc_start: 0.7426 (mttt) cc_final: 0.7073 (mptt) outliers start: 77 outliers final: 48 residues processed: 347 average time/residue: 3.7950 time to fit residues: 1445.4477 Evaluate side-chains 350 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 290 time to evaluate : 4.461 ------------------------------------------------------------------------------- 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 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 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 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 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 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 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain P residue 369 LYS Chi-restraints excluded: chain P residue 378 PHE 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 S residue 370 LYS 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 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 69 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN N 362 HIS N 368 ASN U 362 HIS ** U 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 368 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.197973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.155740 restraints weight = 41170.108| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.29 r_work: 0.3858 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13593 Z= 0.229 Angle : 0.668 5.266 18239 Z= 0.330 Chirality : 0.049 0.154 2001 Planarity : 0.004 0.030 2231 Dihedral : 8.191 58.938 2122 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 5.50 % Allowed : 17.60 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (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 HIS 0.003 0.001 HIS H 330 PHE 0.007 0.001 PHE L 346 TYR 0.016 0.003 TYR V 310 ARG 0.004 0.000 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.02909 ( 328) hydrogen bonds : angle 4.25532 ( 984) covalent geometry : bond 0.00514 (13593) covalent geometry : angle 0.66839 (18239) *********************** 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 391 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 310 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.7484 (m) cc_final: 0.7273 (t) REVERT: D 321 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8118 (mttt) REVERT: D 342 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: E 321 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8008 (mttp) REVERT: F 321 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8112 (mttp) REVERT: H 369 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8077 (ptpp) REVERT: I 340 LYS cc_start: 0.8394 (ttmm) cc_final: 0.8056 (mtpt) REVERT: I 378 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: J 350 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7746 (p) REVERT: J 369 LYS cc_start: 0.8529 (ptpt) cc_final: 0.7935 (ptmt) REVERT: J 370 LYS cc_start: 0.8492 (tttm) cc_final: 0.7921 (ttpt) REVERT: K 343 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7946 (mtpm) REVERT: K 369 LYS cc_start: 0.8229 (ptpt) cc_final: 0.7937 (ptpt) REVERT: K 370 LYS cc_start: 0.8373 (tttm) cc_final: 0.8052 (ttpt) REVERT: L 369 LYS cc_start: 0.8338 (ptpt) cc_final: 0.7909 (ptmt) REVERT: L 370 LYS cc_start: 0.8407 (tttm) cc_final: 0.8027 (ttpt) REVERT: L 375 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7758 (ttmp) REVERT: M 350 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.7990 (p) REVERT: M 352 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8315 (m) REVERT: M 370 LYS cc_start: 0.8337 (tttm) cc_final: 0.7965 (ttpt) REVERT: M 378 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6382 (m-80) REVERT: N 321 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8151 (mttp) REVERT: N 340 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8041 (mtmm) REVERT: N 369 LYS cc_start: 0.8503 (ptpt) cc_final: 0.8002 (ptmt) REVERT: N 370 LYS cc_start: 0.8428 (tttm) cc_final: 0.8070 (ttpt) REVERT: O 317 LYS cc_start: 0.7183 (ptmt) cc_final: 0.6977 (ptmt) REVERT: O 340 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8118 (mttt) REVERT: O 370 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8171 (tttp) REVERT: O 378 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: P 340 LYS cc_start: 0.8417 (ttmm) cc_final: 0.8121 (mttm) REVERT: P 370 LYS cc_start: 0.8537 (tttm) cc_final: 0.8175 (ttpt) REVERT: Q 378 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6276 (m-80) REVERT: R 331 LYS cc_start: 0.8927 (mttp) cc_final: 0.8708 (mtmt) REVERT: R 345 ASP cc_start: 0.8121 (m-30) cc_final: 0.7758 (t0) REVERT: S 317 LYS cc_start: 0.7029 (ptmt) cc_final: 0.6584 (ptmt) REVERT: S 319 THR cc_start: 0.8140 (m) cc_final: 0.7856 (p) REVERT: S 345 ASP cc_start: 0.8154 (m-30) cc_final: 0.7627 (t0) REVERT: S 375 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7723 (ttpp) REVERT: S 378 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.6185 (m-80) REVERT: T 345 ASP cc_start: 0.7976 (m-30) cc_final: 0.7693 (t0) REVERT: T 348 ASP cc_start: 0.7854 (t0) cc_final: 0.7545 (m-30) REVERT: U 345 ASP cc_start: 0.7783 (m-30) cc_final: 0.7279 (t0) REVERT: U 348 ASP cc_start: 0.7606 (t0) cc_final: 0.7301 (m-30) REVERT: U 378 PHE cc_start: 0.6756 (OUTLIER) cc_final: 0.6156 (m-80) REVERT: V 331 LYS cc_start: 0.8964 (mttp) cc_final: 0.8554 (mtpt) REVERT: V 345 ASP cc_start: 0.7788 (m-30) cc_final: 0.7200 (t0) REVERT: V 378 PHE cc_start: 0.6635 (OUTLIER) cc_final: 0.5701 (p90) REVERT: W 343 LYS cc_start: 0.7482 (mttt) cc_final: 0.7118 (mptt) outliers start: 81 outliers final: 57 residues processed: 354 average time/residue: 3.1887 time to fit residues: 1241.8147 Evaluate side-chains 372 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 301 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain C residue 350 VAL 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 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 369 LYS 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 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 J residue 360 ILE 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 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 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain P residue 369 LYS 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 S residue 370 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 55 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 117 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN E 351 GLN L 368 ASN N 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.148437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.114657 restraints weight = 41528.636| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.74 r_work: 0.3809 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.004 0.038 13593 Z= 0.176 Angle : 0.631 5.759 18239 Z= 0.310 Chirality : 0.049 0.136 2001 Planarity : 0.003 0.029 2231 Dihedral : 7.887 57.730 2122 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 5.10 % Allowed : 18.34 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS V 362 PHE 0.005 0.001 PHE T 378 TYR 0.012 0.002 TYR T 310 ARG 0.002 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02770 ( 328) hydrogen bonds : angle 4.20048 ( 984) covalent geometry : bond 0.00396 (13593) covalent geometry : angle 0.63111 (18239) *********************** 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 386 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 311 time to evaluate : 2.255 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: A 320 SER cc_start: 0.7445 (m) cc_final: 0.7226 (t) REVERT: A 350 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7733 (p) REVERT: C 317 LYS cc_start: 0.6955 (ptmt) cc_final: 0.6463 (ptpp) REVERT: C 351 GLN cc_start: 0.7684 (mt0) cc_final: 0.7462 (mt0) REVERT: D 321 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8071 (mttt) REVERT: D 342 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: E 321 LYS cc_start: 0.8509 (mtpt) cc_final: 0.7997 (mttp) REVERT: F 321 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8104 (mttp) REVERT: G 352 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8319 (m) REVERT: H 369 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8067 (ptpp) REVERT: I 340 LYS cc_start: 0.8430 (ttmm) cc_final: 0.8073 (mtpt) REVERT: I 378 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6408 (m-80) REVERT: J 331 LYS cc_start: 0.8793 (mttp) cc_final: 0.8563 (mtpm) REVERT: J 350 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7806 (p) REVERT: J 369 LYS cc_start: 0.8518 (ptpt) cc_final: 0.7930 (ptmt) REVERT: J 370 LYS cc_start: 0.8501 (tttm) cc_final: 0.7928 (ttpt) REVERT: K 343 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7918 (mtpm) REVERT: K 369 LYS cc_start: 0.8240 (ptpt) cc_final: 0.7989 (ptpp) REVERT: K 370 LYS cc_start: 0.8385 (tttm) cc_final: 0.8093 (ttpt) REVERT: L 369 LYS cc_start: 0.8352 (ptpt) cc_final: 