Starting phenix.real_space_refine on Sun May 25 09:40:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fug_29458/05_2025/8fug_29458_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fug_29458/05_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_29458/05_2025/8fug_29458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fug_29458/05_2025/8fug_29458.map" model { file = "/net/cci-nas-00/data/ceres_data/8fug_29458/05_2025/8fug_29458_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fug_29458/05_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-5687/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: 5.44, per 1000 atoms: 0.20 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: 6.21 Conformation dependent library (CDL) restraints added in 1.7 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: 10.07 Time building geometry restraints manager: 7.51 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: 1.530 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: 0.400 Extract box with map and model: 0.860 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 46.520 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.490 ------------------------------------------------------------------------------- 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 : 1.981 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: 2.8876 time to fit residues: 1379.4572 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 : 2.060 ------------------------------------------------------------------------------- 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 = 0.203511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.165745 restraints weight = 41051.895| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.24 r_work: 0.4019 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 4.38050 ( 984) covalent geometry : bond 0.00312 (13593) covalent geometry : angle 0.59332 (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 : 2.082 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: 0.6674 (tm-30) REVERT: A 350 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7671 (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: 0.7956 (t) REVERT: B 370 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8043 (tttp) REVERT: D 321 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8115 (mttt) REVERT: E 321 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7892 (mttp) REVERT: E 370 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7597 (ttpp) REVERT: F 321 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8077 (mttp) REVERT: H 377 THR cc_start: 0.8037 (m) cc_final: 0.7503 (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: 0.7700 (ptmt) REVERT: J 370 LYS cc_start: 0.8140 (tttm) cc_final: 0.7678 (ttpt) REVERT: J 377 THR cc_start: 0.8219 (m) cc_final: 0.7782 (p) REVERT: K 331 LYS cc_start: 0.8635 (mttp) cc_final: 0.8435 (mtpm) REVERT: K 369 LYS cc_start: 0.8150 (ptpt) cc_final: 0.7859 (ptpt) REVERT: L 320 SER cc_start: 0.8203 (m) cc_final: 0.7960 (t) REVERT: L 340 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7713 (mttt) REVERT: L 369 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7791 (ptmt) REVERT: L 370 LYS cc_start: 0.8119 (tttm) cc_final: 0.7750 (ttpt) REVERT: L 378 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: M 331 LYS cc_start: 0.8740 (mttp) cc_final: 0.8509 (mtmt) REVERT: M 340 LYS cc_start: 0.8293 (ttmm) cc_final: 0.7930 (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: 0.7912 (ptmt) REVERT: M 370 LYS cc_start: 0.8080 (tttm) cc_final: 0.7751 (ttpt) REVERT: N 311 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8255 (tmtt) REVERT: N 321 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7967 (mttp) REVERT: N 340 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8071 (mtmm) REVERT: N 369 LYS cc_start: 0.8239 (ptpt) cc_final: 0.7934 (ptmt) REVERT: N 378 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.6093 (m-80) REVERT: O 331 LYS cc_start: 0.8789 (mttp) cc_final: 0.8525 (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: 0.7804 (t0) cc_final: 0.7523 (t70) REVERT: Q 350 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7733 (m) REVERT: Q 378 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.6040 (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: 0.5947 (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: 0.8474 (mtmt) REVERT: S 345 ASP cc_start: 0.7833 (m-30) cc_final: 0.7419 (t0) REVERT: S 373 THR cc_start: 0.8547 (m) cc_final: 0.8001 (p) REVERT: S 375 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7680 (ttpp) REVERT: S 378 PHE cc_start: 0.6592 (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: 0.6719 (OUTLIER) cc_final: 0.5959 (m-80) REVERT: V 331 LYS cc_start: 0.8800 (mttp) cc_final: 0.8457 (mtpt) REVERT: V 378 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5662 (p90) REVERT: W 338 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7683 (tm-30) outliers start: 69 outliers final: 40 residues processed: 366 average time/residue: 2.7268 time to fit residues: 1087.9852 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 : 1.999 ------------------------------------------------------------------------------- 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: 0.4980 chunk 39 optimal weight: 0.8980 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: 2.0184 ------------------------------------------------------------------------------- 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 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 ** O 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 368 ASN ** Q 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 368 ASN ** U 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 368 ASN ** W 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.198829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.157600 restraints weight = 41224.343| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.31 r_work: 0.3909 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13593 Z= 0.217 Angle : 0.655 4.937 18239 Z= 0.324 Chirality : 0.049 0.149 2001 Planarity : 0.004 0.030 2231 Dihedral : 7.898 59.302 2130 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 5.98 % Allowed : 15.01 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.36 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 330 PHE 0.007 0.001 PHE U 346 TYR 0.027 0.004 TYR L 310 ARG 0.001 0.000 ARG N 349 