Starting phenix.real_space_refine on Mon Jan 13 13:06:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdc_43146/01_2025/8vdc_43146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdc_43146/01_2025/8vdc_43146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vdc_43146/01_2025/8vdc_43146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdc_43146/01_2025/8vdc_43146.map" model { file = "/net/cci-nas-00/data/ceres_data/8vdc_43146/01_2025/8vdc_43146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdc_43146/01_2025/8vdc_43146.cif" } resolution = 3.5 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 29496 2.51 5 N 7992 2.21 5 O 9444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 47064 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 10.59, per 1000 atoms: 0.23 Number of scatterers: 47064 At special positions: 0 Unit cell: (179.55, 179.55, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 9444 8.00 N 7992 7.00 C 29496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.40 Conformation dependent library (CDL) restraints added in 4.5 seconds 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10896 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 72 sheets defined 47.5% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG A 59 " --> pdb=" O TYR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 80 Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 132 through 148 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 261 through 282 removed outlier: 3.633A pdb=" N LEU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 445 Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.664A pdb=" N SER C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG C 59 " --> pdb=" O TYR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 93 through 108 Processing helix chain 'C' and resid 117 through 131 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 261 through 282 removed outlier: 3.633A pdb=" N LEU C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS C 304 " --> pdb=" O ARG C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 412 removed outlier: 3.647A pdb=" N ARG C 386 " --> pdb=" O GLY C 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 445 Processing helix chain 'C' and resid 451 through 458 Processing helix chain 'C' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'E' and resid 34 through 40 Processing helix chain 'E' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 3.742A pdb=" N ARG E 59 " --> pdb=" O TYR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 80 Processing helix chain 'E' and resid 93 through 108 Processing helix chain 'E' and resid 117 through 131 Processing helix chain 'E' and resid 132 through 148 Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 261 through 282 removed outlier: 3.632A pdb=" N LEU E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS E 304 " --> pdb=" O ARG E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 371 through 380 removed outlier: 3.708A pdb=" N TYR E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG E 386 " --> pdb=" O GLY E 382 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR E 389 " --> pdb=" O GLN E 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 445 Processing helix chain 'E' and resid 451 through 458 Processing helix chain 'E' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS E 470 " --> pdb=" O GLU E 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 34 through 40 Processing helix chain 'G' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER G 46 " --> pdb=" O VAL G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG G 59 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 80 Processing helix chain 'G' and resid 93 through 108 Processing helix chain 'G' and resid 117 through 131 Processing helix chain 'G' and resid 132 through 148 Processing helix chain 'G' and resid 168 through 170 No H-bonds generated for 'chain 'G' and resid 168 through 170' Processing helix chain 'G' and resid 261 through 282 removed outlier: 3.633A pdb=" N LEU G 282 " --> pdb=" O TYR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS G 304 " --> pdb=" O ARG G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR G 378 " --> pdb=" O GLU G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG G 386 " --> pdb=" O GLY G 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR G 389 " --> pdb=" O GLN G 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG G 400 " --> pdb=" O LYS G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 445 Processing helix chain 'G' and resid 451 through 458 Processing helix chain 'G' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS G 470 " --> pdb=" O GLU G 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 34 through 40 Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.664A pdb=" N SER I 46 " --> pdb=" O VAL I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG I 59 " --> pdb=" O TYR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 80 Processing helix chain 'I' and resid 93 through 108 Processing helix chain 'I' and resid 117 through 131 Processing helix chain 'I' and resid 132 through 148 Processing helix chain 'I' and resid 168 through 170 No H-bonds generated for 'chain 'I' and resid 168 through 170' Processing helix chain 'I' and resid 261 through 282 removed outlier: 3.633A pdb=" N LEU I 282 " --> pdb=" O TYR I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS I 304 " --> pdb=" O ARG I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR I 378 " --> pdb=" O GLU I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 412 removed outlier: 3.647A pdb=" N ARG I 386 " --> pdb=" O GLY I 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR I 389 " --> pdb=" O GLN I 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG I 400 " --> pdb=" O LYS I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 445 Processing helix chain 'I' and resid 451 through 458 Processing helix chain 'I' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS I 470 " --> pdb=" O GLU I 466 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 21 Processing helix chain 'K' and resid 34 through 40 Processing helix chain 'K' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER K 46 " --> pdb=" O VAL K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 68 removed outlier: 3.742A pdb=" N ARG K 59 " --> pdb=" O TYR K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 Processing helix chain 'K' and resid 93 through 108 Processing helix chain 'K' and resid 117 through 131 Processing helix chain 'K' and resid 132 through 148 Processing helix chain 'K' and resid 168 through 170 No H-bonds generated for 'chain 'K' and resid 168 through 170' Processing helix chain 'K' and resid 261 through 282 removed outlier: 3.632A pdb=" N LEU K 282 " --> pdb=" O TYR K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS K 304 " --> pdb=" O ARG K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 371 through 380 removed outlier: 3.708A pdb=" N TYR K 378 " --> pdb=" O GLU K 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG K 386 " --> pdb=" O GLY K 382 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR K 389 " --> pdb=" O GLN K 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG K 400 " --> pdb=" O LYS K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 445 Processing helix chain 'K' and resid 451 through 458 Processing helix chain 'K' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS K 470 " --> pdb=" O GLU K 466 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 34 through 40 Processing helix chain 'M' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER M 46 " --> pdb=" O VAL M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG M 59 " --> pdb=" O TYR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 