0.7893 (ptmt) REVERT: L 370 LYS cc_start: 0.8401 (tttm) cc_final: 0.8035 (ttpt) REVERT: L 375 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7743 (ttmp) REVERT: M 350 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8018 (p) REVERT: M 352 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.8346 (m) REVERT: M 370 LYS cc_start: 0.8348 (tttm) cc_final: 0.7977 (ttpt) REVERT: M 378 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6337 (m-80) REVERT: N 321 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8196 (mttp) REVERT: N 340 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8053 (mtmm) REVERT: N 350 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.7896 (p) REVERT: N 369 LYS cc_start: 0.8554 (ptpt) cc_final: 0.8033 (ptmt) REVERT: N 370 LYS cc_start: 0.8397 (tttm) cc_final: 0.8084 (ttpt) REVERT: O 317 LYS cc_start: 0.7183 (ptmt) cc_final: 0.6940 (ptmt) REVERT: O 340 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8126 (mttt) REVERT: O 378 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: P 340 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8099 (mttm) REVERT: P 370 LYS cc_start: 0.8529 (tttm) cc_final: 0.8170 (ttpt) REVERT: P 378 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.5766 (m-10) REVERT: Q 378 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: R 331 LYS cc_start: 0.8958 (mttp) cc_final: 0.8731 (mtmt) REVERT: R 345 ASP cc_start: 0.8137 (m-30) cc_final: 0.7715 (t0) REVERT: S 317 LYS cc_start: 0.6924 (ptmt) cc_final: 0.6450 (ptmt) REVERT: S 319 THR cc_start: 0.8085 (m) cc_final: 0.7798 (p) REVERT: S 340 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8282 (ttmm) REVERT: S 345 ASP cc_start: 0.8175 (m-30) cc_final: 0.7607 (t0) REVERT: S 375 LYS cc_start: 0.8205 (ttmm) cc_final: 0.7700 (ttpp) REVERT: T 345 ASP cc_start: 0.7997 (m-30) cc_final: 0.7645 (t0) REVERT: U 331 LYS cc_start: 0.8930 (mttp) cc_final: 0.8481 (mtmt) REVERT: U 345 ASP cc_start: 0.7776 (m-30) cc_final: 0.7241 (t0) REVERT: U 348 ASP cc_start: 0.7648 (t0) cc_final: 0.7268 (m-30) REVERT: U 351 GLN cc_start: 0.7375 (mt0) cc_final: 0.7144 (mt0) REVERT: U 370 LYS cc_start: 0.8423 (tttm) cc_final: 0.8078 (tttp) REVERT: U 378 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.6152 (m-80) REVERT: V 331 LYS cc_start: 0.8996 (mttp) cc_final: 0.8571 (mtpt) REVERT: V 345 ASP cc_start: 0.7720 (m-30) cc_final: 0.7116 (t0) REVERT: V 378 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.5596 (p90) REVERT: W 343 LYS cc_start: 0.7384 (mttt) cc_final: 0.6985 (mptt) outliers start: 75 outliers final: 52 residues processed: 351 average time/residue: 2.7389 time to fit residues: 1050.5615 Evaluate side-chains 372 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 304 time to evaluate : 2.062 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain C residue 350 VAL 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 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 H residue 369 LYS Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 352 SER 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 N residue 377 THR 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 P residue 369 LYS Chi-restraints excluded: chain P residue 378 PHE 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 S residue 370 LYS 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 369 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 43 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 97 optimal weight: 0.0770 chunk 123 optimal weight: 1.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 362 HIS N 368 ASN P 368 ASN ** W 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.189890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.159603 restraints weight = 39867.017| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.29 r_work: 0.3885 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13593 Z= 0.136 Angle : 0.597 5.064 18239 Z= 0.293 Chirality : 0.049 0.135 2001 Planarity : 0.003 0.033 2231 Dihedral : 7.504 58.113 2122 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 4.96 % Allowed : 18.55 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (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 HIS 0.002 0.000 HIS V 362 PHE 0.003 0.001 PHE T 378 TYR 0.010 0.002 TYR L 310 ARG 0.001 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02517 ( 328) hydrogen bonds : angle 4.12361 ( 984) covalent geometry : bond 0.00314 (13593) covalent geometry : angle 