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 328) hydrogen bonds : angle 4.27937 ( 984) covalent geometry : bond 0.00486 (13593) covalent geometry : angle 0.65541 (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 423 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 335 time to evaluate : 2.225 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 320 SER cc_start: 0.7495 (m) cc_final: 0.7240 (t) REVERT: A 350 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7765 (p) REVERT: A 368 ASN cc_start: 0.7584 (m110) cc_final: 0.7292 (m110) REVERT: A 370 LYS cc_start: 0.7553 (tttm) cc_final: 0.7302 (tttm) REVERT: B 338 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7997 (tm-30) REVERT: D 321 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8106 (mttt) REVERT: E 321 LYS cc_start: 0.8422 (mtpt) cc_final: 0.7906 (mttp) REVERT: E 370 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7728 (ttpp) REVERT: F 317 LYS cc_start: 0.7448 (ptmt) cc_final: 0.7235 (ptmt) REVERT: F 321 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8150 (mttp) REVERT: F 377 THR cc_start: 0.8417 (m) cc_final: 0.8213 (m) REVERT: H 377 THR cc_start: 0.8199 (m) cc_final: 0.7762 (p) REVERT: I 340 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7977 (mtpt) REVERT: I 369 LYS cc_start: 0.8562 (ptpt) cc_final: 0.8006 (ptmt) REVERT: J 369 LYS cc_start: 0.8370 (ptpt) cc_final: 0.7840 (ptmt) REVERT: J 370 LYS cc_start: 0.8394 (tttm) cc_final: 0.7970 (ttpt) REVERT: K 331 LYS cc_start: 0.8788 (mttp) cc_final: 0.8576 (mtpm) REVERT: K 369 LYS cc_start: 0.8291 (ptpt) cc_final: 0.7994 (ptpt) REVERT: K 370 LYS cc_start: 0.8445 (tttm) cc_final: 0.8158 (ttpt) REVERT: L 369 LYS cc_start: 0.8227 (ptpt) cc_final: 0.7943 (ptmt) REVERT: L 370 LYS cc_start: 0.8392 (tttm) cc_final: 0.8003 (ttpt) REVERT: M 331 LYS cc_start: 0.8813 (mttp) cc_final: 0.8611 (mtmt) REVERT: M 340 LYS cc_start: 0.8423 (ttmm) cc_final: 0.8003 (mtmm) REVERT: M 350 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7801 (p) REVERT: M 369 LYS cc_start: 0.8360 (ptpt) cc_final: 0.8056 (ptmt) REVERT: M 370 LYS cc_start: 0.8387 (tttm) cc_final: 0.8040 (ttpt) REVERT: M 378 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6447 (m-80) REVERT: N 321 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8197 (mttp) REVERT: N 340 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8118 (mtmm) REVERT: N 369 LYS cc_start: 0.8365 (ptpt) cc_final: 0.8008 (ptmt) REVERT: N 370 LYS cc_start: 0.8472 (tttm) cc_final: 0.8124 (ttpt) REVERT: O 317 LYS cc_start: 0.6619 (ptmt) cc_final: 0.6339 (ptmt) REVERT: O 340 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8122 (mttt) REVERT: O 378 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: P 317 LYS cc_start: 0.6665 (ptmt) cc_final: 0.6404 (ptmt) REVERT: P 370 LYS cc_start: 0.8540 (tttm) cc_final: 0.8158 (ttpt) REVERT: Q 370 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8329 (ttmp) REVERT: Q 378 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6179 (m-80) REVERT: R 331 LYS cc_start: 0.8884 (mttp) cc_final: 0.8657 (mtmt) REVERT: R 345 ASP cc_start: 0.8226 (m-30) cc_final: 0.7692 (t0) REVERT: R 370 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8391 (ttmm) REVERT: S 319 THR cc_start: 0.7933 (m) cc_final: 0.7690 (p) REVERT: S 331 LYS cc_start: 0.8808 (mttp) cc_final: 0.8559 (mtmt) REVERT: S 345 ASP cc_start: 0.8032 (m-30) cc_final: 0.7542 (t0) REVERT: S 375 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7751 (ttpp) REVERT: S 378 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6170 (m-80) REVERT: T 345 ASP cc_start: 0.7853 (m-30) cc_final: 0.7530 (t0) REVERT: U 345 ASP cc_start: 0.7642 (m-30) cc_final: 0.7103 (t0) REVERT: U 378 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.6042 (m-80) REVERT: V 331 LYS cc_start: 0.8927 (mttp) cc_final: 0.8537 (mtpt) REVERT: V 345 ASP cc_start: 0.7738 (m-30) cc_final: 0.7182 (t0) REVERT: V 378 PHE cc_start: 0.6599 (OUTLIER) cc_final: 0.5635 (p90) REVERT: W 343 LYS cc_start: 0.7478 (mttt) cc_final: 0.7138 (mptt) outliers start: 88 outliers final: 47 residues processed: 381 average time/residue: 2.7850 time to fit residues: 1161.2584 Evaluate side-chains 361 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 303 time to evaluate : 1.948 ------------------------------------------------------------------------------- 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 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 338 GLU 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 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 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 377 THR Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 319 THR Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 370 LYS Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 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 S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 352 SER Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 48 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 156 optimal weight: 0.0770 chunk 119 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN D 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 368 ASN K 336 GLN ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 ASN N 368 ASN P 368 ASN R 368 ASN T 362 HIS ** U 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 368 ASN ** W 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.200403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.159429 restraints weight = 41626.075| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.32 r_work: 0.3924 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13593 Z= 0.172 Angle : 0.625 4.934 18239 Z= 0.305 Chirality : 0.049 0.148 2001 Planarity : 0.003 0.029 2231 Dihedral : 7.404 58.123 2122 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer: Outliers : 5.91 % Allowed : 17.32 % Favored : 76.77 % 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: -3.43 (0.18), 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 0.004 0.000 HIS V 362 PHE 0.005 0.001 PHE T 378 TYR 0.012 0.002 TYR T 310 ARG 0.003 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 328) hydrogen bonds : angle 4.22074 ( 984) covalent geometry : bond 0.00385 (13593) covalent geometry : angle 0.62515 (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 389 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 302 time to evaluate : 2.029 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: 0.7479 (m) cc_final: 0.7279 (t) REVERT: A 350 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7682 (p) REVERT: A 368 ASN cc_start: 0.7417 (m110) cc_final: 0.7135 (m110) REVERT: A 370 LYS cc_start: 0.7618 (tttm) cc_final: 0.7352 (tttm) REVERT: B 338 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7970 (tm-30) REVERT: D 321 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8099 (mttt) REVERT: E 321 LYS cc_start: 0.8455 (mtpt) cc_final: 0.7966 (mttp) REVERT: F 321 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8108 (mttp) REVERT: I 340 LYS cc_start: 0.8285 (ttmm) cc_final: 0.7965 (mtpt) REVERT: J 350 VAL cc_start: 0.8084 (OUTLIER) cc_final: 0.7573 (p) REVERT: J 369 LYS cc_start: 0.8472 (ptpt) cc_final: 0.7868 (ptmt) REVERT: K 331 LYS cc_start: 0.8724 (mttp) cc_final: 0.8516 (mtpm) REVERT: K 369 LYS cc_start: 0.8262 (ptpt) cc_final: 0.7976 (ptpt) REVERT: K 370 LYS cc_start: 0.8315 (tttm) cc_final: 0.7990 (ttpt) REVERT: L 350 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.7851 (p) REVERT: L 369 LYS cc_start: 0.8243 (ptpt) cc_final: 0.7860 (ptmt) REVERT: L 370 LYS cc_start: 0.8352 (tttm) cc_final: 0.7997 (ttpt) REVERT: M 331 LYS cc_start: 0.8807 (mttp) cc_final: 0.8581 (mtmt) REVERT: M 340 LYS cc_start: 0.8416 (ttmm) cc_final: 0.7989 (mtmm) REVERT: M 350 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.7868 (p) REVERT: M 369 LYS cc_start: 0.8342 (ptpt) cc_final: 0.8089 (ptmt) REVERT: M 370 LYS cc_start: 0.8306 (tttm) cc_final: 0.7923 (ttpt) REVERT: M 378 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6415 (m-80) REVERT: N 311 LYS cc_start: 0.8515 (tmtt) cc_final: 0.8255 (tptt) REVERT: N 321 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8170 (mttp) REVERT: N 340 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8051 (mtmm) REVERT: N 350 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7756 (p) REVERT: N 369 LYS cc_start: 0.8408 (ptpt) cc_final: 0.8033 (ptmt) REVERT: N 370 LYS cc_start: 0.8393 (tttm) cc_final: 0.8057 (ttpt) REVERT: N 378 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: O 321 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8060 (mttp) REVERT: O 340 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8103 (mttt) REVERT: O 370 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8133 (tttp) REVERT: O 378 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6140 (m-80) REVERT: P 317 LYS cc_start: 0.6671 (ptmt) cc_final: 0.6466 (ptmt) REVERT: P 370 LYS cc_start: 0.8467 (tttm) cc_final: 0.8122 (ttpt) REVERT: Q 378 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6204 (m-80) REVERT: R 331 LYS cc_start: 0.8881 (mttp) cc_final: 0.8676 (mtmt) REVERT: R 340 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8188 (mtmp) REVERT: R 345 ASP cc_start: 0.8203 (m-30) cc_final: 0.7701 (t0) REVERT: S 319 THR cc_start: 0.8070 (m) cc_final: 0.7811 (p) REVERT: S 331 LYS cc_start: 0.8793 (mttp) cc_final: 0.8542 (mtmt) REVERT: S 345 ASP cc_start: 0.8104 (m-30) cc_final: 0.7579 (t0) REVERT: S 375 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7694 (ttpp) REVERT: S 378 PHE cc_start: 0.6591 (OUTLIER) cc_final: 0.6236 (m-80) REVERT: T 345 ASP cc_start: 0.7922 (m-30) cc_final: 0.7567 (t0) REVERT: U 345 ASP cc_start: 0.7695 (m-30) cc_final: 0.7198 (t0) REVERT: U 378 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6186 (m-80) REVERT: V 331 LYS cc_start: 0.8931 (mttp) cc_final: 0.8556 (mtpt) REVERT: V 345 ASP cc_start: 0.7770 (m-30) cc_final: 0.7213 (t0) REVERT: V 378 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.5619 (p90) REVERT: W 343 LYS cc_start: 0.7439 (mttt) cc_final: 0.7112 (mptt) outliers start: 87 outliers final: 51 residues processed: 354 average time/residue: 2.7202 time to fit residues: 1051.5191 Evaluate side-chains 359 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 293 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 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 H residue 369 LYS 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 352 SER Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 378 PHE 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 369 LYS Chi-restraints excluded: chain O residue 370 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 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 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 352 SER Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 356 SER Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 0.0870 chunk 50 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS K 336 GLN ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 336 GLN ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 362 HIS ** S 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.201159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.159452 restraints weight = 41448.941| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.32 r_work: 0.3919 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13593 Z= 0.164 Angle : 0.605 5.197 18239 Z= 0.296 Chirality : 0.049 0.167 2001 Planarity : 0.003 0.032 2231 Dihedral : 7.505 58.961 2122 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 5.50 % Allowed : 17.32 % Favored : 77.17 % 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: -3.45 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS V 362 PHE 0.005 0.001 PHE T 378 TYR 0.012 0.002 TYR V 310 ARG 0.006 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02606 ( 328) hydrogen bonds : angle 4.16050 ( 984) covalent geometry : bond 0.00370 (13593) covalent geometry : angle 0.60529 (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 383 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 302 time to evaluate : 1.999 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: A 320 SER cc_start: 0.7453 (m) cc_final: 0.7211 (t) REVERT: A 350 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7710 (p) REVERT: A 368 ASN cc_start: 0.7379 (m110) cc_final: 0.7099 (m110) REVERT: B 338 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7962 (tm-30) REVERT: C 343 LYS cc_start: 0.8443 (mttp) cc_final: 0.7792 (mtpp) REVERT: D 321 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8101 (mttt) REVERT: D 342 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: E 321 LYS cc_start: 0.8458 (mtpt) cc_final: 0.7964 (mttp) REVERT: F 321 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8096 (mttp) REVERT: F 349 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7058 (mtp180) REVERT: G 352 