80 Processing helix chain 'M' and resid 93 through 108 Processing helix chain 'M' and resid 117 through 131 Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 168 through 170 No H-bonds generated for 'chain 'M' and resid 168 through 170' Processing helix chain 'M' and resid 261 through 282 removed outlier: 3.633A pdb=" N LEU M 282 " --> pdb=" O TYR M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS M 304 " --> pdb=" O ARG M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 356 Processing helix chain 'M' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR M 378 " --> pdb=" O GLU M 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG M 386 " --> pdb=" O GLY M 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR M 389 " --> pdb=" O GLN M 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG M 400 " --> pdb=" O LYS M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 445 Processing helix chain 'M' and resid 451 through 458 Processing helix chain 'M' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS M 470 " --> pdb=" O GLU M 466 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 34 through 40 Processing helix chain 'O' and resid 42 through 55 removed outlier: 3.664A pdb=" N SER O 46 " --> pdb=" O VAL O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG O 59 " --> pdb=" O TYR O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL O 75 " --> pdb=" O THR O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 80 Processing helix chain 'O' and resid 93 through 108 Processing helix chain 'O' and resid 117 through 131 Processing helix chain 'O' and resid 132 through 148 Processing helix chain 'O' and resid 168 through 170 No H-bonds generated for 'chain 'O' and resid 168 through 170' Processing helix chain 'O' and resid 261 through 282 removed outlier: 3.633A pdb=" N LEU O 282 " --> pdb=" O TYR O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS O 304 " --> pdb=" O ARG O 301 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 356 Processing helix chain 'O' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR O 378 " --> pdb=" O GLU O 374 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 412 removed outlier: 3.647A pdb=" N ARG O 386 " --> pdb=" O GLY O 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR O 389 " --> pdb=" O GLN O 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG O 400 " --> pdb=" O LYS O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 445 Processing helix chain 'O' and resid 451 through 458 Processing helix chain 'O' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS O 470 " --> pdb=" O GLU O 466 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 34 through 40 Processing helix chain 'Q' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER Q 46 " --> pdb=" O VAL Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 68 removed outlier: 3.742A pdb=" N ARG Q 59 " --> pdb=" O TYR Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL Q 75 " --> pdb=" O THR Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 80 Processing helix chain 'Q' and resid 93 through 108 Processing helix chain 'Q' and resid 117 through 131 Processing helix chain 'Q' and resid 132 through 148 Processing helix chain 'Q' and resid 168 through 170 No H-bonds generated for 'chain 'Q' and resid 168 through 170' Processing helix chain 'Q' and resid 261 through 282 removed outlier: 3.632A pdb=" N LEU Q 282 " --> pdb=" O TYR Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS Q 304 " --> pdb=" O ARG Q 301 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 356 Processing helix chain 'Q' and resid 371 through 380 removed outlier: 3.708A pdb=" N TYR Q 378 " --> pdb=" O GLU Q 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG Q 386 " --> pdb=" O GLY Q 382 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR Q 389 " --> pdb=" O GLN Q 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG Q 400 " --> pdb=" O LYS Q 396 " (cutoff:3.500A) Processing helix chain 'Q' and resid 435 through 445 Processing helix chain 'Q' and resid 451 through 458 Processing helix chain 'Q' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS Q 470 " --> pdb=" O GLU Q 466 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 21 Processing helix chain 'S' and resid 34 through 40 Processing helix chain 'S' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER S 46 " --> pdb=" O VAL S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG S 59 " --> pdb=" O TYR S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL S 75 " --> pdb=" O THR S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 80 Processing helix chain 'S' and resid 93 through 108 Processing helix chain 'S' and resid 117 through 131 Processing helix chain 'S' and resid 132 through 148 Processing helix chain 'S' and resid 168 through 170 No H-bonds generated for 'chain 'S' and resid 168 through 170' Processing helix chain 'S' and resid 261 through 282 removed outlier: 3.633A pdb=" N LEU S 282 " --> pdb=" O TYR S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS S 304 " --> pdb=" O ARG S 301 " (cutoff:3.500A) Processing helix chain 'S' and resid 338 through 356 Processing helix chain 'S' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR S 378 " --> pdb=" O GLU S 374 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG S 386 " --> pdb=" O GLY S 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR S 389 " --> pdb=" O GLN S 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG S 400 " --> pdb=" O LYS S 396 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 445 Processing helix chain 'S' and resid 451 through 458 Processing helix chain 'S' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS S 470 " --> pdb=" O GLU S 466 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 34 through 40 Processing helix chain 'U' and resid 42 through 55 removed outlier: 3.664A pdb=" N SER U 46 " --> pdb=" O VAL U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG U 59 " --> pdb=" O TYR U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL U 75 " --> pdb=" O THR U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 80 Processing helix chain 'U' and resid 93 through 108 Processing helix chain 'U' and resid 117 through 131 Processing helix chain 'U' and resid 132 through 148 Processing helix chain 'U' and resid 168 through 170 No H-bonds generated for 'chain 'U' and resid 168 through 170' Processing helix chain 'U' and resid 261 through 282 removed outlier: 3.633A pdb=" N LEU U 282 " --> pdb=" O TYR U 278 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS U 304 " --> pdb=" O ARG U 301 " (cutoff:3.500A) Processing helix chain 'U' and resid 338 through 356 Processing helix chain 'U' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR U 378 " --> pdb=" O GLU U 374 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 412 removed outlier: 3.647A pdb=" N ARG U 386 " --> pdb=" O GLY U 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR U 389 " --> pdb=" O GLN U 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG U 400 " --> pdb=" O LYS U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 435 through 445 Processing helix chain 'U' and resid 451 through 458 Processing helix chain 'U' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS U 470 " --> pdb=" O GLU U 466 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 21 Processing helix chain 'W' and resid 34 through 40 Processing helix chain 'W' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER W 46 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 68 removed outlier: 3.742A pdb=" N ARG W 59 " --> pdb=" O TYR W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL W 75 " --> pdb=" O THR W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 80 Processing helix chain 'W' and resid 93 through 108 Processing