0.59704 (18239) *********************** 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 384 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 311 time to evaluate : 2.169 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: A 350 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7691 (p) REVERT: C 317 LYS cc_start: 0.7059 (ptmt) cc_final: 0.6551 (ptpp) REVERT: D 321 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8103 (mttt) REVERT: E 321 LYS cc_start: 0.8481 (mtpt) cc_final: 0.7984 (mttp) REVERT: F 321 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8120 (mttp) REVERT: I 340 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8072 (mtpt) REVERT: I 378 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6342 (m-80) REVERT: J 350 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7668 (p) REVERT: J 369 LYS cc_start: 0.8493 (ptpt) cc_final: 0.7897 (ptmt) REVERT: J 370 LYS cc_start: 0.8447 (tttm) cc_final: 0.7863 (ttpt) REVERT: K 343 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7888 (mtpm) REVERT: K 350 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7751 (p) REVERT: K 369 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7886 (ptpt) REVERT: K 370 LYS cc_start: 0.8236 (tttm) cc_final: 0.7947 (ttpt) REVERT: L 350 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.7854 (p) REVERT: L 369 LYS cc_start: 0.8300 (ptpt) cc_final: 0.7880 (ptmt) REVERT: L 370 LYS cc_start: 0.8336 (tttm) cc_final: 0.7977 (ttpt) REVERT: L 375 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7716 (ttmp) REVERT: L 378 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6591 (m-80) REVERT: M 350 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.7961 (p) REVERT: M 352 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8293 (m) REVERT: M 370 LYS cc_start: 0.8212 (tttm) cc_final: 0.7860 (ttpt) REVERT: M 378 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.6306 (m-80) REVERT: N 321 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8198 (mttp) REVERT: N 331 LYS cc_start: 0.8884 (mttt) cc_final: 0.8647 (mtpm) REVERT: N 340 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8066 (mtmm) REVERT: N 350 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7839 (p) REVERT: N 369 LYS cc_start: 0.8458 (ptpt) cc_final: 0.7966 (ptmt) REVERT: N 370 LYS cc_start: 0.8304 (tttm) cc_final: 0.8004 (ttpt) REVERT: O 340 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8122 (mttt) REVERT: O 378 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6069 (m-80) REVERT: P 340 LYS cc_start: 0.8395 (ttmm) cc_final: 0.8100 (mttm) REVERT: P 370 LYS cc_start: 0.8445 (tttm) cc_final: 0.8030 (ttpt) REVERT: Q 378 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.6202 (m-80) REVERT: R 345 ASP cc_start: 0.8061 (m-30) cc_final: 0.7699 (t0) REVERT: R 370 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8095 (ttmm) REVERT: S 317 LYS cc_start: 0.6981 (ptmt) cc_final: 0.6608 (ptmt) REVERT: S 319 THR cc_start: 0.8023 (m) cc_final: 0.7778 (p) REVERT: S 340 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8229 (ttmm) REVERT: S 345 ASP cc_start: 0.8137 (m-30) cc_final: 0.7627 (t0) REVERT: S 350 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7532 (p) REVERT: S 375 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7694 (ttpp) REVERT: T 345 ASP cc_start: 0.7930 (m-30) cc_final: 0.7653 (t0) REVERT: T 348 ASP cc_start: 0.7859 (t0) cc_final: 0.7538 (m-30) REVERT: U 331 LYS cc_start: 0.8886 (mttp) cc_final: 0.8415 (mtpt) REVERT: U 345 ASP cc_start: 0.7747 (m-30) cc_final: 0.7296 (t0) REVERT: U 348 ASP cc_start: 0.7617 (t0) cc_final: 0.7303 (m-30) REVERT: U 370 LYS cc_start: 0.8327 (tttm) cc_final: 0.7993 (tttp) REVERT: U 378 PHE cc_start: 0.6697 (OUTLIER) cc_final: 0.6129 (m-80) REVERT: V 331 LYS cc_start: 0.8968 (mttp) cc_final: 0.8594 (mtpt) REVERT: V 345 ASP cc_start: 0.7702 (m-30) cc_final: 0.7146 (t0) REVERT: V 378 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.5539 (p90) REVERT: W 343 LYS cc_start: 0.7382 (mttt) cc_final: 0.7051 (mptt) outliers start: 73 outliers final: 41 residues processed: 352 average time/residue: 2.7290 time to fit residues: 1050.7614 Evaluate side-chains 357 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 299 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER 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 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 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 