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8316 (m) REVERT: I 340 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8045 (mtpt) REVERT: J 350 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7608 (p) REVERT: J 369 LYS cc_start: 0.8471 (ptpt) cc_final: 0.7858 (ptmt) REVERT: K 343 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7933 (mtpm) REVERT: K 350 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7722 (p) REVERT: K 369 LYS cc_start: 0.8223 (ptpt) cc_final: 0.7929 (ptpt) REVERT: K 370 LYS cc_start: 0.8290 (tttm) cc_final: 0.7894 (ttpt) REVERT: L 350 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.7846 (p) REVERT: L 369 LYS cc_start: 0.8194 (ptpt) cc_final: 0.7919 (ptmt) REVERT: L 370 LYS cc_start: 0.8354 (tttm) cc_final: 0.7999 (ttpt) REVERT: M 331 LYS cc_start: 0.8806 (mttp) cc_final: 0.8553 (mtmt) REVERT: M 340 LYS cc_start: 0.8419 (ttmm) cc_final: 0.7958 (mtmm) REVERT: M 350 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.7924 (p) REVERT: M 352 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8320 (m) REVERT: M 369 LYS cc_start: 0.8335 (ptpt) cc_final: 0.8078 (ptmt) REVERT: M 370 LYS cc_start: 0.8308 (tttm) cc_final: 0.7933 (ttpt) REVERT: M 378 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: N 311 LYS cc_start: 0.8525 (tmtt) cc_final: 0.8253 (tptt) REVERT: N 321 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8183 (mttp) REVERT: N 331 LYS cc_start: 0.8887 (mttt) cc_final: 0.8647 (mtpm) REVERT: N 340 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8068 (mtmm) REVERT: N 350 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.7770 (p) REVERT: N 369 LYS cc_start: 0.8394 (ptpt) cc_final: 0.7994 (ptmt) REVERT: N 370 LYS cc_start: 0.8394 (tttm) cc_final: 0.8072 (ttpt) REVERT: O 321 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8065 (mttp) REVERT: O 340 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8115 (mttt) REVERT: O 370 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8084 (tttp) REVERT: O 378 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.6144 (m-80) REVERT: P 317 LYS cc_start: 0.6695 (ptmt) cc_final: 0.6445 (ptmt) REVERT: P 370 LYS cc_start: 0.8491 (tttm) cc_final: 0.8129 (ttpt) REVERT: P 378 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.5798 (m-10) REVERT: Q 378 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.6200 (m-80) REVERT: R 340 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8216 (mtmp) REVERT: R 345 ASP cc_start: 0.8169 (m-30) cc_final: 0.7708 (t0) REVERT: S 319 THR cc_start: 0.8047 (m) cc_final: 0.7787 (p) REVERT: S 331 LYS cc_start: 0.8777 (mttp) cc_final: 0.8530 (mtmt) REVERT: S 345 ASP cc_start: 0.8180 (m-30) cc_final: 0.7607 (t0) REVERT: S 375 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7695 (ttpp) REVERT: S 378 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: T 345 ASP cc_start: 0.7913 (m-30) cc_final: 0.7595 (t0) REVERT: U 345 ASP cc_start: 0.7777 (m-30) cc_final: 0.7234 (t0) REVERT: U 378 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6161 (m-80) REVERT: V 331 LYS cc_start: 0.8937 (mttp) cc_final: 0.8552 (mtpt) REVERT: V 345 ASP cc_start: 0.7761 (m-30) cc_final: 0.7197 (t0) REVERT: V 378 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.5606 (p90) REVERT: W 343 LYS cc_start: 0.7441 (mttt) cc_final: 0.7067 (mptt) outliers start: 81 outliers final: 44 residues processed: 346 average time/residue: 2.7198 time to fit residues: 1029.4556 Evaluate side-chains 361 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 296 time to evaluate : 2.076 ------------------------------------------------------------------------------- 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 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 349 ARG Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 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 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 336 GLN ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 336 GLN ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4470 r_free = 0.4470 target = 0.151903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.118773 restraints weight = 41343.802| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.72 r_work: 0.3880 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13593 Z= 0.148 Angle : 0.593 4.825 18239 Z= 0.289 Chirality : 0.049 0.138 2001 Planarity : 0.003 0.049 2231 Dihedral : 7.334 58.406 2122 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 5.30 % Allowed : 17.60 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.48 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (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 T 378 TYR 0.011 0.002 TYR T 310 ARG 0.008 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02520 ( 328) hydrogen bonds : angle 4.12081 ( 984) covalent geometry : bond 0.00335 (13593) covalent geometry : angle 0.59267 (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 390 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 312 time to evaluate : 2.166 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: A 320 SER cc_start: 0.7420 (m) cc_final: 0.7146 (t) REVERT: A 350 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7694 (p) REVERT: A 368 ASN cc_start: 0.7288 (m110) cc_final: 0.6987 (m110) REVERT: A 370 LYS cc_start: 0.7596 (tttm) cc_final: 0.7353 (ttpp) REVERT: D 321 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8073 (mttt) REVERT: D 342 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: E 321 LYS cc_start: 0.8478 (mtpt) cc_final: 0.7956 (mttp) REVERT: F 321 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8124 (mttp) REVERT: F 349 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7051 (mtp180) REVERT: I 340 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8086 (mtpt) REVERT: I 378 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6246 (m-80) REVERT: J 350 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7704 (p) REVERT: J 369 LYS cc_start: 0.8448 (ptpt) cc_final: 0.7836 (ptmt) REVERT: K 343 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7924 (mtpm) REVERT: K 350 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7736 (p) REVERT: K 369 LYS cc_start: 0.8242 (ptpt) cc_final: 0.7930 (ptpt) REVERT: K 370 LYS cc_start: 0.8325 (tttm) cc_final: 0.8050 (ttpt) REVERT: L 350 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.7882 (p) REVERT: L 369 LYS cc_start: 0.8212 (ptpt) cc_final: 0.7820 (ptmt) REVERT: L 370 LYS cc_start: 0.8333 (tttm) cc_final: 0.7969 (ttpt) REVERT: M 331 LYS cc_start: 0.8809 (mttp) cc_final: 0.8521 (mtmt) REVERT: M 340 LYS cc_start: 0.8467 (ttmm) cc_final: 0.7974 (mtmm) REVERT: M 350 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.7983 (p) REVERT: M 352 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8326 (m) REVERT: M 369 LYS cc_start: 0.8373 (ptpt) cc_final: 0.8114 (ptmt) REVERT: M 370 LYS cc_start: 0.8306 (tttm) cc_final: 0.7905 (ttpt) REVERT: M 378 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6390 (m-80) REVERT: N 311 LYS cc_start: 0.8556 (tmtt) cc_final: 0.8305 (tptt) REVERT: N 321 LYS cc_start: 0.8557 (mtpt) cc_final: 0.8190 (mttp) REVERT: N 331 LYS cc_start: 0.8923 (mttt) cc_final: 0.8654 (mtpm) REVERT: N 340 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8069 (mtmm) REVERT: N 350 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.7811 (p) REVERT: N 369 LYS cc_start: 0.8453 (ptpt) cc_final: 0.7925 (ptmt) REVERT: N 370 LYS cc_start: 0.8367 (tttm) cc_final: 0.8014 (ttpt) REVERT: O 340 LYS cc_start: 0.8536 (ttmm) cc_final: 0.8157 (mttt) REVERT: O 378 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6137 (m-80) REVERT: P 370 LYS cc_start: 0.8493 (tttm) cc_final: 0.8128 (ttpt) REVERT: Q 378 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6286 (m-80) REVERT: R 345 ASP cc_start: 0.8201 (m-30) cc_final: 0.7731 (t0) REVERT: S 319 THR cc_start: 0.8050 (m) cc_final: 0.7768 (p) REVERT: S 331 LYS cc_start: 0.8826 (mttp) cc_final: 0.8558 (mtmt) REVERT: S 340 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8187 (ttmm) REVERT: S 345 ASP cc_start: 0.8211 (m-30) cc_final: 0.7577 (t0) REVERT: S 375 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7678 (ttpp) REVERT: S 378 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.6233 (m-80) REVERT: T 345 ASP cc_start: 0.7994 (m-30) cc_final: 0.7630 (t0) REVERT: U 331 LYS cc_start: 0.8933 (mttp) cc_final: 0.8468 (mtmt) REVERT: U 345 ASP cc_start: 0.7777 (m-30) cc_final: 0.7216 (t0) REVERT: U 378 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.6074 (m-80) REVERT: V 331 LYS cc_start: 0.9011 (mttp) cc_final: 0.8584 (mtpt) REVERT: V 345 ASP cc_start: 0.7771 (m-30) cc_final: 0.7141 (t0) REVERT: V 378 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.5612 (p90) REVERT: W 343 LYS cc_start: 0.7449 (mttt) cc_final: 0.7023 (mptt) outliers start: 78 outliers final: 48 residues processed: 355 average time/residue: 2.6755 time to fit residues: 1040.4916 Evaluate side-chains 368 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 303 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain C residue 350 VAL 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 349 ARG 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 343 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 369 LYS Chi-restraints excluded: chain O residue 377 THR Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain 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 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: 4.9990 chunk 62 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN F 362 HIS ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 336 GLN ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 336 GLN N 362 HIS ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.198860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.156463 restraints weight = 41263.897| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.33 r_work: 0.3868 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13593 Z= 0.211 Angle : 0.639 5.277 18239 Z= 0.315 Chirality : 0.049 0.137 2001 Planarity : 0.004 0.062 2231 Dihedral : 7.980 57.837 2122 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.49 % Favored : 87.51 % Rotamer: Outliers : 5.50 % Allowed : 17.80 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (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 0.001 HIS H 330 PHE 0.006 0.001 PHE U 346 TYR 0.015 0.003 TYR T 310 ARG 0.011 0.001 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02573 ( 328) hydrogen bonds : angle 4.16471 ( 984) covalent geometry : bond 0.00470 (13593) covalent geometry : angle 0.63937 (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 395 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 314 time to evaluate : 2.356 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 350 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7766 (p) REVERT: A 370 LYS cc_start: 0.7564 (tttm) cc_final: 0.7270 (tttm) REVERT: C 317 LYS cc_start: 0.7079 (ptmt) cc_final: 0.6572 (ptpp) REVERT: D 321 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8138 (mttt) REVERT: D 342 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: E 321 LYS cc_start: 0.8489 (mtpt) cc_final: 0.7979 (mttp) REVERT: F 321 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8138 (mttp) REVERT: F 349 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7050 (mtp180) REVERT: I 340 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8075 (mtpt) REVERT: I 343 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7864 (mppt) REVERT: I 378 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6400 (m-80) REVERT: J 350 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7767 (p) REVERT: J 369 LYS cc_start: 0.8501 (ptpt) cc_final: 0.7899 (ptmt) REVERT: K 343 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7912 (mtpm) REVERT: K 350 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7777 (p) REVERT: K 369 LYS cc_start: 0.8307 (ptpt) cc_final: 0.7998 (ptpt) REVERT: K 370 LYS cc_start: 0.8394 (tttm) cc_final: 0.8126 (ttpt) REVERT: L 369 LYS cc_start: 0.8276 (ptpt) cc_final: 0.7884 (ptmt) REVERT: L 370 LYS cc_start: 0.8383 (tttm) cc_final: 0.8034 (ttpt) REVERT: M 331 LYS cc_start: 0.8771 (mttp) cc_final: 0.8524 (mtmt) REVERT: M 340 LYS cc_start: 0.8471 (ttmm) cc_final: 0.7960 (mtmm) REVERT: M 350 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.7982 (p) REVERT: M 352 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8315 (m) REVERT: M 369 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8163 (ptmt) REVERT: M 370 LYS cc_start: 0.8336 (tttm) cc_final: 0.7960 (ttpt) REVERT: M 378 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6367 (m-80) REVERT: N 321 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8189 (mttp) REVERT: N 331 LYS cc_start: 0.8907 (mttt) cc_final: 0.8681 (mtpm) REVERT: N 340 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8099 (mtmm) REVERT: N 350 