Starting phenix.real_space_refine on Mon Jan 13 19:04:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vd8_43145/01_2025/8vd8_43145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vd8_43145/01_2025/8vd8_43145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vd8_43145/01_2025/8vd8_43145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vd8_43145/01_2025/8vd8_43145.map" model { file = "/net/cci-nas-00/data/ceres_data/8vd8_43145/01_2025/8vd8_43145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vd8_43145/01_2025/8vd8_43145.cif" } resolution = 3.2 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= -0.001 sd= 0.007 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 30036 2.51 5 N 8112 2.21 5 O 9600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 47880 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: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} 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: 9.34, per 1000 atoms: 0.20 Number of scatterers: 47880 At special positions: 0 Unit cell: (179.55, 179.55, 154.28, 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 9600 8.00 N 8112 7.00 C 30036 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: 8.44 Conformation dependent library (CDL) restraints added in 4.3 seconds 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11088 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 72 sheets defined 50.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL A 27 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG A 59 " --> pdb=" O TYR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) 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: 3.940A pdb=" N THR A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR A 423 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL C 27 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG C 59 " --> pdb=" O TYR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) 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: 3.939A pdb=" N THR C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 4.183A pdb=" N LYS C 304 " --> pdb=" O ARG C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 358 Processing helix chain 'C' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET C 376 " --> pdb=" O SER C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR C 423 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 479 removed outlier: 3.758A pdb=" N VAL C 469 " --> pdb=" O PRO C 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'E' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL E 27 " --> pdb=" O GLU E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 40 Processing helix chain 'E' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG E 59 " --> pdb=" O TYR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 132 removed outlier: 3.943A pdb=" N ALA E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) 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: 3.940A pdb=" N THR E 275 " --> pdb=" O ALA E 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS E 304 " --> pdb=" O ARG E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 358 Processing helix chain 'E' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET E 376 " --> pdb=" O SER E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR E 389 " --> pdb=" O GLN E 385 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR E 423 " --> pdb=" O ASP E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU E 458 " --> pdb=" O THR E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL E 469 " --> pdb=" O PRO E 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS E 470 " --> pdb=" O GLU E 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 98 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL G 27 " --> pdb=" O GLU G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 40 Processing helix chain 'G' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER G 46 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG G 59 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR G 97 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA G 123 " --> pdb=" O ASP G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP G 143 " --> pdb=" O SER G 139 " (cutoff:3.500A) 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: 3.940A pdb=" N THR G 275 " --> pdb=" O ALA G 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 282 " --> pdb=" O TYR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS G 304 " --> pdb=" O ARG G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 358 Processing helix chain 'G' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET G 376 " --> pdb=" O SER G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR G 389 " --> pdb=" O GLN G 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY G 397 " --> pdb=" O LEU G 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG G 400 " --> pdb=" O LYS G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR G 423 " --> pdb=" O ASP G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU G 458 " --> pdb=" O THR G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL G 469 " --> pdb=" O PRO G 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS G 470 " --> pdb=" O GLU G 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 98 Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL I 27 " --> pdb=" O GLU I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 40 Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER I 46 " --> pdb=" O VAL I 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS I 47 " --> pdb=" O ASN I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG I 59 " --> pdb=" O TYR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP I 143 " --> pdb=" O SER I 139 " (cutoff:3.500A) 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: 3.939A pdb=" N THR I 275 " --> pdb=" O ALA I 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 282 " --> pdb=" O TYR I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 305 removed outlier: 4.183A pdb=" N LYS I 304 " --> pdb=" O ARG I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 