helix chain 'W' and resid 117 through 131 Processing helix chain 'W' and resid 132 through 148 Processing helix chain 'W' and resid 168 through 170 No H-bonds generated for 'chain 'W' and resid 168 through 170' Processing helix chain 'W' and resid 261 through 282 removed outlier: 3.632A pdb=" N LEU W 282 " --> pdb=" O TYR W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS W 304 " --> pdb=" O ARG W 301 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 356 Processing helix chain 'W' and resid 371 through 380 removed outlier: 3.708A pdb=" N TYR W 378 " --> pdb=" O GLU W 374 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG W 386 " --> pdb=" O GLY W 382 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR W 389 " --> pdb=" O GLN W 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG W 400 " --> pdb=" O LYS W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 435 through 445 Processing helix chain 'W' and resid 451 through 458 Processing helix chain 'W' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS W 470 " --> pdb=" O GLU W 466 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP A 177 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER A 184 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER A 234 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU A 219 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU A 232 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ASN A 221 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=3, first strand: chain 'A' and resid 162 through 167 removed outlier: 3.942A pdb=" N TYR A 151 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP A 329 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 310 through 312 Processing sheet with id=6, first strand: chain 'A' and resid 315 through 317 Processing sheet with id=7, first strand: chain 'C' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP C 177 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER C 184 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER C 234 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU C 219 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU C 232 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASN C 221 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=9, first strand: chain 'C' and resid 162 through 167 removed outlier: 3.943A pdb=" N TYR C 151 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP C 329 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 310 through 312 Processing sheet with id=12, first strand: chain 'C' and resid 315 through 317 Processing sheet with id=13, first strand: chain 'E' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP E 177 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER E 184 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER E 234 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU E 219 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU E 232 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASN E 221 " --> pdb=" O PRO E 230 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'E' and resid 112 through 114 Processing sheet with id=15, first strand: chain 'E' and resid 162 through 167 removed outlier: 3.942A pdb=" N TYR E 151 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'E' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP E 329 " --> pdb=" O LYS E 290 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'E' and resid 310 through 312 Processing sheet with id=18, first strand: chain 'E' and resid 315 through 317 Processing sheet with id=19, first strand: chain 'G' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP G 177 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER G 184 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER G 234 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU G 219 " --> pdb=" O GLU G 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU G 232 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ASN G 221 " --> pdb=" O PRO G 230 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'G' and resid 112 through 114 Processing sheet with id=21, first strand: chain 'G' and resid 162 through 167 removed outlier: 3.942A pdb=" N TYR G 151 " --> pdb=" O SER G 167 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'G' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP G 329 " --> pdb=" O LYS G 290 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'G' and resid 310 through 312 Processing sheet with id=24, first strand: chain 'G' and resid 315 through 317 Processing sheet with id=25, first strand: chain 'I' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP I 177 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER I 184 " --> pdb=" O ASP I 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER I 234 " --> pdb=" O ARG I 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU I 219 " --> pdb=" O GLU I 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU I 232 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASN I 221 " --> pdb=" O PRO I 230 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'I' and resid 112 through 114 Processing sheet with id=27, first strand: chain 'I' and resid 162 through 167 removed outlier: 3.943A pdb=" N TYR I 151 " --> pdb=" O SER I 167 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'I' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP I 329 " --> pdb=" O LYS I 290 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'I' and resid 310 through 312 Processing sheet with id=30, first strand: chain 'I' and resid 315 through 317 Processing sheet with id=31, first strand: chain 'K' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP K 177 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER K 184 " --> pdb=" O ASP K 177 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER K 234 " --> pdb=" O ARG K 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU K 219 " --> pdb=" O GLU K 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU K 232 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASN K 221 " --> pdb=" O PRO K 230 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'K' and resid 112 through 114 Processing sheet with id=33, first strand: chain 'K' and resid 162 through 167 removed outlier: 3.942A pdb=" N TYR K 151 " --> pdb=" O SER K 167 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'K' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP K 329 " --> pdb=" O LYS K 290 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'K' and resid 310 through 312 Processing sheet with id=36, first strand: chain 'K' and resid 315 through 317 Processing sheet with id=37, first strand: chain 'M' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP M 177 " --> pdb=" O SER M 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER M 184 " --> pdb=" O ASP M 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER M 234 " --> pdb=" O ARG M 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU M 219 " --> pdb=" O GLU M 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU M 232 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ASN M 221 " --> pdb=" O PRO M 230 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'M' and resid 112 through 114 Processing sheet with id=39, first strand: chain 'M' and resid 162 through 167 removed outlier: 3.942A pdb=" N TYR M 151 " --> pdb=" O SER M 167 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'M' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP M 329 " --> pdb=" O LYS M 290 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'M' and resid 310 through 312 Processing sheet with id=42, first strand: chain 'M' and resid 315 through 317 Processing sheet with id=43, first strand: chain 'O' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP O 177 " --> pdb=" O