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 378 PHE 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 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 P residue 369 LYS 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 R residue 370 LYS Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 370 LYS 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 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 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 368 ASN O 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.150239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.114915 restraints weight = 41311.723| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.82 r_work: 0.3801 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4676 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= 0.176 Angle : 0.626 5.726 18239 Z= 0.307 Chirality : 0.048 0.136 2001 Planarity : 0.004 0.032 2231 Dihedral : 7.610 57.487 2120 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 4.82 % Allowed : 19.43 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.000 HIS B 330 PHE 0.004 0.001 PHE I 346 TYR 0.012 0.002 TYR V 310 ARG 0.001 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02549 ( 328) hydrogen bonds : angle 4.10638 ( 984) covalent geometry : bond 0.00400 (13593) covalent geometry : angle 0.62629 (18239) *********************** 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 375 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 304 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7737 (p) REVERT: A 370 LYS cc_start: 0.7548 (tttm) cc_final: 0.7262 (tttm) REVERT: C 317 LYS cc_start: 0.6919 (ptmt) cc_final: 0.6416 (ptpp) REVERT: D 321 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8094 (mttt) REVERT: E 321 LYS cc_start: 0.8480 (mtpt) cc_final: 0.7954 (mttp) REVERT: F 321 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8152 (mttp) REVERT: I 340 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8141 (mtpt) REVERT: I 378 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6376 (m-80) REVERT: J 350 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7715 (p) REVERT: J 369 LYS cc_start: 0.8550 (ptpt) cc_final: 0.7960 (ptmt) REVERT: K 343 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7897 (mtpm) REVERT: K 350 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7807 (p) REVERT: K 369 LYS cc_start: 0.8274 (ptpt) cc_final: 0.7988 (ptpt) REVERT: K 370 LYS cc_start: 0.8388 (tttm) cc_final: 0.8108 (ttpt) REVERT: L 350 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.7910 (p) REVERT: L 369 LYS cc_start: 0.8330 (ptpt) cc_final: 0.7881 (ptmt) REVERT: L 370 LYS cc_start: 0.8431 (tttm) cc_final: 0.8071 (ttpt) REVERT: L 375 LYS cc_start: 0.8064 (ttmt) cc_final: 0.7714 (ttmp) REVERT: L 378 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6590 (m-80) REVERT: M 350 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8038 (p) REVERT: M 352 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8338 (m) REVERT: M 370 LYS cc_start: 0.8330 (tttm) cc_final: 0.7967 (ttpt) REVERT: M 378 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6311 (m-80) REVERT: N 321 LYS cc_start: 0.8554 (mtpt) cc_final: 0.8217 (mttp) REVERT: N 331 LYS cc_start: 0.8957 (mttt) cc_final: 0.8710 (mtpm) REVERT: N 340 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8081 (mtmm) REVERT: N 350 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.7864 (p) REVERT: N 369 LYS cc_start: 0.8592 (ptpt) cc_final: 0.8072 (ptmt) REVERT: N 370 LYS cc_start: 0.8393 (tttm) cc_final: 0.8094 (ttpt) REVERT: O 317 LYS cc_start: 0.7223 (ptmt) cc_final: 0.6972 (ptmt) REVERT: O 340 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8138 (mttt) REVERT: O 378 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6089 (m-80) REVERT: P 340 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8122 (mttm) REVERT: P 370 LYS cc_start: 0.8573 (tttm) cc_final: 0.8211 (ttpt) REVERT: Q 378 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6267 (m-80) REVERT: R 317 LYS cc_start: 0.6814 (ptmt) cc_final: 0.6489 (ptmt) REVERT: R 345 ASP cc_start: 0.8134 (m-30) cc_final: 0.7698 (t0) REVERT: S 317 LYS cc_start: 0.6982 (ptmt) cc_final: 0.6585 (ptmt) REVERT: S 319 THR cc_start: 0.8089 (m) cc_final: 0.7817 (p) REVERT: S 340 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8312 (ttmm) REVERT: S 345 ASP cc_start: 0.8180 (m-30) cc_final: 0.7625 (t0) REVERT: S 375 