358 Processing helix chain 'I' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET I 376 " --> pdb=" O SER I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR I 389 " --> pdb=" O GLN I 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY I 397 " --> pdb=" O LEU I 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG I 400 " --> pdb=" O LYS I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR I 423 " --> pdb=" O ASP I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 446 Processing helix chain 'I' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU I 458 " --> pdb=" O THR I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 479 removed outlier: 3.758A pdb=" N VAL I 469 " --> pdb=" O PRO I 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS I 470 " --> pdb=" O GLU I 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 98 Processing helix chain 'K' and resid 16 through 21 Processing helix chain 'K' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL K 27 " --> pdb=" O GLU K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 40 Processing helix chain 'K' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER K 46 " --> pdb=" O VAL K 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG K 59 " --> pdb=" O TYR K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR K 97 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 132 removed outlier: 3.943A pdb=" N ALA K 123 " --> pdb=" O ASP K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP K 143 " --> pdb=" O SER K 139 " (cutoff:3.500A) 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: 3.940A pdb=" N THR K 275 " --> pdb=" O ALA K 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU K 282 " --> pdb=" O TYR K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS K 304 " --> pdb=" O ARG K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 358 Processing helix chain 'K' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET K 376 " --> pdb=" O SER K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR K 389 " --> pdb=" O GLN K 385 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY K 397 " --> pdb=" O LEU K 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 400 " --> pdb=" O LYS K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR K 423 " --> pdb=" O ASP K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 446 Processing helix chain 'K' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU K 458 " --> pdb=" O THR K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL K 469 " --> pdb=" O PRO K 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS K 470 " --> pdb=" O GLU K 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL M 27 " --> pdb=" O GLU M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 40 Processing helix chain 'M' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER M 46 " --> pdb=" O VAL M 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG M 59 " --> pdb=" O TYR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR M 97 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA M 123 " --> pdb=" O ASP M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP M 143 " --> pdb=" O SER M 139 " (cutoff:3.500A) 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: 3.940A pdb=" N THR M 275 " --> pdb=" O ALA M 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU M 282 " --> pdb=" O TYR M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS M 304 " --> pdb=" O ARG M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 358 Processing helix chain 'M' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET M 376 " --> pdb=" O SER M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR M 389 " --> pdb=" O GLN M 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY M 397 " --> pdb=" O LEU M 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG M 400 " --> pdb=" O LYS M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR M 423 " --> pdb=" O ASP M 420 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 446 Processing helix chain 'M' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU M 458 " --> pdb=" O THR M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL M 469 " --> pdb=" O PRO M 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS M 470 " --> pdb=" O GLU M 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 98 Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL O 27 " --> pdb=" O GLU O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 40 Processing helix chain 'O' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER O 46 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS O 47 " --> pdb=" O ASN O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG O 59 " --> pdb=" O TYR O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL O 75 " --> pdb=" O THR O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR O 97 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA O 123 " --> pdb=" O ASP O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP O 143 " --> pdb=" O SER O 139 " (cutoff:3.500A) 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: 3.939A pdb=" N THR O 275 " --> pdb=" O ALA O 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU O 282 " --> pdb=" O TYR O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 305 removed outlier: 4.183A pdb=" N LYS O 304 " --> pdb=" O ARG O 301 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 358 Processing helix chain 'O' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET O 376 " --> pdb=" O SER O 372 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR O 389 " --> pdb=" O GLN O 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY O 397 " --> pdb=" O LEU O 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG O 400 " --> pdb=" O LYS O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR O 423 " --> pdb=" O ASP O 420 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 446 Processing helix chain 'O' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU O 458 " --> pdb=" O THR O 454 " (cutoff:3.500A) Processing helix chain 'O' and resid 464 through 479 removed outlier: 3.758A