SER O 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER O 184 " --> pdb=" O ASP O 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER O 234 " --> pdb=" O ARG O 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU O 219 " --> pdb=" O GLU O 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU O 232 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASN O 221 " --> pdb=" O PRO O 230 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'O' and resid 112 through 114 Processing sheet with id=45, first strand: chain 'O' and resid 162 through 167 removed outlier: 3.943A pdb=" N TYR O 151 " --> pdb=" O SER O 167 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'O' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP O 329 " --> pdb=" O LYS O 290 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 310 through 312 Processing sheet with id=48, first strand: chain 'O' and resid 315 through 317 Processing sheet with id=49, first strand: chain 'Q' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP Q 177 " --> pdb=" O SER Q 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER Q 184 " --> pdb=" O ASP Q 177 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER Q 234 " --> pdb=" O ARG Q 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU Q 219 " --> pdb=" O GLU Q 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU Q 232 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASN Q 221 " --> pdb=" O PRO Q 230 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'Q' and resid 112 through 114 Processing sheet with id=51, first strand: chain 'Q' and resid 162 through 167 removed outlier: 3.942A pdb=" N TYR Q 151 " --> pdb=" O SER Q 167 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'Q' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP Q 329 " --> pdb=" O LYS Q 290 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'Q' and resid 310 through 312 Processing sheet with id=54, first strand: chain 'Q' and resid 315 through 317 Processing sheet with id=55, first strand: chain 'S' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP S 177 " --> pdb=" O SER S 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER S 184 " --> pdb=" O ASP S 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER S 234 " --> pdb=" O ARG S 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU S 219 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU S 232 " --> pdb=" O LEU S 219 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ASN S 221 " --> pdb=" O PRO S 230 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'S' and resid 112 through 114 Processing sheet with id=57, first strand: chain 'S' and resid 162 through 167 removed outlier: 3.942A pdb=" N TYR S 151 " --> pdb=" O SER S 167 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'S' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP S 329 " --> pdb=" O LYS S 290 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'S' and resid 310 through 312 Processing sheet with id=60, first strand: chain 'S' and resid 315 through 317 Processing sheet with id=61, first strand: chain 'U' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP U 177 " --> pdb=" O SER U 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER U 184 " --> pdb=" O ASP U 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER U 234 " --> pdb=" O ARG U 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU U 219 " --> pdb=" O GLU U 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU U 232 " --> pdb=" O LEU U 219 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASN U 221 " --> pdb=" O PRO U 230 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'U' and resid 112 through 114 Processing sheet with id=63, first strand: chain 'U' and resid 162 through 167 removed outlier: 3.943A pdb=" N TYR U 151 " --> pdb=" O SER U 167 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'U' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP U 329 " --> pdb=" O LYS U 290 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'U' and resid 310 through 312 Processing sheet with id=66, first strand: chain 'U' and resid 315 through 317 Processing sheet with id=67, first strand: chain 'W' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP W 177 " --> pdb=" O SER W 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER W 184 " --> pdb=" O ASP W 177 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER W 234 " --> pdb=" O ARG W 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU W 219 " --> pdb=" O GLU W 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU W 232 " --> pdb=" O LEU W 219 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASN W 221 " --> pdb=" O PRO W 230 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'W' and resid 112 through 114 Processing sheet with id=69, first strand: chain 'W' and resid 162 through 167 removed outlier: 3.942A pdb=" N TYR W 151 " --> pdb=" O SER W 167 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'W' and resid 285 through 290 removed outlier: 3.863A pdb=" N ASP W 329 " --> pdb=" O LYS W 290 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'W' and resid 310 through 312 Processing sheet with id=72, first strand: chain 'W' and resid 315 through 317 2304 hydrogen bonds defined for protein. 6552 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: 14.70 Time building geometry restraints manager: 10.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15712 1.34 - 1.45: 5700 1.45 - 1.57: 26192 1.57 - 1.69: 0 1.69 - 1.80: 264 Bond restraints: 47868 Sorted by residual: bond pdb=" N ASN K 16 " pdb=" CA ASN K 16 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.33e+00 bond pdb=" N ASN Q 16 " pdb=" CA ASN Q 16 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.33e+00 bond pdb=" N ASN W 16 " pdb=" CA ASN W 16 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.33e+00 bond pdb=" N ASN E 16 " pdb=" CA ASN E 16 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.33e+00 bond pdb=" N ASN O 16 " pdb=" CA ASN O 16 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.32e+00 ... (remaining 47863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 56692 1.10 - 2.20: 6568 2.20 - 3.29: 996 3.29 - 4.39: 232 4.39 - 5.49: 12 Bond angle restraints: 64500 Sorted by residual: angle pdb=" N HIS U 92 " pdb=" CA HIS U 92 " pdb=" C HIS U 92 " ideal model delta sigma weight residual 113.38 116.47 -3.09 1.23e+00 6.61e-01 6.32e+00 angle pdb=" N HIS C 92 " pdb=" CA HIS C 92 " pdb=" C HIS C 92 " ideal model delta sigma weight residual 113.38 116.47 -3.09 1.23e+00 6.61e-01 6.32e+00 angle pdb=" N HIS O 92 " pdb=" CA HIS O 92 " pdb=" C HIS O 92 " ideal model delta sigma weight residual 113.38 116.47 -3.09 1.23e+00 6.61e-01 6.32e+00 angle pdb=" N HIS I 92 " pdb=" CA HIS I 92 " pdb=" C HIS I 92 " ideal model delta sigma weight residual 113.38 116.47 -3.09 1.23e+00 6.61e-01 6.32e+00 angle pdb=" N HIS S 92 " pdb=" CA HIS S 92 " pdb=" C HIS S 92 " ideal model delta sigma weight residual 113.38 116.46 -3.08 1.23e+00 6.61e-01 6.29e+00 ... (remaining 64495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 26796 17.68 - 35.36: 1944 35.36 - 53.04: 312 53.04 - 70.72: 84 70.72 - 88.40: 48 Dihedral angle restraints: 29184 sinusoidal: 12204 harmonic: 16980 Sorted by residual: dihedral pdb=" CA ILE W 444 " pdb=" C ILE W 444 " pdb=" N ASP W 445 " pdb=" CA ASP W 445 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ILE E 444 " pdb=" C ILE E 444 " pdb=" N ASP E 445 " pdb=" CA ASP E 445 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ILE Q 444 " pdb=" C ILE Q 444 " pdb=" N ASP Q 445 " pdb=" CA ASP Q 445 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 29181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3490 0.031 - 0.061: 2232 0.061 - 0.092: 828 0.092 - 0.123: 350 0.123 - 0.153: 72 Chirality