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.7860 (p) REVERT: N 369 LYS cc_start: 0.8479 (ptpt) cc_final: 0.8021 (ptmt) REVERT: N 370 LYS cc_start: 0.8389 (tttm) cc_final: 0.8065 (ttpt) REVERT: O 317 LYS cc_start: 0.7267 (ptmt) cc_final: 0.7051 (ptmt) REVERT: O 321 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8087 (mttp) REVERT: O 340 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8112 (mttt) REVERT: O 378 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: P 370 LYS cc_start: 0.8549 (tttm) cc_final: 0.8183 (ttpt) REVERT: Q 378 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: R 317 LYS cc_start: 0.6827 (ptmt) cc_final: 0.6495 (ptmt) REVERT: R 340 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8257 (mtmp) REVERT: R 345 ASP cc_start: 0.8098 (m-30) cc_final: 0.7730 (t0) REVERT: S 317 LYS cc_start: 0.7001 (ptmt) cc_final: 0.6572 (ptmt) REVERT: S 319 THR cc_start: 0.8135 (m) cc_final: 0.7865 (p) REVERT: S 331 LYS cc_start: 0.8788 (mttp) cc_final: 0.8527 (mtmt) REVERT: S 345 ASP cc_start: 0.8123 (m-30) cc_final: 0.7632 (t0) REVERT: S 375 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7741 (ttpp) REVERT: S 378 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.6168 (m-80) REVERT: T 345 ASP cc_start: 0.7924 (m-30) cc_final: 0.7636 (t0) REVERT: U 331 LYS cc_start: 0.8913 (mttp) cc_final: 0.8485 (mtmt) REVERT: U 345 ASP cc_start: 0.7759 (m-30) cc_final: 0.7268 (t0) REVERT: U 370 LYS cc_start: 0.8472 (tttp) cc_final: 0.8194 (tttp) REVERT: U 378 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6038 (m-80) REVERT: V 331 LYS cc_start: 0.8983 (mttp) cc_final: 0.8577 (mtpt) REVERT: V 345 ASP cc_start: 0.7729 (m-30) cc_final: 0.7169 (t0) REVERT: V 378 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.5594 (p90) REVERT: W 343 LYS cc_start: 0.7417 (mttt) cc_final: 0.7057 (mptt) outliers start: 81 outliers final: 53 residues processed: 359 average time/residue: 2.7584 time to fit residues: 1080.2364 Evaluate side-chains 382 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 310 time to evaluate : 2.040 ------------------------------------------------------------------------------- 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 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 349 ARG Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 343 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 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain 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 376 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 ASN K 336 GLN ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 ASN M 336 GLN N 368 ASN ** O 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 368 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.198190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.155278 restraints weight = 41432.873| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.34 r_work: 0.3852 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13593 Z= 0.215 Angle : 0.652 5.601 18239 Z= 0.321 Chirality : 0.049 0.136 2001 Planarity : 0.004 0.061 2231 Dihedral : 8.013 57.680 2122 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer: Outliers : 5.16 % Allowed : 18.27 % 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: -3.50 (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 B 330 PHE 0.005 0.001 PHE U 346 TYR 0.015 0.003 TYR V 310 ARG 0.012 0.001 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02655 ( 328) hydrogen bonds : angle 4.16458 ( 984) covalent geometry : bond 0.00479 (13593) covalent geometry : angle 0.65151 (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 385 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 309 time to evaluate : 2.018 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: A 350 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7764 (p) REVERT: C 317 LYS cc_start: 0.7080 (ptmt) cc_final: 0.6568 (ptpp) REVERT: D 321 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8123 (mttt) REVERT: D 342 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: E 321 LYS cc_start: 0.8495 (mtpt) cc_final: 0.7999 (mttp) REVERT: F 321 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8134 (mttp) REVERT: F 349 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7043 (mtp180) REVERT: I 340 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8100 (mtpt) REVERT: I 378 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6357 (m-80) REVERT: J 350 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7800 (p) REVERT: J 369 LYS cc_start: 0.8533 (ptpt) cc_final: 0.7920 (ptmt) REVERT: K 343 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7907 (mtpm) REVERT: K 369 LYS cc_start: 0.8307 (ptpt) cc_final: 0.8008 (ptpt) REVERT: K 370 LYS cc_start: 0.8386 (tttm) cc_final: 0.8106 (ttpt) REVERT: L 369 LYS cc_start: 0.8305 (ptpt) cc_final: 0.7887 (ptmt) REVERT: L 370 LYS cc_start: 0.8370 (tttm) cc_final: 0.8034 (ttpt) REVERT: L 375 LYS cc_start: 0.8043 (ttmt) cc_final: 0.7690 (ttmp) REVERT: M 331 LYS cc_start: 0.8776 (mttp) cc_final: 0.8567 (mtmt) REVERT: M 340 LYS cc_start: 0.8463 (ttmm) cc_final: 0.7987 (mtmm) REVERT: M 350 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.8020 (p) REVERT: M 352 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8304 (m) REVERT: M 369 LYS cc_start: 0.8465 (ptpt) cc_final: 0.8172 (ptmt) REVERT: M 370 LYS cc_start: 0.8325 (tttm) cc_final: 0.7946 (ttpt) REVERT: M 378 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6356 (m-80) REVERT: N 321 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8199 (mttp) REVERT: N 340 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8079 (mtmm) REVERT: N 350 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.7888 (p) REVERT: N 369 LYS cc_start: 0.8527 (ptpt) cc_final: 0.8047 (ptmt) REVERT: N 370 LYS cc_start: 0.8383 (tttm) cc_final: 0.8070 (ttpt) REVERT: O 317 LYS cc_start: 0.7395 (ptmt) cc_final: 0.7164 (ptmt) REVERT: O 321 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8106 (mttp) REVERT: O 340 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8101 (mttt) REVERT: O 378 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.6083 (m-80) REVERT: P 370 LYS cc_start: 0.8536 (tttm) cc_final: 0.8188 (ttpt) REVERT: Q 378 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6274 (m-80) REVERT: R 317 LYS cc_start: 0.6902 (ptmt) cc_final: 0.6558 (ptmt) REVERT: R 338 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: R 345 ASP cc_start: 0.8069 (m-30) cc_final: 