pdb=" N VAL O 469 " --> pdb=" O PRO O 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS O 470 " --> pdb=" O GLU O 466 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 98 Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL Q 27 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 40 Processing helix chain 'Q' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER Q 46 " --> pdb=" O VAL Q 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG Q 59 " --> pdb=" O TYR Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL Q 75 " --> pdb=" O THR Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR Q 97 " --> pdb=" O ASP Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 132 removed outlier: 3.943A pdb=" N ALA Q 123 " --> pdb=" O ASP Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP Q 143 " --> pdb=" O SER Q 139 " (cutoff:3.500A) 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: 3.940A pdb=" N THR Q 275 " --> pdb=" O ALA Q 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU Q 282 " --> pdb=" O TYR Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS Q 304 " --> pdb=" O ARG Q 301 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 358 Processing helix chain 'Q' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET Q 376 " --> pdb=" O SER Q 372 " (cutoff:3.500A) Processing helix chain 'Q' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR Q 389 " --> pdb=" O GLN Q 385 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY Q 397 " --> pdb=" O LEU Q 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Q 400 " --> pdb=" O LYS Q 396 " (cutoff:3.500A) Processing helix chain 'Q' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR Q 423 " --> pdb=" O ASP Q 420 " (cutoff:3.500A) Processing helix chain 'Q' and resid 435 through 446 Processing helix chain 'Q' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU Q 458 " --> pdb=" O THR Q 454 " (cutoff:3.500A) Processing helix chain 'Q' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL Q 469 " --> pdb=" O PRO Q 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS Q 470 " --> pdb=" O GLU Q 466 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 98 Processing helix chain 'S' and resid 16 through 21 Processing helix chain 'S' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL S 27 " --> pdb=" O GLU S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 40 Processing helix chain 'S' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER S 46 " --> pdb=" O VAL S 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS S 47 " --> pdb=" O ASN S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG S 59 " --> pdb=" O TYR S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL S 75 " --> pdb=" O THR S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR S 97 " --> pdb=" O ASP S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA S 123 " --> pdb=" O ASP S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP S 143 " --> pdb=" O SER S 139 " (cutoff:3.500A) 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: 3.940A pdb=" N THR S 275 " --> pdb=" O ALA S 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU S 282 " --> pdb=" O TYR S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS S 304 " --> pdb=" O ARG S 301 " (cutoff:3.500A) Processing helix chain 'S' and resid 338 through 358 Processing helix chain 'S' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET S 376 " --> pdb=" O SER S 372 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR S 389 " --> pdb=" O GLN S 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY S 397 " --> pdb=" O LEU S 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG S 400 " --> pdb=" O LYS S 396 " (cutoff:3.500A) Processing helix chain 'S' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR S 423 " --> pdb=" O ASP S 420 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 446 Processing helix chain 'S' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU S 458 " --> pdb=" O THR S 454 " (cutoff:3.500A) Processing helix chain 'S' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL S 469 " --> pdb=" O PRO S 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS S 470 " --> pdb=" O GLU S 466 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 98 Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL U 27 " --> pdb=" O GLU U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 40 Processing helix chain 'U' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER U 46 " --> pdb=" O VAL U 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS U 47 " --> pdb=" O ASN U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG U 59 " --> pdb=" O TYR U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL U 75 " --> pdb=" O THR U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR U 97 " --> pdb=" O ASP U 93 " (cutoff:3.500A) Processing helix chain 'U' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA U 123 " --> pdb=" O ASP U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP U 143 " --> pdb=" O SER U 139 " (cutoff:3.500A) 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: 3.939A pdb=" N THR U 275 " --> pdb=" O ALA U 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU U 282 " --> pdb=" O TYR U 278 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 305 removed outlier: 4.183A pdb=" N LYS U 304 " --> pdb=" O ARG U 301 " (cutoff:3.500A) Processing helix chain 'U' and resid 338 through 358 Processing helix chain 'U' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET U 376 " --> pdb=" O SER U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR U 389 " --> pdb=" O GLN U 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY U 397 " --> pdb=" O LEU U 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG U 400 " --> pdb=" O LYS U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR U 423 " --> pdb=" O ASP U 420 " (cutoff:3.500A) Processing helix chain 'U' and resid 435 through 446 Processing helix chain 'U' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU U 458 " --> pdb=" O THR U 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 464 through 479 