restraints: 6972 Sorted by residual: chirality pdb=" CA ILE W 175 " pdb=" N ILE W 175 " pdb=" C ILE W 175 " pdb=" CB ILE W 175 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE Q 175 " pdb=" N ILE Q 175 " pdb=" C ILE Q 175 " pdb=" CB ILE Q 175 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE E 175 " pdb=" N ILE E 175 " pdb=" C ILE E 175 " pdb=" CB ILE E 175 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 6969 not shown) Planarity restraints: 8484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS W 388 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C LYS W 388 " 0.055 2.00e-02 2.50e+03 pdb=" O LYS W 388 " -0.020 2.00e-02 2.50e+03 pdb=" N THR W 389 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 388 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C LYS Q 388 " 0.055 2.00e-02 2.50e+03 pdb=" O LYS Q 388 " -0.020 2.00e-02 2.50e+03 pdb=" N THR Q 389 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 388 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" C LYS A 388 " 0.054 2.00e-02 2.50e+03 pdb=" O LYS A 388 " -0.020 2.00e-02 2.50e+03 pdb=" N THR A 389 " -0.018 2.00e-02 2.50e+03 ... (remaining 8481 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 18452 2.88 - 3.39: 44860 3.39 - 3.89: 75120 3.89 - 4.40: 89024 4.40 - 4.90: 148088 Nonbonded interactions: 375544 Sorted by model distance: nonbonded pdb=" OG SER O 145 " pdb=" OD2 ASP O 257 " model vdw 2.377 3.040 nonbonded pdb=" OG SER I 145 " pdb=" OD2 ASP I 257 " model vdw 2.377 3.040 nonbonded pdb=" OG SER U 145 " pdb=" OD2 ASP U 257 " model vdw 2.377 3.040 nonbonded pdb=" OG SER C 145 " pdb=" OD2 ASP C 257 " model vdw 2.377 3.040 nonbonded pdb=" OG SER E 145 " pdb=" OD2 ASP E 257 " model vdw 2.378 3.040 ... (remaining 375539 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: 0.30 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.360 Check model and map are aligned: 0.270 Set scattering table: 0.320 Process input model: 66.510 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.200 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:1.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 47868 Z= 0.392 Angle : 0.752 5.491 64500 Z= 0.449 Chirality : 0.046 0.153 6972 Planarity : 0.010 0.087 8484 Dihedral : 13.426 88.398 18288 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -1.87 (0.09), residues: 5688 helix: -1.40 (0.08), residues: 2388 sheet: -0.02 (0.16), residues: 1020 loop : -1.47 (0.10), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 238 PHE 0.023 0.004 PHE S 173 TYR 0.039 0.004 TYR E 66 ARG 0.015 0.003 ARG W 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 4.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 ARG cc_start: 0.5030 (tpt170) cc_final: 0.3085 (ptp-110) REVERT: C 154 MET cc_start: 0.8744 (ttm) cc_final: 0.8285 (mtp) REVERT: C 279 MET cc_start: 0.8950 (mmm) cc_final: 0.8729 (mmm) REVERT: C 320 GLU cc_start: 0.7402 (pt0) cc_final: 0.7180 (tm-30) REVERT: E 239 SER cc_start: 0.8583 (m) cc_final: 0.8377 (p) REVERT: E 279 MET cc_start: 0.8878 (mmm) cc_final: 0.8578 (mmt) REVERT: E 355 MET cc_start: 0.9009 (ttp) cc_final: 0.8584 (ttm) REVERT: I 80 ARG cc_start: 0.5031 (tpt170) cc_final: 0.3089 (ptp-110) REVERT: I 154 MET cc_start: 0.8743 (ttm) cc_final: 0.8284 (mtp) REVERT: I 279 MET cc_start: 0.8952 (mmm) cc_final: 0.8730 (mmm) REVERT: I 320 GLU cc_start: 0.7403 (pt0) cc_final: 0.7177 (tm-30) REVERT: K 239 SER cc_start: 0.8583 (m) cc_final: 0.8375 (p) REVERT: K 279 MET cc_start: 0.8878 (mmm) cc_final: 0.8578 (mmt) REVERT: K 355 MET cc_start: 0.9007 (ttp) cc_final: 0.8587 (ttm) REVERT: O 80 ARG cc_start: 0.5027 (tpt170) cc_final: 0.3087 (ptp-110) REVERT: O 154 MET cc_start: 0.8743 (ttm) cc_final: 0.8283 (mtp) REVERT: O 279 MET cc_start: 0.8950 (mmm) cc_final: 0.8725 (mmm) REVERT: O 320 GLU cc_start: 0.7403 (pt0) cc_final: 0.7179 (tm-30) REVERT: Q 239 SER cc_start: 0.8586 (m) cc_final: 0.8381 (p) REVERT: Q 279 MET cc_start: 0.8878 (mmm) cc_final: 0.8578 (mmt) REVERT: Q 355 MET cc_start: 0.9015 (ttp) cc_final: 0.8584 (ttm) REVERT: U 80 ARG cc_start: 0.5027 (tpt170) cc_final: 0.3085 (ptp-110) REVERT: U 154 MET cc_start: 0.8746 (ttm) cc_final: 0.8284 (mtp) REVERT: U 279 MET cc_start: 0.8948 (mmm) cc_final: 0.8724 (mmm) REVERT: U 320 GLU cc_start: 0.7402 (pt0) cc_final: 0.7179 (tm-30) REVERT: W 239 SER cc_start: 0.8585 (m) cc_final: 0.8378 (p) REVERT: W 279 MET cc_start: 0.8880 (mmm) cc_final: 0.8574 (mmt) REVERT: W 355 MET cc_start: 0.9018 (ttp) cc_final: 0.8581 (ttm) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.6187 time to fit residues: 409.8663 Evaluate side-chains 216 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 476 optimal weight: 6.9990 chunk 427 optimal weight: 4.9990 chunk 237 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 442 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 329 optimal weight: 0.5980 chunk 512 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 40 GLN A 73 ASN A 354 HIS C 26 ASN C 73 ASN E 26 ASN E 73 ASN E 354 HIS G 26 ASN G 40 GLN G 73 ASN G 354 HIS I 26 ASN K 26 ASN K 73 ASN K 354 HIS M 26 ASN M 40 GLN M 73 ASN M 354 HIS O 26 ASN O 73 ASN Q 26 ASN Q 354 HIS S 26 ASN S 40 GLN S 73 ASN S 354 HIS U 26 ASN U 73 ASN W 26 ASN W 73 ASN W 354 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.066414 restraints weight = 115983.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.068181 restraints weight = 72683.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.069282 restraints weight = 55241.878| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 47868 Z= 0.231 Angle : 0.552 7.404 64500 Z= 0.310 Chirality : 0.042 0.141 6972 Planarity : 0.004 0.041 8484 Dihedral : 5.105 28.892 6444 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.38 % Allowed : 4.86 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.11), residues: 5688 helix: 0.84 (0.10), residues: 2508 sheet: -0.07 (0.15), residues: 1116 loop : -0.80 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 238 PHE 0.018 0.002 PHE U 173 TYR 0.017 0.002 TYR W 66 ARG 0.004 0.000 ARG I 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 4.204 Fit side-chains REVERT: C 85 MET cc_start: 0.6122 (pmm) cc_final: 0.5562 (pmm) REVERT: C 93 ASP cc_start: 0.7900 (t0) cc_final: 0.7642 (t0) REVERT: C 320 GLU cc_start: 0.7568 (pt0) cc_final: 0.7163 (tm-30) REVERT: I 85 MET cc_start: 0.6114 (pmm) cc_final: 0.5568 (pmm) REVERT: I 93 ASP cc_start: 0.7898 (t0) cc_final: 0.7640 (t0) REVERT: I 320 GLU cc_start: 0.7578 (pt0) cc_final: 0.7164 (tm-30) REVERT: O 85 MET cc_start: 0.6108 (pmm) cc_final: 0.5550 (pmm) REVERT: O 93 ASP cc_start: 0.7895 (t0) cc_final: 0.7636 (t0) REVERT: O 320 GLU cc_start: 0.7571 (pt0) cc_final: 0.7167 (tm-30) REVERT: U 85 MET cc_start: 0.6101 (pmm) cc_final: 0.5545 (pmm) REVERT: U 93 ASP cc_start: 0.7906 (t0) cc_final: 0.7639 (t0) REVERT: U 320 GLU cc_start: 0.7569 (pt0) cc_final: 0.7164 (tm-30) outliers start: 20 outliers final: 12 residues processed: 284 average time/residue: 0.5065 time to fit residues: 234.4948 Evaluate side-chains 220 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 4.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain V residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 300 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 435 optimal weight: 7.9990 chunk 512 optimal weight: 5.9990 chunk 427 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 393 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 407 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 418 ASN C 354 HIS G 303 GLN I 73 ASN I 354 HIS K 303 GLN M 303 GLN O 354 HIS Q 73 ASN Q 303 GLN S 303 GLN S 418 ASN U 354 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.078161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.062217 restraints weight = 116868.