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7712 (ttpp) REVERT: T 345 ASP cc_start: 0.7985 (m-30) cc_final: 0.7638 (t0) REVERT: U 331 LYS cc_start: 0.8932 (mttp) cc_final: 0.8445 (mtpt) REVERT: U 345 ASP cc_start: 0.7770 (m-30) cc_final: 0.7236 (t0) REVERT: U 348 ASP cc_start: 0.7666 (t0) cc_final: 0.7257 (m-30) REVERT: U 370 LYS cc_start: 0.8402 (tttm) cc_final: 0.8105 (tttp) REVERT: U 378 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: V 331 LYS cc_start: 0.8999 (mttp) cc_final: 0.8578 (mtpt) REVERT: V 345 ASP cc_start: 0.7705 (m-30) cc_final: 0.7099 (t0) REVERT: V 378 PHE cc_start: 0.6615 (OUTLIER) cc_final: 0.5606 (p90) REVERT: W 343 LYS cc_start: 0.7331 (mttt) cc_final: 0.6919 (mptt) outliers start: 71 outliers final: 48 residues processed: 346 average time/residue: 2.6813 time to fit residues: 1016.2413 Evaluate side-chains 359 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 296 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER 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 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 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 L residue 352 SER 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 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 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 P residue 369 LYS 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 S residue 370 LYS 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 378 PHE Chi-restraints excluded: chain W residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 26 optimal weight: 0.0270 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.147144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.113425 restraints weight = 42020.725| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.77 r_work: 0.3815 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4723 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= 0.151 Angle : 0.611 5.710 18239 Z= 0.300 Chirality : 0.048 0.134 2001 Planarity : 0.004 0.033 2231 Dihedral : 7.396 57.534 2120 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 4.48 % Allowed : 19.90 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (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 HIS 0.002 0.000 HIS V 362 PHE 0.004 0.001 PHE C 378 TYR 0.010 0.002 TYR V 310 ARG 0.001 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02480 ( 328) hydrogen bonds : angle 4.08388 ( 984) covalent geometry : bond 0.00344 (13593) covalent geometry : angle 0.61143 (18239) *********************** 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 369 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 303 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7720 (p) REVERT: A 370 LYS cc_start: 0.7553 (tttm) cc_final: 0.7271 (tttm) REVERT: C 317 LYS cc_start: 0.6912 (ptmt) cc_final: 0.6394 (ptpp) REVERT: D 321 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8082 (mttt) REVERT: E 321 LYS cc_start: 0.8470 (mtpt) cc_final: 0.7945 (mttp) REVERT: F 321 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8159 (mttp) REVERT: H 378 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.5982 (m-80) REVERT: I 340 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8111 (mtpt) REVERT: I 378 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6322 (m-80) REVERT: J 350 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7701 (p) REVERT: J 369 LYS cc_start: 0.8518 (ptpt) cc_final: 0.7912 (ptmt) REVERT: K 350 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7763 (p) REVERT: K 369 LYS cc_start: 0.8244 (ptpt) cc_final: 0.7946 (ptpt) REVERT: K 370 LYS cc_start: 0.8356 (tttm) cc_final: 0.8067 (ttpt) REVERT: L 350 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.7934 (p) REVERT: L 369 LYS cc_start: 0.8314 (ptpt) cc_final: 0.7887 (ptmt) REVERT: L 370 LYS cc_start: 0.8405 (tttm) cc_final: 0.8057 (ttpt) REVERT: L 375 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7704 (ttmp) REVERT: L 378 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.6476 (m-80) REVERT: M 350 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8022 (p) REVERT: M 370 LYS cc_start: 0.8273 (tttm) cc_final: 0.7920 (ttpt) REVERT: M 378 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6277 (m-80) REVERT: N 321 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8229 (mttp) REVERT: N 331 LYS cc_start: 0.8938 (mttt) cc_final: 0.8690 (mtpm) REVERT: N 340 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8073 (mtmm) REVERT: N 350 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.7860 (p) REVERT: N 369 LYS cc_start: 0.8519 (ptpt) cc_final: 0.8006 (ptmt) REVERT: N 370 LYS cc_start: 0.8386 (tttm) cc_final: 0.8072 (ttpt) REVERT: O 340 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8133 (mttt) REVERT: O 378 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6082 (m-80) REVERT: P 340 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8111 (mttm) REVERT: P 370 LYS cc_start: 0.8555 (tttm) cc_final: 0.8163 (ttpt) REVERT: Q 378 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.6247 (m-80) REVERT: R 317 LYS cc_start: 0.6814 (ptmt) cc_final: 0.6477 (ptmt) REVERT: R 345 ASP cc_start: 0.8129 (m-30) cc_final: 0.7721 (t0) REVERT: S 317 LYS cc_start: 0.6952 (ptmt) cc_final: 0.6552 (ptmt) REVERT: S 319 THR cc_start: 0.8089 (m) cc_final: 0.7862 (p) REVERT: S 340 LYS cc_start: 0.8557 (ttmm) cc_final: 0.8275 (ttmm) REVERT: S 345 ASP cc_start: 0.8142 (m-30) cc_final: 0.7617 (t0) REVERT: S 350 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7578 (p) REVERT: S 375 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7700 (ttpp) REVERT: T 345 ASP cc_start: 0.7964 (m-30) cc_final: 0.7634 (t0) REVERT: U 331 LYS cc_start: 0.8926 (mttp) cc_final: 0.8438 (mtpt) REVERT: U 345 ASP cc_start: 0.7765 (m-30) cc_final: 0.7244 (t0) REVERT: U 348 ASP cc_start: 0.7669 (t0) cc_final: 0.7261 (m-30) REVERT: U 370 LYS cc_start: 0.8371 (tttm) cc_final: 0.8074 (tttp) REVERT: U 378 PHE cc_start: 0.6692 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: V 331 LYS cc_start: 0.9014 (mttp) cc_final: 0.8599 (mtpt) REVERT: V 345 ASP cc_start: 0.7714 (m-30) cc_final: 0.7090 (t0) REVERT: V 378 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.5612 (p90) REVERT: W 343 LYS cc_start: 0.7319 (mttt) cc_final: 0.6907 (mptt) outliers start: 66 outliers final: 45 residues processed: 344 average time/residue: 2.6507 time to fit residues: 997.1776 Evaluate side-chains 360 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 300 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER 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 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 H residue 378 PHE 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 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 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 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 P residue 369 LYS 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 S residue 370 LYS 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 378 PHE Chi-restraints excluded: chain W residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.146862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.113100 restraints weight = 41784.681| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.77 r_work: 0.3808 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13593 Z= 0.155 Angle : 0.618 6.200 18239 Z= 0.302 Chirality : 0.048 0.133 2001 Planarity : 0.004 0.033 2231 Dihedral : 7.388 56.970 2120 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 4.21 % Allowed : 20.52 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS W 362 PHE 0.003 0.001 PHE M 346 TYR 0.011 0.002 TYR V 310 ARG 0.002 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02442 ( 328) hydrogen bonds : angle 4.04347 ( 984) covalent geometry : bond 0.00354 (13593) covalent geometry : angle 0.61754 (18239) ********************** 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 370 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7709 (p) REVERT: A 370 LYS cc_start: 0.7546 (tttm) cc_final: 0.7267 (tttm) REVERT: C 317 LYS cc_start: 0.6953 (ptmt) cc_final: 0.6438 (ptpp) REVERT: D 321 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8074 (mttt) REVERT: E 321 LYS cc_start: 0.8487 (mtpt) cc_final: 0.7962 (mttp) REVERT: F 321 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8153 (mttp) REVERT: H 378 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.5993 (m-80) REVERT: I 340 LYS cc_start: 0.8450 (ttmm) cc_final: 0.8108 (mtpt) REVERT: I 378 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6318 (m-80) REVERT: J 350 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7712 (p) REVERT: J 369 LYS cc_start: 0.8535 (ptpt) cc_final: 0.7929 (ptmt) REVERT: K 350 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7790 (p) REVERT: K 369 LYS cc_start: 0.8251 (ptpt) cc_final: 0.7976 (ptpt) REVERT: K 370 LYS cc_start: 0.8372 (tttm) cc_final: 