removed outlier: 3.758A pdb=" N VAL U 469 " --> pdb=" O PRO U 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS U 470 " --> pdb=" O GLU U 466 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 98 Processing helix chain 'W' and resid 16 through 21 Processing helix chain 'W' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL W 27 " --> pdb=" O GLU W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 34 through 40 Processing helix chain 'W' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER W 46 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS W 47 " --> pdb=" O ASN W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG W 59 " --> pdb=" O TYR W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL W 75 " --> pdb=" O THR W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR W 97 " --> pdb=" O ASP W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 removed outlier: 3.943A pdb=" N ALA W 123 " --> pdb=" O ASP W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP W 143 " --> pdb=" O SER W 139 " (cutoff:3.500A) 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: 3.940A pdb=" N THR W 275 " --> pdb=" O ALA W 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU W 282 " --> pdb=" O TYR W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS W 304 " --> pdb=" O ARG W 301 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 358 Processing helix chain 'W' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET W 376 " --> pdb=" O SER W 372 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR W 389 " --> pdb=" O GLN W 385 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY W 397 " --> pdb=" O LEU W 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG W 400 " --> pdb=" O LYS W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR W 423 " --> pdb=" O ASP W 420 " (cutoff:3.500A) Processing helix chain 'W' and resid 435 through 446 Processing helix chain 'W' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU W 458 " --> pdb=" O THR W 454 " (cutoff:3.500A) Processing helix chain 'W' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL W 469 " --> pdb=" O PRO W 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS W 470 " --> pdb=" O GLU W 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 92 through 98 Processing sheet with id=1, first strand: chain 'A' and resid 29 through 31 removed outlier: 7.053A pdb=" N TYR A 29 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP A 177 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 184 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER A 234 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LEU A 219 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU A 232 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 11.211A 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: 4.029A 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 291 Processing sheet with id=5, first strand: chain 'A' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN A 294 " --> pdb=" O ALA B 107 " (cutoff:3.500A) 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 29 through 31 removed outlier: 7.054A pdb=" N TYR C 29 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP C 177 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER C 184 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER C 234 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU C 219 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU C 232 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 11.210A 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: 4.028A 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 291 Processing sheet with id=11, first strand: chain 'C' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN C 294 " --> pdb=" O ALA D 107 " (cutoff:3.500A) 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 29 through 31 removed outlier: 7.053A pdb=" N TYR E 29 " --> pdb=" O TYR E 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP E 177 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER E 184 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER E 234 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU E 219 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU E 232 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 11.210A 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: 4.029A 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 291 Processing sheet with id=17, first strand: chain 'E' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN E 294 " --> pdb=" O ALA F 107 " (cutoff:3.500A) 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 29 through 31 removed outlier: 7.053A pdb=" N TYR G 29 " --> pdb=" O TYR G 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP G 177 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER G 184 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER G 234 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LEU G 219 " --> pdb=" O GLU G 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU G 232 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 11.211A 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: 4.029A 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 291 Processing sheet with id=23, first strand: chain 'G' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN G 294 " --> pdb=" O ALA H 107 " (cutoff:3.500A) 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 29 through 31 removed outlier: 7.054A pdb=" N TYR I 29 " --> pdb=" O TYR I 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP I 177 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER I 184 " --> pdb=" O ASP I 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER I 234 " --> pdb=" O ARG I 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU I 219 " --> pdb=" O GLU I 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU I 232 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 11.210A 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: 4.028A 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 291 Processing sheet with id=29, first strand: chain 