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.064093 restraints weight = 67032.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.065275 restraints weight = 48437.696| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 47868 Z= 0.407 Angle : 0.609 9.491 64500 Z= 0.333 Chirality : 0.045 0.146 6972 Planarity : 0.004 0.044 8484 Dihedral : 5.127 29.648 6444 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.04 % Allowed : 5.57 % Favored : 93.39 % 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: 0.10 (0.11), residues: 5688 helix: 1.11 (0.11), residues: 2508 sheet: -0.36 (0.14), residues: 1116 loop : -0.89 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 238 PHE 0.017 0.002 PHE A 173 TYR 0.021 0.002 TYR W 66 ARG 0.005 0.001 ARG V 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 4.139 Fit side-chains REVERT: B 103 LYS cc_start: 0.8596 (tppt) cc_final: 0.8178 (ttpp) REVERT: C 320 GLU cc_start: 0.7538 (pt0) cc_final: 0.7203 (tm-30) REVERT: D 103 LYS cc_start: 0.8636 (tppt) cc_final: 0.7998 (ttpp) REVERT: E 279 MET cc_start: 0.8968 (tpp) cc_final: 0.8512 (mmt) REVERT: H 103 LYS cc_start: 0.8599 (tppt) cc_final: 0.8177 (ttpp) REVERT: I 320 GLU cc_start: 0.7541 (pt0) cc_final: 0.7205 (tm-30) REVERT: J 103 LYS cc_start: 0.8638 (tppt) cc_final: 0.7996 (ttpp) REVERT: K 279 MET cc_start: 0.8972 (tpp) cc_final: 0.8516 (mmt) REVERT: N 103 LYS cc_start: 0.8600 (tppt) cc_final: 0.8180 (ttpp) REVERT: O 320 GLU cc_start: 0.7538 (pt0) cc_final: 0.7208 (tm-30) REVERT: P 103 LYS cc_start: 0.8640 (tppt) cc_final: 0.7998 (ttpp) REVERT: Q 279 MET cc_start: 0.8965 (tpp) cc_final: 0.8510 (mmt) REVERT: T 103 LYS cc_start: 0.8600 (tppt) cc_final: 0.8181 (ttpp) REVERT: U 320 GLU cc_start: 0.7538 (pt0) cc_final: 0.7204 (tm-30) REVERT: V 103 LYS cc_start: 0.8629 (tppt) cc_final: 0.7995 (ttpp) REVERT: W 279 MET cc_start: 0.8964 (tpp) cc_final: 0.8509 (mmt) outliers start: 54 outliers final: 48 residues processed: 252 average time/residue: 0.5382 time to fit residues: 218.4932 Evaluate side-chains 246 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 362 MET Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain S residue 362 MET Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 196 ILE Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 324 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 391 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 516 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 460 optimal weight: 0.9990 chunk 357 optimal weight: 2.9990 chunk 521 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 418 ASN M 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.079984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.064283 restraints weight = 115431.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.066197 restraints weight = 65350.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.067423 restraints weight = 46863.481| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 47868 Z= 0.214 Angle : 0.483 7.710 64500 Z= 0.268 Chirality : 0.040 0.140 6972 Planarity : 0.003 0.041 8484 Dihedral : 4.666 26.218 6444 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.46 % Allowed : 6.07 % Favored : 92.47 % 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: 0.56 (0.11), residues: 5688 helix: 1.70 (0.11), residues: 2520 sheet: -0.35 (0.14), residues: 1116 loop : -0.83 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS U 238 PHE 0.023 0.002 PHE M 173 TYR 0.017 0.001 TYR M 84 ARG 0.005 0.000 ARG J 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 222 time to evaluate : 4.195 Fit side-chains REVERT: A 53 MET cc_start: 0.8619 (mtm) cc_final: 0.8276 (ttp) REVERT: C 93 ASP cc_start: 0.7865 (t0) cc_final: 0.7575 (t0) REVERT: C 320 GLU cc_start: 0.7485 (pt0) cc_final: 0.7123 (tm-30) REVERT: D 103 LYS cc_start: 0.8650 (tppt) cc_final: 0.8152 (ttpp) REVERT: E 279 MET cc_start: 0.8989 (tpp) cc_final: 0.8531 (mmt) REVERT: G 53 MET cc_start: 0.8623 (mtm) cc_final: 0.8278 (ttp) REVERT: I 93 ASP cc_start: 0.7865 (t0) cc_final: 0.7572 (t0) REVERT: I 320 GLU cc_start: 0.7502 (pt0) cc_final: 0.7127 (tm-30) REVERT: J 103 LYS cc_start: 0.8652 (tppt) cc_final: 0.8150 (ttpp) REVERT: K 279 MET cc_start: 0.8988 (tpp) cc_final: 0.8531 (mmt) REVERT: M 53 MET cc_start: 0.8613 (mtm) cc_final: 0.8272 (ttp) REVERT: O 93 ASP cc_start: 0.7869 (t0) cc_final: 0.7575 (t0) REVERT: O 320 GLU cc_start: 0.7496 (pt0) cc_final: 0.7129 (tm-30) REVERT: P 103 LYS cc_start: 0.8652 (tppt) cc_final: 0.8189 (ttpp) REVERT: Q 279 MET cc_start: 0.8985 (tpp) cc_final: 0.8525 (mmt) REVERT: S 53 MET cc_start: 0.8611 (mtm) cc_final: 0.8273 (ttp) REVERT: U 93 ASP cc_start: 0.7871 (t0) cc_final: 0.7577 (t0) REVERT: U 320 GLU cc_start: 0.7486 (pt0) cc_final: 0.7130 (tm-30) REVERT: V 103 LYS cc_start: 0.8648 (tppt) cc_final: 0.8188 (ttpp) REVERT: W 279 MET cc_start: 0.8986 (tpp) cc_final: 0.8527 (mmt) outliers start: 76 outliers final: 60 residues processed: 290 average time/residue: 0.5245 time to fit residues: 244.8068 Evaluate side-chains 264 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 469 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 409 optimal weight: 0.7980 chunk 543 optimal weight: 7.9990 chunk 550 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 452 optimal weight: 0.9980 chunk 228 optimal weight: 0.0870 chunk 423 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 HIS I 136 HIS O 136 HIS U 136 HIS W 303 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.063266 restraints weight = 115600.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.065181 restraints weight = 65584.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.066407 restraints weight = 47031.389| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 47868 Z= 0.281 Angle : 0.515 8.809 64500 Z= 0.282 Chirality : 0.041 0.133 6972 Planarity : 0.003 0.041 8484 Dihedral : 4.668 26.434 6444 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.50 % Allowed : 6.39 % Favored : 92.11 % 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: 0.58 (0.11), residues: 5688 helix: 1.80 (0.11), residues: 2520 sheet: -0.36 (0.15), residues: 1116 loop : -0.93 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 238 PHE 0.022 0.002 PHE M 173 TYR 0.018 0.002 TYR M 84 ARG 0.005 0.000 ARG V 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 212 time to evaluate : 4.144 Fit side-chains REVERT: A 53 MET cc_start: 0.8665 (mtm) cc_final: 0.8398 (ttp) REVERT: B 103 LYS cc_start: 0.8720 (tppt) cc_final: 0.8259 (ttpp) REVERT: C 320 GLU cc_start: 0.7490 (pt0) cc_final: 0.7117 (tm-30) REVERT: G 53 MET cc_start: 0.8669 (mtm) cc_final: 0.8397 (ttp) REVERT: H 103 LYS cc_start: 0.8721 (tppt) cc_final: 0.8258 (ttpp) REVERT: I 320 GLU cc_start: 0.7502 (pt0) cc_final: 0.7122 (tm-30) REVERT: M 53 MET cc_start: 0.8659 (mtm) cc_final: 0.8391 (ttp) REVERT: N 103 LYS cc_start: 0.8725 (tppt) cc_final: 0.8260 (ttpp) REVERT: O 320 GLU cc_start: 0.7496 (pt0) cc_final: 0.7123 (tm-30) REVERT: S 53 MET cc_start: 0.8667 (mtm) cc_final: 0.8398 (ttp) REVERT: T 103 LYS cc_start: 0.8720 (tppt) cc_final: 0.8258 (ttpp) REVERT: U 320 GLU cc_start: 0.7490 (pt0) cc_final: 0.7126 (tm-30) outliers start: 78 outliers final: 68 residues processed: 282 average time/residue: 0.5160 time to fit residues: 234.6225 Evaluate side-chains 266 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 198 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 263 THR Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 196 ILE Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 181 optimal weight: 0.0370 chunk 169 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 323 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 529 optimal weight: 4.9990 chunk 477 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 427 optimal weight: 3.