0.8075 (ttpt) REVERT: L 350 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.7938 (p) REVERT: L 369 LYS cc_start: 0.8330 (ptpt) cc_final: 0.7894 (ptmt) REVERT: L 370 LYS cc_start: 0.8418 (tttm) cc_final: 0.8070 (ttpt) REVERT: L 375 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7702 (ttmp) REVERT: L 378 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: M 350 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.7907 (p) REVERT: M 370 LYS cc_start: 0.8279 (tttm) cc_final: 0.7929 (ttpt) REVERT: M 378 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: N 321 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8210 (mttp) REVERT: N 331 LYS cc_start: 0.8949 (mttt) cc_final: 0.8711 (mtpm) REVERT: N 340 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8076 (mtmm) REVERT: N 350 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.7879 (p) REVERT: N 369 LYS cc_start: 0.8549 (ptpt) cc_final: 0.8031 (ptmt) REVERT: N 370 LYS cc_start: 0.8400 (tttm) cc_final: 0.8076 (ttpt) REVERT: O 340 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8138 (mttt) REVERT: O 350 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.7827 (p) REVERT: O 378 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6076 (m-80) REVERT: P 340 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8116 (mttm) REVERT: P 370 LYS cc_start: 0.8558 (tttm) cc_final: 0.8163 (ttpt) REVERT: Q 378 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6262 (m-80) REVERT: R 317 LYS cc_start: 0.6849 (ptmt) cc_final: 0.6503 (ptmt) REVERT: R 345 ASP cc_start: 0.8124 (m-30) cc_final: 0.7712 (t0) REVERT: S 317 LYS cc_start: 0.7004 (ptmt) cc_final: 0.6602 (ptmt) REVERT: S 319 THR cc_start: 0.8075 (m) cc_final: 0.7832 (p) REVERT: S 340 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8281 (ttmm) REVERT: S 345 ASP cc_start: 0.8143 (m-30) cc_final: 0.7632 (t0) REVERT: S 350 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7574 (p) REVERT: S 375 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7693 (ttpp) REVERT: T 345 ASP cc_start: 0.7985 (m-30) cc_final: 0.7663 (t0) REVERT: U 331 LYS cc_start: 0.8924 (mttp) cc_final: 0.8444 (mtpt) REVERT: U 345 ASP cc_start: 0.7771 (m-30) cc_final: 0.7243 (t0) REVERT: U 348 ASP cc_start: 0.7692 (t0) cc_final: 0.7290 (m-30) REVERT: U 370 LYS cc_start: 0.8367 (tttm) cc_final: 0.8062 (tttp) REVERT: U 378 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: V 331 LYS cc_start: 0.9020 (mttp) cc_final: 0.8609 (mtpt) REVERT: V 345 ASP cc_start: 0.7708 (m-30) cc_final: 0.7072 (t0) REVERT: V 378 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.5632 (p90) REVERT: W 343 LYS cc_start: 0.7304 (mttt) cc_final: 0.6905 (mptt) outliers start: 62 outliers final: 43 residues processed: 347 average time/residue: 2.9114 time to fit residues: 1115.8764 Evaluate side-chains 361 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 302 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER 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 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 H residue 378 PHE 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 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 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 360 ILE Chi-restraints excluded: chain N residue 377 THR 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 S residue 370 LYS 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 378 PHE Chi-restraints excluded: chain W residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 118 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.147116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.113388 restraints weight = 41710.655| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.76 r_work: 0.3817 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13593 Z= 0.150 Angle : 0.615 6.086 18239 Z= 0.301 Chirality : 0.048 0.129 2001 Planarity : 0.004 0.033 2231 Dihedral : 7.329 56.910 2120 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 4.42 % Allowed : 20.38 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS W 362 PHE 0.004 0.001 PHE M 346 TYR 0.010 0.002 TYR V 310 ARG 0.001 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02438 ( 328) hydrogen bonds : angle 4.05330 ( 984) covalent geometry : bond 0.00342 (13593) covalent geometry : angle 0.61549 (18239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24722.77 seconds wall clock time: 429 minutes 45.21 seconds (25785.21 seconds total)