'I' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN I 294 " --> pdb=" O ALA J 107 " (cutoff:3.500A) 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 29 through 31 removed outlier: 7.053A pdb=" N TYR K 29 " --> pdb=" O TYR K 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP K 177 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER K 184 " --> pdb=" O ASP K 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER K 234 " --> pdb=" O ARG K 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU K 219 " --> pdb=" O GLU K 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU K 232 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 11.210A 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: 4.029A 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 291 Processing sheet with id=35, first strand: chain 'K' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN K 294 " --> pdb=" O ALA L 107 " (cutoff:3.500A) 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 29 through 31 removed outlier: 7.053A pdb=" N TYR M 29 " --> pdb=" O TYR M 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP M 177 " --> pdb=" O SER M 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER M 184 " --> pdb=" O ASP M 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER M 234 " --> pdb=" O ARG M 217 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LEU M 219 " --> pdb=" O GLU M 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU M 232 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 11.211A 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: 4.029A 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 291 Processing sheet with id=41, first strand: chain 'M' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN M 294 " --> pdb=" O ALA N 107 " (cutoff:3.500A) 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 29 through 31 removed outlier: 7.054A pdb=" N TYR O 29 " --> pdb=" O TYR O 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP O 177 " --> pdb=" O SER O 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER O 184 " --> pdb=" O ASP O 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER O 234 " --> pdb=" O ARG O 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU O 219 " --> pdb=" O GLU O 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU O 232 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 11.210A 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: 4.028A 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 291 Processing sheet with id=47, first strand: chain 'O' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN O 294 " --> pdb=" O ALA P 107 " (cutoff:3.500A) 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 29 through 31 removed outlier: 7.053A pdb=" N TYR Q 29 " --> pdb=" O TYR Q 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP Q 177 " --> pdb=" O SER Q 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER Q 184 " --> pdb=" O ASP Q 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER Q 234 " --> pdb=" O ARG Q 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU Q 219 " --> pdb=" O GLU Q 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU Q 232 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 11.210A 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: 4.029A 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 291 Processing sheet with id=53, first strand: chain 'Q' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN Q 294 " --> pdb=" O ALA R 107 " (cutoff:3.500A) 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 29 through 31 removed outlier: 7.053A pdb=" N TYR S 29 " --> pdb=" O TYR S 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP S 177 " --> pdb=" O SER S 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER S 184 " --> pdb=" O ASP S 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER S 234 " --> pdb=" O ARG S 217 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LEU S 219 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU S 232 " --> pdb=" O LEU S 219 " (cutoff:3.500A) removed outlier: 11.211A 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: 4.029A 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 291 Processing sheet with id=59, first strand: chain 'S' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN S 294 " --> pdb=" O ALA T 107 " (cutoff:3.500A) 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 29 through 31 removed outlier: 7.054A pdb=" N TYR U 29 " --> pdb=" O TYR U 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP U 177 " --> pdb=" O SER U 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER U 184 " --> pdb=" O ASP U 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER U 234 " --> pdb=" O ARG U 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU U 219 " --> pdb=" O GLU U 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU U 232 " --> pdb=" O LEU U 219 " (cutoff:3.500A) removed outlier: 11.210A 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: 4.028A 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 291 Processing sheet with id=65, first strand: chain 'U' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN U 294 " --> pdb=" O ALA V 107 " (cutoff:3.500A) 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 29 through 31 removed outlier: 7.053A pdb=" N TYR W 29 " --> pdb=" O TYR W 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP W 177 " --> pdb=" O SER W 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER W 184 " --> pdb=" O ASP W 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER W 234 " --> pdb=" O ARG W 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU W 219 " --> pdb=" O GLU W 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU W 232 " --> pdb=" O LEU W 219 " (cutoff:3.500A) removed outlier: 11.210A 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: 4.029A 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 291 Processing sheet with id=71, first strand: chain 'W' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN W 294 " --> pdb=" O ALA X 107 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'W' and resid 315 through 317 2328 hydrogen bonds defined for protein. 