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 HIS K 136 HIS Q 136 HIS W 136 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.079986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.064228 restraints weight = 115497.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.066155 restraints weight = 65327.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.067388 restraints weight = 46757.031| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 47868 Z= 0.211 Angle : 0.472 7.249 64500 Z= 0.261 Chirality : 0.039 0.136 6972 Planarity : 0.003 0.038 8484 Dihedral : 4.469 24.465 6444 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.42 % Allowed : 6.74 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.11), residues: 5688 helix: 2.01 (0.11), residues: 2520 sheet: -0.35 (0.15), residues: 1116 loop : -0.92 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 238 PHE 0.019 0.001 PHE M 173 TYR 0.017 0.001 TYR M 84 ARG 0.005 0.000 ARG J 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 211 time to evaluate : 4.185 Fit side-chains REVERT: A 53 MET cc_start: 0.8630 (mtm) cc_final: 0.8417 (ttp) REVERT: B 103 LYS cc_start: 0.8647 (tppt) cc_final: 0.8254 (ttpp) REVERT: C 93 ASP cc_start: 0.7867 (t0) cc_final: 0.7573 (t0) REVERT: C 320 GLU cc_start: 0.7463 (pt0) cc_final: 0.7106 (tm-30) REVERT: D 103 LYS cc_start: 0.8841 (tppt) cc_final: 0.8136 (ttpp) REVERT: F 103 LYS cc_start: 0.8634 (tppt) cc_final: 0.8330 (ttpp) REVERT: G 53 MET cc_start: 0.8632 (mtm) cc_final: 0.8417 (ttp) REVERT: H 103 LYS cc_start: 0.8647 (tppt) cc_final: 0.8256 (ttpp) REVERT: I 93 ASP cc_start: 0.7867 (t0) cc_final: 0.7578 (t0) REVERT: I 320 GLU cc_start: 0.7477 (pt0) cc_final: 0.7113 (tm-30) REVERT: J 103 LYS cc_start: 0.8841 (tppt) cc_final: 0.8138 (ttpp) REVERT: L 103 LYS cc_start: 0.8632 (tppt) cc_final: 0.8329 (ttpp) REVERT: M 53 MET cc_start: 0.8621 (mtm) cc_final: 0.8408 (ttp) REVERT: N 103 LYS cc_start: 0.8650 (tppt) cc_final: 0.8254 (ttpp) REVERT: O 93 ASP cc_start: 0.7868 (t0) cc_final: 0.7575 (t0) REVERT: O 320 GLU cc_start: 0.7474 (pt0) cc_final: 0.7115 (tm-30) REVERT: P 103 LYS cc_start: 0.8839 (tppt) cc_final: 0.8135 (ttpp) REVERT: Q 302 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8356 (mtmm) REVERT: S 53 MET cc_start: 0.8625 (mtm) cc_final: 0.8410 (ttp) REVERT: T 103 LYS cc_start: 0.8647 (tppt) cc_final: 0.8250 (ttpp) REVERT: U 93 ASP cc_start: 0.7876 (t0) cc_final: 0.7579 (t0) REVERT: U 320 GLU cc_start: 0.7461 (pt0) cc_final: 0.7113 (tm-30) REVERT: V 103 LYS cc_start: 0.8837 (tppt) cc_final: 0.8134 (ttpp) outliers start: 74 outliers final: 64 residues processed: 277 average time/residue: 0.5268 time to fit residues: 235.8615 Evaluate side-chains 261 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 197 time to evaluate : 4.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 263 THR Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 196 ILE Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 460 optimal weight: 5.9990 chunk 406 optimal weight: 3.9990 chunk 399 optimal weight: 5.9990 chunk 274 optimal weight: 6.9990 chunk 530 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 504 optimal weight: 3.9990 chunk 391 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.078443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.062534 restraints weight = 116143.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.064393 restraints weight = 66418.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.065613 restraints weight = 47839.548| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 47868 Z= 0.351 Angle : 0.545 8.958 64500 Z= 0.296 Chirality : 0.042 0.131 6972 Planarity : 0.004 0.037 8484 Dihedral : 4.709 26.716 6444 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.38 % Allowed : 7.12 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.11), residues: 5688 helix: 1.75 (0.11), residues: 2520 sheet: -0.32 (0.15), residues: 1104 loop : -1.08 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS U 238 PHE 0.022 0.002 PHE S 173 TYR 0.018 0.002 TYR A 84 ARG 0.005 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 197 time to evaluate : 4.255 Fit side-chains REVERT: A 53 MET cc_start: 0.8626 (mtm) cc_final: 0.8393 (ttp) REVERT: B 103 LYS cc_start: 0.8640 (tppt) cc_final: 0.8326 (ttpp) REVERT: C 320 GLU cc_start: 0.7502 (pt0) cc_final: 0.7125 (tm-30) REVERT: D 103 LYS cc_start: 0.8916 (tppt) cc_final: 0.8128 (ttpp) REVERT: F 103 LYS cc_start: 0.8577 (tppt) cc_final: 0.8297 (ttpp) REVERT: G 53 MET cc_start: 0.8627 (mtm) cc_final: 0.8394 (ttp) REVERT: H 103 LYS cc_start: 0.8643 (tppt) cc_final: 0.8327 (ttpp) REVERT: I 320 GLU cc_start: 0.7518 (pt0) cc_final: 0.7126 (tm-30) REVERT: J 103 LYS cc_start: 0.8918 (tppt) cc_final: 0.8125 (ttpp) REVERT: L 103 LYS cc_start: 0.8577 (tppt) cc_final: 0.8295 (ttpp) REVERT: M 53 MET cc_start: 0.8615 (mtm) cc_final: 0.8382 (ttp) REVERT: N 103 LYS cc_start: 0.8643 (tppt) cc_final: 0.8330 (ttpp) REVERT: O 320 GLU cc_start: 0.7508 (pt0) cc_final: 0.7128 (tm-30) REVERT: P 103 LYS cc_start: 0.8913 (tppt) cc_final: 0.8124 (ttpp) REVERT: S 53 MET cc_start: 0.8623 (mtm) cc_final: 0.8395 (ttp) REVERT: T 103 LYS cc_start: 0.8641 (tppt) cc_final: 0.8326 (ttpp) REVERT: U 320 GLU cc_start: 0.7511 (pt0) cc_final: 0.7127 (tm-30) REVERT: V 103 LYS cc_start: 0.8914 (tppt) cc_final: 0.8127 (ttpp) outliers start: 72 outliers final: 68 residues processed: 269 average time/residue: 0.5393 time to fit residues: 233.4554 Evaluate side-chains 260 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 192 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 263 THR Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 196 ILE Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 160 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 482 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 519 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 521 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.079045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.061958 restraints weight = 115915.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.063866 restraints weight = 66570.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.065054 restraints weight = 48329.496| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 47868 Z= 0.299 Angle : 0.512 8.489 64500 Z= 0.280 Chirality : 0.041 0.129 6972 Planarity : 0.003 0.037 8484 Dihedral : 4.598 26.273 6444 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.46 % Allowed : 6.85 % Favored : 91.69 % 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: 0.52 (0.11), residues: 5688 helix: 1.83 (0.11), residues: 2520 sheet: -0.38 (0.15), residues: 1104 loop : -1.10 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 238 PHE 0.020 0.002 PHE A 173 TYR 0.018 0.002 TYR A 84 ARG 0.006 0.000 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 192 time to evaluate : 4.236 Fit side-chains REVERT: B 103 LYS cc_start: 0.8649 (tppt) cc_final: 0.8306 (ttpp) REVERT: C 320 GLU cc_start: 0.7595 (pt0) cc_final: 0.7074 (tm-30) REVERT: D 103 LYS cc_start: 0.8869 (tppt) cc_final: 0.8036 (ttpp) REVERT: F 103 LYS cc_start: 0.8565 (tppt) cc_final: 0.8264 (ttpp) REVERT: H 103 LYS cc_start: 0.8648 (tppt) cc_final: 0.8307 (ttpp) REVERT: I 320 GLU cc_start: 0.7599 (pt0) cc_final: 0.7080 (tm-30) REVERT: J 103 LYS cc_start: 0.8871 (tppt) cc_final: 0.8037 (ttpp) REVERT: L 103 LYS cc_start: 0.8571 (tppt) cc_final: 0.8265 (ttpp) REVERT: N 103 LYS cc_start: 0.8653 (tppt) cc_final: 0.8307 (ttpp) REVERT: O 320 GLU cc_start: 0.7596 (pt0) cc_final: 0.7075 (tm-30) REVERT: P 103 LYS cc_start: 0.8869 (tppt) cc_final: 0.8031 (ttpp) REVERT: T 103 LYS cc_start: 0.8650 (tppt) cc_final: 0.8302 (ttpp) REVERT: U 320 GLU cc_start: 0.7598 (pt0) cc_final: 0.7072 (tm-30) REVERT: V 103 LYS cc_start: 0.8872 (tppt) cc_final: 0.8034 (ttpp) outliers start: 76 outliers final: 76 residues processed: 268 average time/residue: 0.5202 time to fit residues: 225.6097 Evaluate side-chains 268 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 192 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 339 VAL Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 339 VAL Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 263 THR Chi-restraints excluded: chain U residue 339 VAL Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 196 ILE Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 118 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 326 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 461 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 294 ASN K 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.079357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.062233 restraints weight = 115827.