0.7706 (t0) REVERT: S 317 LYS cc_start: 0.7063 (ptmt) cc_final: 0.6704 (ptmt) REVERT: S 319 THR cc_start: 0.8185 (m) cc_final: 0.7910 (p) REVERT: S 345 ASP cc_start: 0.8107 (m-30) cc_final: 0.7654 (t0) REVERT: S 375 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7753 (ttpp) REVERT: T 345 ASP cc_start: 0.7929 (m-30) cc_final: 0.7647 (t0) REVERT: U 331 LYS cc_start: 0.8904 (mttp) cc_final: 0.8469 (mtmt) REVERT: U 345 ASP cc_start: 0.7759 (m-30) cc_final: 0.7280 (t0) REVERT: U 378 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.6060 (m-80) REVERT: V 331 LYS cc_start: 0.8985 (mttp) cc_final: 0.8579 (mtpt) REVERT: V 345 ASP cc_start: 0.7683 (m-30) cc_final: 0.7158 (t0) REVERT: V 378 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.5687 (p90) REVERT: W 343 LYS cc_start: 0.7354 (mttt) cc_final: 0.7031 (mptt) outliers start: 76 outliers final: 54 residues processed: 353 average time/residue: 2.7566 time to fit residues: 1060.3907 Evaluate side-chains 371 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 301 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 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 F residue 338 GLU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 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 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 338 GLU 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 319 THR 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 356 SER Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN G 368 ASN K 336 GLN ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 ASN M 336 GLN N 368 ASN ** O 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.196555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.152372 restraints weight = 41837.839| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.35 r_work: 0.3815 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13593 Z= 0.263 Angle : 0.697 6.052 18239 Z= 0.345 Chirality : 0.049 0.135 2001 Planarity : 0.004 0.061 2231 Dihedral : 8.461 57.288 2120 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer: Outliers : 5.37 % Allowed : 18.48 % Favored : 76.15 % 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 0.003 0.001 HIS J 330 PHE 0.007 0.001 PHE U 346 TYR 0.018 0.004 TYR T 310 ARG 0.015 0.001 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02734 ( 328) hydrogen bonds : angle 4.22102 ( 984) covalent geometry : bond 0.00584 (13593) covalent geometry : angle 0.69697 (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 389 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 310 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7816 (p) REVERT: A 370 LYS cc_start: 0.7612 (tttm) cc_final: 0.7309 (tttm) REVERT: C 317 LYS cc_start: 0.7165 (ptmt) cc_final: 0.6661 (ptpp) REVERT: D 321 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8159 (mttt) REVERT: D 342 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: E 321 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8071 (mttp) REVERT: F 321 LYS cc_start: 0.8497 (mtpt) cc_final: 0.8151 (mttp) REVERT: F 349 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7060 (mtp180) REVERT: H 369 LYS cc_start: 0.8472 (ptpt) cc_final: 0.8165 (ptpp) REVERT: I 340 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8102 (mtpt) REVERT: I 378 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6425 (m-80) REVERT: J 369 LYS cc_start: 0.8589 (ptpt) cc_final: 0.7994 (ptmt) REVERT: K 343 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7919 (mtpm) REVERT: K 369 LYS cc_start: 0.8354 (ptpt) cc_final: 0.8053 (ptpt) REVERT: K 370 LYS cc_start: 0.8451 (tttm) cc_final: 0.8132 (ttpt) REVERT: L 369 LYS cc_start: 0.8337 (ptpt) cc_final: 0.7958 (ptmt) REVERT: L 370 LYS cc_start: 0.8406 (tttm) cc_final: 0.8079 (ttpt) REVERT: L 375 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7713 (ttmp) REVERT: M 340 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8007 (mtmm) REVERT: M 369 LYS cc_start: 0.8497 (ptpt) cc_final: 0.8084 (ptmt) REVERT: M 370 LYS cc_start: 0.8380 (tttm) cc_final: 0.8010 (ttpt) REVERT: M 378 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6358 (m-80) REVERT: N 321 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8223 (mttp) REVERT: N 340 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8084 (mtmm) REVERT: N 350 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.7960 (p) REVERT: N 369 LYS cc_start: 0.8604 (ptpt) cc_final: 0.8084 (ptmt) REVERT: N 370 LYS cc_start: 0.8463 (tttm) cc_final: 0.8144 (ttpt) REVERT: O 340 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8196 (mttt) REVERT: O 378 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6109 (m-80) REVERT: P 370 LYS cc_start: 0.8594 (tttm) cc_final: 0.8223 (ttpt) REVERT: Q 378 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6345 (m-80) REVERT: R 317 LYS cc_start: 0.7141 (ptmt) cc_final: 0.6880 (ptmt) REVERT: R 345 ASP cc_start: 0.8072 (m-30) cc_final: 0.7723 (t0) REVERT: S 317 LYS cc_start: 0.7220 (ptmt) cc_final: 0.6837 (ptmt) REVERT: S 319 THR cc_start: 0.8214 (m) cc_final: 0.7976 (p) REVERT: S 345 ASP cc_start: 0.8122 (m-30) cc_final: 0.7709 (t0) REVERT: S 375 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7793 (ttpp) REVERT: T 345 ASP cc_start: 0.7940 (m-30) cc_final: 0.7709 (t0) REVERT: U 331 LYS cc_start: 0.8911 (mttp) cc_final: 0.8505 (mtmt) REVERT: U 345 ASP cc_start: 0.7797 (m-30) cc_final: 0.7338 (t0) REVERT: U 370 LYS cc_start: 0.8491 (tttp) cc_final: 0.8156 (tttp) REVERT: U 378 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.6027 (m-80) REVERT: V 331 LYS cc_start: 0.8959 (mttp) cc_final: 0.8573 (mtpt) REVERT: V 345 ASP cc_start: 0.7747 (m-30) cc_final: 0.7236 (t0) REVERT: V 378 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.5652 (p90) REVERT: W 343 LYS cc_start: 0.7356 (mttt) cc_final: 0.7033 (mptt) REVERT: W 378 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6441 (m-80) outliers start: 79 outliers final: 59 residues processed: 354 average time/residue: 2.7269 time to fit residues: 1055.1176 Evaluate side-chains 367 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 296 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 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 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 F residue 338 GLU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain I residue 378 PHE Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 343 LYS Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 