6624 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: 14.71 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: 15746 1.34 - 1.45: 6690 1.45 - 1.57: 26008 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 48708 Sorted by residual: bond pdb=" N ASN K 16 " pdb=" CA ASN K 16 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N ASN Q 16 " pdb=" CA ASN Q 16 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N ASN W 16 " pdb=" CA ASN W 16 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N ASN E 16 " pdb=" CA ASN E 16 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N ASN S 16 " pdb=" CA ASN S 16 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.50e+00 ... (remaining 48703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 52064 0.86 - 1.73: 10026 1.73 - 2.59: 2652 2.59 - 3.46: 706 3.46 - 4.32: 204 Bond angle restraints: 65652 Sorted by residual: angle pdb=" C TYR K 334 " pdb=" N LYS K 335 " pdb=" CA LYS K 335 " ideal model delta sigma weight residual 120.71 124.89 -4.18 1.42e+00 4.96e-01 8.66e+00 angle pdb=" C TYR E 334 " pdb=" N LYS E 335 " pdb=" CA LYS E 335 " ideal model delta sigma weight residual 120.71 124.89 -4.18 1.42e+00 4.96e-01 8.66e+00 angle pdb=" C TYR Q 334 " pdb=" N LYS Q 335 " pdb=" CA LYS Q 335 " ideal model delta sigma weight residual 120.71 124.89 -4.18 1.42e+00 4.96e-01 8.66e+00 angle pdb=" C TYR W 334 " pdb=" N LYS W 335 " pdb=" CA LYS W 335 " ideal model delta sigma weight residual 120.71 124.89 -4.18 1.42e+00 4.96e-01 8.66e+00 angle pdb=" C TYR I 334 " pdb=" N LYS I 335 " pdb=" CA LYS I 335 " ideal model delta sigma weight residual 120.71 124.89 -4.18 1.42e+00 4.96e-01 8.66e+00 ... (remaining 65647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 27152 17.67 - 35.35: 2020 35.35 - 53.02: 272 53.02 - 70.69: 148 70.69 - 88.37: 60 Dihedral angle restraints: 29652 sinusoidal: 12372 harmonic: 17280 Sorted by residual: dihedral pdb=" CA LEU E 39 " pdb=" C LEU E 39 " pdb=" N GLN E 40 " pdb=" CA GLN E 40 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LEU W 39 " pdb=" C LEU W 39 " pdb=" N GLN W 40 " pdb=" CA GLN W 40 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LEU K 39 " pdb=" C LEU K 39 " pdb=" N GLN K 40 " pdb=" CA GLN K 40 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 29649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4554 0.042 - 0.085: 1922 0.085 - 0.127: 552 0.127 - 0.170: 52 0.170 - 0.212: 12 Chirality restraints: 7092 Sorted by residual: chirality pdb=" CA HIS I 92 " pdb=" N HIS I 92 " pdb=" C HIS I 92 " pdb=" CB HIS I 92 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA HIS C 92 " pdb=" N HIS C 92 " pdb=" C HIS C 92 " pdb=" CB HIS C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA HIS U 92 " pdb=" N HIS U 92 " pdb=" C HIS U 92 " pdb=" CB HIS U 92 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 7089 not shown) Planarity restraints: 8640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 58 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PRO C 58 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO C 58 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG C 59 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO I 58 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PRO I 58 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO I 58 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG I 59 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO U 58 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PRO U 58 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO U 58 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG U 59 " 0.020 2.00e-02 2.50e+03 ... (remaining 8637 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 3178 2.72 - 3.27: 48538 3.27 - 3.81: 75094 3.81 - 4.36: 99434 4.36 - 4.90: 165488 Nonbonded interactions: 391732 Sorted by model distance: nonbonded pdb=" NZ LYS K 70 " pdb=" OD1 ASP M 23 " model vdw 2.181 3.120 nonbonded pdb=" NZ LYS E 70 " pdb=" OD1 ASP G 23 " model vdw 2.181 3.120 nonbonded pdb=" OD1 ASP A 23 " pdb=" NZ LYS W 70 " model vdw 2.181 3.120 nonbonded pdb=" NZ LYS Q 70 " pdb=" OD1 ASP S 23 " model vdw 2.181 3.120 nonbonded pdb=" NZ LYS M 70 " pdb=" OD1 ASP O 23 " model vdw 2.181 3.120 ... (remaining 391727 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: 0.29 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.270 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 64.260 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.007 0.055 48708 Z= 0.479 Angle : 0.813 4.322 65652 Z= 0.485 Chirality : 0.048 0.212 7092 Planarity : 0.010 0.103 8640 Dihedral : 13.728 88.365 18564 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: -0.87 (0.09), residues: 5784 helix: -0.75 (0.09), residues: 2424 sheet: 0.58 (0.14), residues: 1044 loop : -0.75 (0.11), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS U 238 PHE 0.028 0.004 PHE I 367 TYR 0.040 0.005 TYR C 332 ARG 0.016 0.002 ARG Q 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1128 time to evaluate : 4.107 Fit side-chains REVERT: A 27 VAL cc_start: 0.8888 (t) cc_final: 0.8624 (m) REVERT: A 85 MET cc_start: 0.3220 (mtm) cc_final: 0.3016 (mtp) REVERT: A 403 LYS cc_start: 0.8006 (tppt) cc_final: 0.7772 (mmtt) REVERT: A 422 ASN cc_start: 0.7779 (m-40) cc_final: 0.7538 (m-40) REVERT: B 94 ASN cc_start: 0.7137 (t0) cc_final: 0.6628 (m110) REVERT: B 101 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7291 (mtp180) REVERT: C 47 LYS cc_start: 0.7600 (mttt) cc_final: 0.7294 (mmtt) REVERT: C 85 MET cc_start: 0.3328 (mtm) cc_final: 0.2633 (mtp) REVERT: C 213 HIS cc_start: 0.8536 (m170) cc_final: 0.8221 (m-70) REVERT: C 216 TYR cc_start: 0.8850 (m-80) cc_final: 0.8329 (m-80) REVERT: C 217 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.7386 (mtt-85) REVERT: C 280 SER cc_start: 0.9005 (t) cc_final: 0.8767 (m) REVERT: C 371 GLN cc_start: 0.5537 (mt0) cc_final: 0.4249 (mt0) REVERT: C 386 ARG cc_start: 0.8742 (mtt180) cc_final: 0.8366 (mtt180) REVERT: C 396 LYS cc_start: 0.9179 (ttmm) cc_final: 0.8933 (ttmt) REVERT: C 403 LYS cc_start: 0.7847 (tppt) cc_final: 0.7618 (mmtt) REVERT: C 425 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.7009 (mtm180) REVERT: D 94 ASN cc_start: 0.7476 (t0) cc_final: 0.6876 (m110) REVERT: D 101 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7222 (mmm160) REVERT: E 154 MET cc_start: 0.8986 (ttm) cc_final: 0.8509 (mtp) REVERT: E 208 ASP cc_start: 0.7698 (m-30) cc_final: 0.7426 (m-30) REVERT: E 217 ARG cc_start: 0.7910 (mtt-85) cc_final: 0.7362 (mtm-85) REVERT: E 280 SER cc_start: 0.8919 (t) cc_final: 0.8655 (p) REVERT: E 386 ARG cc_start: 0.8915 (mtt180) cc_final: 0.8572 (mtt90) REVERT: E 471 LYS cc_start: 0.7399 (mttt) cc_final: 0.6884 (tttt) REVERT: E 476 GLU cc_start: 0.6492 (tp30) cc_final: 0.6139 (mm-30) REVERT: F 101 ARG cc_start: 0.7499 (mtp180) cc_final: 0.6123 (mtp180) REVERT: G 27 VAL cc_start: 0.8887 (t) cc_final: 0.8628 (m) REVERT: G 85 MET cc_start: 0.3220 (mtm) cc_final: 0.3014 (mtp) REVERT: G 403 LYS cc_start: 0.8009 (tppt) cc_final: 0.7772 (mmtt) REVERT: G 422 ASN cc_start: 0.7778 (m-40) cc_final: 0.7536 (m-40) REVERT: H 94 ASN cc_start: 0.7136 (t0) cc_final: 0.6627 (m110) REVERT: H 101 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7291 (mtp180) REVERT: I 47 LYS cc_start: 0.7596 (mttt) cc_final: 0.7291 (mmtt) REVERT: I 85 MET cc_start: 0.3333 (mtm) cc_final: 0.2641 (mtp) REVERT: I 213 HIS cc_start: 0.8537 (m170) cc_final: 0.8223 (m-70) REVERT: I 216 TYR cc_start: 0.8849 (m-80) cc_final: 0.8329 (m-80) REVERT: I 217 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.7388 (mtt-85) REVERT: I 280 SER cc_start: 0.9010 (t) cc_final: 0.8768 (m) REVERT: I 371 GLN cc_start: 0.5536 (mt0) cc_final: 0.4254 (mt0) REVERT: I 386 ARG cc_start: 0.8743 (mtt180) cc_final: 0.8367 (mtt180) REVERT: I 396 LYS cc_start: 0.9179 (ttmm) cc_final: 0.8933 (ttmt) REVERT: I 403 LYS cc_start: 0.7843 (tppt) cc_final: 0.7616 (mmtt) REVERT: I 425 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.7011 (mtm180) REVERT: J 94 ASN cc_start: 0.7475 (t0) cc_final: 0.6876 (m110) REVERT: J 101 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7224 (mmm160) REVERT: K 154 MET cc_start: 0.8985 (ttm) cc_final: 0.8509 (mtp) REVERT: K 208 ASP cc_start: 0.7693 (m-30) cc_final: 0.7424 (m-30) REVERT: K 217 ARG cc_start: 0.7911 (mtt-85) cc_final: 0.7363 (mtm-85) REVERT: K 280 SER cc_start: 0.8921 (t) cc_final: 0.8657 (p) REVERT: K 386 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8570 (mtt90) REVERT: K 471 LYS cc_start: 0.7394 (mttt) cc_final: 0.6877 (tttt) REVERT: K 476 GLU cc_start: 0.6498 (tp30) cc_final: 0.6140 (mm-30) REVERT: L 101 ARG cc_start: 0.7497 (mtp180) cc_final: 0.6123 (mtp180) REVERT: M 27 VAL cc_start: 0.8884 (t) cc_final: 0.8622 (m) REVERT: M 85 MET cc_start: 0.3210 (mtm) cc_final: 0.3005 (mtp) REVERT: M 403 LYS cc_start: 0.8005 (tppt) cc_final: 0.7770 (mmtt) REVERT: M 422 ASN cc_start: 0.7779 (m-40) cc_final: 0.7537 (m-40) REVERT: N 94 ASN cc_start: 0.7138 (t0) cc_final: 0.6627 (m110) REVERT: N 101 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7292 (mtp180) REVERT: O 47 LYS cc_start: 0.7597 (mttt) cc_final: 0.7294 (mmtt) REVERT: O 85 MET cc_start: 0.3334 (mtm) cc_final: 0.2643 (mtp) REVERT: O 213 HIS cc_start: 0.8538 (m170) cc_final: 0.8226 (m-70) REVERT: O 216 TYR cc_start: 0.8845 (m-80) cc_final: 0.8324 (m-80) REVERT: O 217 ARG cc_start: 0.7885 (mtt-85) cc_final: 0.7388 (mtt-85) REVERT: O 280 SER cc_start: 0.9016 (t) cc_final: 0.8775 (m) REVERT: O 371 GLN cc_start: 0.5540 (mt0) cc_final: 0.4251 (mt0) REVERT: O 386 ARG cc_start: 0.8745 (mtt180) cc_final: 0.8369 (mtt180) REVERT: O 396 LYS cc_start: 0.9176 (ttmm) cc_final: 0.8929 (ttmt) REVERT: O 403 LYS cc_start: 0.7840 (tppt) cc_final: 0.7612 (mmtt) REVERT: O 425 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.7010 (mtm180) REVERT: P 94 ASN cc_start: 0.7477 (t0) cc_final: 0.6880 (m110) REVERT: P 101 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7222 (mmm160) REVERT: Q 154 MET cc_start: 0.8984 (ttm) cc_final: 0.8511 (mtp) REVERT: Q 208 ASP cc_start: 0.7694 (m-30) cc_final: 0.7423 (m-30) REVERT: Q 217 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7365 (mtm-85) REVERT: Q 280 SER cc_start: 0.8924 (t) cc_final: 0.8660 (p) REVERT: Q 386 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8570 (mtt90) REVERT: Q 471 LYS cc_start: 0.7393 (mttt) cc_final: 0.6879 (tttt) REVERT: Q 476 GLU cc_start: 0.6501 (tp30) cc_final: 0.6142 (mm-30) REVERT: R 101 ARG cc_start: 0.7504 (mtp180) cc_final: 0.6129 (mtp180) REVERT: S 27 VAL cc_start: 0.8888 (t) cc_final: 0.8624 (m) REVERT: S 85 MET cc_start: 0.3217 (mtm) cc_final: 0.3012 (mtp) REVERT: S 403 LYS cc_start: 0.8004 (tppt) cc_final: 0.7769 (mmtt) REVERT: S 422 ASN cc_start: 0.7777 (m-40) cc_final: 0.7537 (m-40) REVERT: T 94 ASN cc_start: 0.7139 (t0) cc_final: 0.6625 (m110) REVERT: T 101 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7291 (mtp180) REVERT: U 47 LYS cc_start: 0.7598 (mttt) cc_final: 0.7293 (mmtt) REVERT: U 85 MET cc_start: 0.3329 (mtm) cc_final: 0.2636 (mtp) REVERT: U 213 HIS cc_start: 0.8537 (m170) cc_final: 0.8223 (m-70) REVERT: U 216 TYR cc_start: 0.8846 (m-80) cc_final: 0.8325 (m-80) REVERT: U 217 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.7383 (mtt-85) REVERT: U 280 SER cc_start: 0.9016 (t) cc_final: 0.8773 (m) REVERT: U 371 GLN cc_start: 0.5543 (mt0) cc_final: 0.4259 (mt0) REVERT: U 386 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8370 (mtt180) REVERT: U 396 LYS cc_start: 0.9178 (ttmm) cc_final: 0.8930 (ttmt) REVERT: U 403 LYS cc_start: 0.7843 (tppt) cc_final: 0.7616 (mmtt) REVERT: U 425 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.7006 (mtm180) REVERT: V 94 ASN cc_start: 0.7476 (t0) cc_final: 0.6875 (m110) REVERT: V 101 ARG cc_start: 0.7645 (mtp180) cc_final: 0.7223 (mmm160) REVERT: W 154 MET cc_start: 0.8983 (ttm) cc_final: 0.8508 (mtp) REVERT: W 208 ASP cc_start: 0.7697 (m-30) cc_final: 0.7424 (m-30) REVERT: W 217 ARG cc_start: 0.7913 (mtt-85) cc_final: 0.7365 (mtm-85) REVERT: W 280 SER cc_start: 0.8925 (t) cc_final: 0.8659 (p) REVERT: W 386 ARG cc_start: 0.8912 (mtt180) cc_final: 