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.064160 restraints weight = 66616.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.065355 restraints weight = 48250.563| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 47868 Z= 0.259 Angle : 0.490 8.225 64500 Z= 0.269 Chirality : 0.040 0.132 6972 Planarity : 0.003 0.037 8484 Dihedral : 4.519 25.665 6444 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.46 % Allowed : 6.93 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.11), residues: 5688 helix: 1.90 (0.11), residues: 2520 sheet: -0.38 (0.15), residues: 1104 loop : -1.09 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS U 238 PHE 0.019 0.002 PHE M 173 TYR 0.019 0.001 TYR G 84 ARG 0.007 0.000 ARG T 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 192 time to evaluate : 4.234 Fit side-chains REVERT: B 103 LYS cc_start: 0.8626 (tppt) cc_final: 0.8310 (ttpp) REVERT: C 320 GLU cc_start: 0.7583 (pt0) cc_final: 0.7065 (tm-30) REVERT: D 103 LYS cc_start: 0.8849 (tppt) cc_final: 0.7999 (ttpp) REVERT: F 103 LYS cc_start: 0.8614 (tppt) cc_final: 0.8374 (ttpp) REVERT: H 103 LYS cc_start: 0.8626 (tppt) cc_final: 0.8312 (ttpp) REVERT: I 320 GLU cc_start: 0.7586 (pt0) cc_final: 0.7071 (tm-30) REVERT: J 103 LYS cc_start: 0.8850 (tppt) cc_final: 0.8000 (ttpp) REVERT: L 103 LYS cc_start: 0.8619 (tppt) cc_final: 0.8377 (ttpp) REVERT: N 103 LYS cc_start: 0.8631 (tppt) cc_final: 0.8310 (ttpp) REVERT: O 320 GLU cc_start: 0.7590 (pt0) cc_final: 0.7067 (tm-30) REVERT: P 103 LYS cc_start: 0.8848 (tppt) cc_final: 0.7992 (ttpp) REVERT: T 103 LYS cc_start: 0.8629 (tppt) cc_final: 0.8307 (ttpp) REVERT: U 320 GLU cc_start: 0.7590 (pt0) cc_final: 0.7063 (tm-30) REVERT: V 103 LYS cc_start: 0.8850 (tppt) cc_final: 0.8000 (ttpp) outliers start: 76 outliers final: 76 residues processed: 268 average time/residue: 0.5272 time to fit residues: 228.8990 Evaluate side-chains 268 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 192 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 339 VAL Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 339 VAL Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 263 THR Chi-restraints excluded: chain U residue 339 VAL Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 196 ILE Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 113 optimal weight: 6.9990 chunk 423 optimal weight: 0.3980 chunk 323 optimal weight: 4.9990 chunk 513 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 242 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 141 optimal weight: 0.0770 chunk 374 optimal weight: 0.9990 chunk 373 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 294 ASN W 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.067599 restraints weight = 116974.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.069394 restraints weight = 74201.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.070467 restraints weight = 56876.544| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 47868 Z= 0.119 Angle : 0.421 7.846 64500 Z= 0.233 Chirality : 0.037 0.144 6972 Planarity : 0.003 0.037 8484 Dihedral : 4.091 20.421 6444 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.92 % Allowed : 7.47 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.11), residues: 5688 helix: 2.21 (0.11), residues: 2520 sheet: -0.32 (0.15), residues: 1104 loop : -0.92 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 238 PHE 0.016 0.001 PHE O 173 TYR 0.018 0.001 TYR G 84 ARG 0.008 0.000 ARG B 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 4.272 Fit side-chains REVERT: B 103 LYS cc_start: 0.8639 (tppt) cc_final: 0.8319 (ttpp) REVERT: C 85 MET cc_start: 0.5975 (pmm) cc_final: 0.5569 (pmm) REVERT: C 93 ASP cc_start: 0.7885 (t0) cc_final: 0.7565 (t0) REVERT: C 320 GLU cc_start: 0.7526 (pt0) cc_final: 0.7314 (tm-30) REVERT: D 103 LYS cc_start: 0.8983 (tppt) cc_final: 0.8276 (ttpp) REVERT: E 302 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8233 (mtmm) REVERT: F 103 LYS cc_start: 0.8662 (tppt) cc_final: 0.8388 (ttpp) REVERT: H 103 LYS cc_start: 0.8640 (tppt) cc_final: 0.8319 (ttpp) REVERT: I 85 MET cc_start: 0.5980 (pmm) cc_final: 0.5569 (pmm) REVERT: I 93 ASP cc_start: 0.7882 (t0) cc_final: 0.7541 (t0) REVERT: I 320 GLU cc_start: 0.7531 (pt0) cc_final: 0.7321 (tm-30) REVERT: J 103 LYS cc_start: 0.8985 (tppt) cc_final: 0.8277 (ttpp) REVERT: K 302 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8235 (mtmm) REVERT: L 103 LYS cc_start: 0.8660 (tppt) cc_final: 0.8390 (ttpp) REVERT: N 103 LYS cc_start: 0.8639 (tppt) cc_final: 0.8320 (ttpp) REVERT: O 85 MET cc_start: 0.5959 (pmm) cc_final: 0.5550 (pmm) REVERT: O 93 ASP cc_start: 0.7884 (t0) cc_final: 0.7539 (t0) REVERT: O 320 GLU cc_start: 0.7536 (pt0) cc_final: 0.7321 (tm-30) REVERT: P 103 LYS cc_start: 0.8985 (tppt) cc_final: 0.8275 (ttpp) REVERT: R 103 LYS cc_start: 0.8752 (tppt) cc_final: 0.8263 (ttpp) REVERT: T 103 LYS cc_start: 0.8638 (tppt) cc_final: 0.8319 (ttpp) REVERT: U 85 MET cc_start: 0.5953 (pmm) cc_final: 0.5558 (pmm) REVERT: U 93 ASP cc_start: 0.7891 (t0) cc_final: 0.7541 (t0) REVERT: U 320 GLU cc_start: 0.7527 (pt0) cc_final: 0.7318 (tm-30) REVERT: V 103 LYS cc_start: 0.8982 (tppt) cc_final: 0.8281 (ttpp) REVERT: W 302 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8234 (mtmm) REVERT: X 103 LYS cc_start: 0.8754 (tppt) cc_final: 0.8263 (ttpp) outliers start: 48 outliers final: 44 residues processed: 267 average time/residue: 0.5579 time to fit residues: 239.0763 Evaluate side-chains 251 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 263 THR Chi-restraints excluded: chain U residue 339 VAL Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 196 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 225 optimal weight: 3.9990 chunk 329 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 396 optimal weight: 0.0770 chunk 58 optimal weight: 0.9990 chunk 431 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 543 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.063904 restraints weight = 114613.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.065824 restraints weight = 66135.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.067012 restraints weight = 48007.144| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 47868 Z= 0.180 Angle : 0.448 7.151 64500 Z= 0.244 Chirality : 0.038 0.131 6972 Planarity : 0.003 0.037 8484 Dihedral : 4.150 20.057 6444 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.92 % Allowed : 7.78 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.11), residues: 5688 helix: 2.26 (0.11), residues: 2520 sheet: -0.31 (0.15), residues: 1104 loop : -0.90 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS U 354 PHE 0.017 0.001 PHE O 173 TYR 0.019 0.001 TYR A 84 ARG 0.007 0.000 ARG N 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8339.01 seconds wall clock time: 148 minutes 14.49 seconds (8894.49 seconds total)