319 THR Chi-restraints excluded: chain R residue 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 319 THR 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 319 THR Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 356 SER Chi-restraints excluded: chain W residue 369 LYS Chi-restraints excluded: chain W residue 378 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN E 351 GLN K 336 GLN M 336 GLN N 368 ASN ** O 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 368 ASN ** S 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.147849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.114324 restraints weight = 41571.892| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.76 r_work: 0.3842 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13593 Z= 0.127 Angle : 0.614 6.214 18239 Z= 0.300 Chirality : 0.049 0.132 2001 Planarity : 0.004 0.030 2231 Dihedral : 7.348 57.628 2120 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 4.08 % Allowed : 20.18 % 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: -3.55 (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 V 362 PHE 0.003 0.001 PHE J 378 TYR 0.009 0.002 TYR L 310 ARG 0.004 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02484 ( 328) hydrogen bonds : angle 4.05927 ( 984) covalent geometry : bond 0.00288 (13593) covalent geometry : angle 0.61355 (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 365 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 305 time to evaluate : 1.991 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: A 350 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7690 (p) REVERT: A 370 LYS cc_start: 0.7567 (tttm) cc_final: 0.7273 (tttm) REVERT: B 378 PHE cc_start: 0.7283 (m-80) cc_final: 0.7039 (m-80) REVERT: C 317 LYS cc_start: 0.7008 (ptmt) cc_final: 0.6501 (ptpp) REVERT: D 321 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8122 (mttt) REVERT: E 321 LYS cc_start: 0.8507 (mtpt) cc_final: 0.7986 (mttp) REVERT: F 321 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8150 (mttp) REVERT: F 349 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7041 (mtp180) REVERT: I 340 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8103 (mtpt) REVERT: I 378 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: J 350 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7818 (p) REVERT: J 369 LYS cc_start: 0.8458 (ptpt) cc_final: 0.7848 (ptmt) REVERT: J 370 LYS cc_start: 0.8423 (tttm) cc_final: 0.7813 (ttpt) REVERT: K 350 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7737 (p) REVERT: K 369 LYS cc_start: 0.8319 (ptpt) cc_final: 0.8022 (ptpt) REVERT: L 369 LYS cc_start: 0.8244 (ptpt) cc_final: 0.7830 (ptmt) REVERT: L 370 LYS cc_start: 0.8325 (tttm) cc_final: 0.7981 (ttpt) REVERT: L 375 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7666 (ttmp) REVERT: M 350 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.8041 (p) REVERT: M 352 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8341 (m) REVERT: M 370 LYS cc_start: 0.8306 (tttm) cc_final: 0.7933 (ttpt) REVERT: M 378 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: N 321 LYS cc_start: 0.8562 (mtpt) cc_final: 0.8215 (mttp) REVERT: N 331 LYS cc_start: 0.8942 (mttt) cc_final: 0.8693 (mtpm) REVERT: N 340 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8026 (mtmm) REVERT: N 350 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.7951 (p) REVERT: N 369 LYS cc_start: 0.8464 (ptpt) cc_final: 0.7951 (ptmt) REVERT: N 370 LYS cc_start: 0.8378 (tttm) cc_final: 0.8064 (ttpt) REVERT: O 321 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8074 (mttp) REVERT: O 340 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8165 (mttt) REVERT: O 378 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6068 (m-80) REVERT: P 370 LYS cc_start: 0.8508 (tttm) cc_final: 0.8075 (ttpt) REVERT: Q 378 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6277 (m-80) REVERT: R 317 LYS cc_start: 0.6948 (ptmt) cc_final: 0.6688 (ptmt) REVERT: R 345 ASP cc_start: 0.8097 (m-30) cc_final: 0.7672 (t0) REVERT: S 317 LYS cc_start: 0.6905 (ptmt) cc_final: 0.6482 (ptmt) REVERT: S 319 THR cc_start: 0.8114 (m) cc_final: 0.7867 (p) REVERT: S 345 ASP cc_start: 0.8141 (m-30) cc_final: 0.7619 (t0) REVERT: S 375 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7707 (ttpp) REVERT: T 345 ASP cc_start: 0.7990 (m-30) cc_final: 0.7641 (t0) REVERT: U 331 LYS cc_start: 0.8916 (mttp) cc_final: 0.8451 (mtmt) REVERT: U 345 ASP cc_start: 0.7718 (m-30) cc_final: 0.7212 (t0) REVERT: U 378 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6084 (m-80) REVERT: V 331 LYS cc_start: 0.9015 (mttp) cc_final: 0.8605 (mtpt) REVERT: V 345 ASP cc_start: 0.7641 (m-30) cc_final: 0.7081 (t0) REVERT: V 378 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.5601 (p90) REVERT: W 343 LYS cc_start: 0.7286 (mttt) cc_final: 0.6890 (mptt) outliers start: 60 outliers final: 39 residues processed: 346 average time/residue: 2.6909 time to fit residues: 1026.9942 Evaluate side-chains 345 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 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 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 349 ARG 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 I residue 350 VAL Chi-restraints excluded: chain I residue 378 PHE Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 118 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 ** K 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 336 GLN ** O 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 = 0.4464 r_free = 0.4464 target = 0.198662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.154065 restraints weight = 41432.338| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.34 r_work: 0.3829 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13593 Z= 0.227 Angle : 0.666 6.032 18239 Z= 0.328 Chirality : 0.049 0.134 2001 Planarity : 0.004 0.038 2231 Dihedral : 8.039 57.307 2120 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 4.01 % Allowed : 20.65 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 330 PHE 0.006 0.001 PHE I 346 TYR 0.017 0.003 TYR V 310 ARG 0.004 0.001 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02505 ( 328) hydrogen bonds : angle 4.09890 ( 984) covalent geometry : bond 0.00510 (13593) covalent geometry : angle 0.66610 (18239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22262.43 seconds wall clock time: 382 minutes 24.75 seconds (22944.75 seconds total)