0.8571 (mtt90) REVERT: W 471 LYS cc_start: 0.7392 (mttt) cc_final: 0.6878 (tttt) REVERT: W 476 GLU cc_start: 0.6496 (tp30) cc_final: 0.6143 (mm-30) REVERT: X 101 ARG cc_start: 0.7501 (mtp180) cc_final: 0.6127 (mtp180) outliers start: 0 outliers final: 0 residues processed: 1128 average time/residue: 0.5959 time to fit residues: 1018.2382 Evaluate side-chains 662 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 662 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 10.0000 chunk 436 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 451 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 336 optimal weight: 6.9990 chunk 523 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 354 HIS C 224 ASN C 270 ASN C 354 HIS C 358 ASN C 452 GLN E 224 ASN E 270 ASN E 354 HIS E 358 ASN G 270 ASN G 354 HIS I 224 ASN I 270 ASN I 354 HIS I 358 ASN I 452 GLN K 224 ASN K 270 ASN K 354 HIS K 358 ASN M 270 ASN M 354 HIS O 224 ASN O 270 ASN O 354 HIS O 358 ASN O 452 GLN Q 224 ASN Q 270 ASN Q 354 HIS Q 358 ASN S 41 ASN S 270 ASN S 354 HIS U 224 ASN U 270 ASN U 354 HIS U 358 ASN U 452 GLN W 224 ASN W 270 ASN W 354 HIS W 358 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.143059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.112980 restraints weight = 57332.653| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.68 r_work: 0.2999 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 48708 Z= 0.396 Angle : 0.645 6.133 65652 Z= 0.353 Chirality : 0.044 0.179 7092 Planarity : 0.005 0.041 8640 Dihedral : 5.458 21.487 6552 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.21 % Allowed : 7.52 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 5784 helix: 0.62 (0.10), residues: 2484 sheet: 0.74 (0.14), residues: 1116 loop : -0.59 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS W 354 PHE 0.014 0.002 PHE O 367 TYR 0.017 0.002 TYR G 345 ARG 0.003 0.001 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 748 time to evaluate : 4.169 Fit side-chains REVERT: A 27 VAL cc_start: 0.8609 (t) cc_final: 0.8307 (m) REVERT: A 76 GLU cc_start: 0.7070 (tt0) cc_final: 0.6687 (pt0) REVERT: A 247 GLU cc_start: 0.8183 (tt0) cc_final: 0.7943 (tt0) REVERT: A 295 LEU cc_start: 0.7675 (tp) cc_final: 0.7359 (tp) REVERT: A 403 LYS cc_start: 0.8484 (tppt) cc_final: 0.8198 (mmtt) REVERT: A 422 ASN cc_start: 0.7955 (m-40) cc_final: 0.7611 (m-40) REVERT: B 101 ARG cc_start: 0.8000 (mtp180) cc_final: 0.6958 (mpt-90) REVERT: C 85 MET cc_start: 0.3236 (mtm) cc_final: 0.2797 (mtp) REVERT: C 213 HIS cc_start: 0.8625 (m170) cc_final: 0.8354 (m-70) REVERT: C 217 ARG cc_start: 0.7910 (mtt-85) cc_final: 0.7703 (mtt180) REVERT: C 362 MET cc_start: 0.7608 (mmp) cc_final: 0.7299 (mmm) REVERT: C 374 GLU cc_start: 0.6425 (pt0) cc_final: 0.6221 (mt-10) REVERT: C 386 ARG cc_start: 0.8662 (mtt180) cc_final: 0.8354 (mtt180) REVERT: C 403 LYS cc_start: 0.8617 (tppt) cc_final: 0.8152 (mmtt) REVERT: C 425 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7140 (mtm180) REVERT: C 471 LYS cc_start: 0.7101 (mttt) cc_final: 0.6874 (mttt) REVERT: D 94 ASN cc_start: 0.7319 (t0) cc_final: 0.6596 (m110) REVERT: D 101 ARG cc_start: 0.7786 (mtp180) cc_final: 0.7516 (mmm160) REVERT: D 103 LYS cc_start: 0.8942 (tptp) cc_final: 0.8696 (tttp) REVERT: E 89 ARG cc_start: 0.6904 (mtm180) cc_final: 0.6697 (mtt180) REVERT: E 322 ARG cc_start: 0.7838 (mtp180) cc_final: 0.7500 (ttm110) REVERT: E 386 ARG cc_start: 0.8953 (mtt180) cc_final: 0.8543 (mtt90) REVERT: E 471 LYS cc_start: 0.7520 (mttt) cc_final: 0.6654 (tttt) REVERT: G 27 VAL cc_start: 0.8609 (t) cc_final: 0.8305 (m) REVERT: G 76 GLU cc_start: 0.7058 (tt0) cc_final: 0.6685 (pt0) REVERT: G 247 GLU cc_start: 0.8182 (tt0) cc_final: 0.7943 (tt0) REVERT: G 295 LEU cc_start: 0.7679 (tp) cc_final: 0.7363 (tp) REVERT: G 403 LYS cc_start: 0.8478 (tppt) cc_final: 0.8191 (mmtt) REVERT: G 422 ASN cc_start: 0.7960 (m-40) cc_final: 0.7613 (m-40) REVERT: H 101 ARG cc_start: 0.8000 (mtp180) cc_final: 0.6969 (mpt-90) REVERT: I 85 MET cc_start: 0.3242 (mtm) cc_final: 0.2822 (mtp) REVERT: I 213 HIS cc_start: 0.8616 (m170) cc_final: 0.8346 (m-70) REVERT: I 217 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7709 (mtt180) REVERT: I 362 MET cc_start: 0.7622 (mmp) cc_final: 0.7317 (mmm) REVERT: I 374 GLU cc_start: 0.6415 (pt0) cc_final: 0.6210 (mt-10) REVERT: I 386 ARG cc_start: 0.8660 (mtt180) cc_final: 0.8352 (mtt180) REVERT: I 403 LYS cc_start: 0.8609 (tppt) cc_final: 0.8151 (mmtt) REVERT: I 425 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7139 (mtm180) REVERT: I 471 LYS cc_start: 0.7104 (mttt) cc_final: 0.6876 (mttt) REVERT: J 94 ASN cc_start: 0.7307 (t0) cc_final: 0.6591 (m110) REVERT: J 101 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7524 (mmm160) REVERT: J 103 LYS cc_start: 0.8943 (tptp) cc_final: 0.8698 (tttp) REVERT: K 322 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7528 (ttm110) REVERT: K 386 ARG cc_start: 0.8953 (mtt180) cc_final: 0.8542 (mtt90) REVERT: K 471 LYS cc_start: 0.7504 (mttt) cc_final: 0.6640 (tttt) REVERT: M 27 VAL cc_start: 0.8609 (t) cc_final: 0.8304 (m) REVERT: M 76 GLU cc_start: 0.7058 (tt0) cc_final: 0.6673 (pt0) REVERT: M 247 GLU cc_start: 0.8187 (tt0) cc_final: 0.7949 (tt0) REVERT: M 295 LEU cc_start: 0.7685 (tp) cc_final: 0.7369 (tp) REVERT: M 403 LYS cc_start: 0.8475 (tppt) cc_final: 0.8184 (mmtt) REVERT: M 422 ASN cc_start: 0.7953 (m-40) cc_final: 0.7605 (m-40) REVERT: N 101 ARG cc_start: 0.7993 (mtp180) cc_final: 0.6974 (mpt-90) REVERT: O 85 MET cc_start: 0.3224 (mtm) cc_final: 0.2800 (mtp) REVERT: O 213 HIS cc_start: 0.8613 (m170) cc_final: 0.8343 (m-70) REVERT: O 217 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7722 (mtt180) REVERT: O 362 MET cc_start: 0.7617 (mmp) cc_final: 0.7308 (mmm) REVERT: O 374 GLU cc_start: 0.6412 (pt0) cc_final: 0.6201 (mt-10) REVERT: O 386 ARG cc_start: 0.8668 (mtt180) cc_final: 0.8361 (mtt180) REVERT: O 403 LYS cc_start: 0.8613 (tppt) cc_final: 0.8149 (mmtt) REVERT: O 425 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7133 (mtm180) REVERT: O 471 LYS cc_start: 0.7085 (mttt) cc_final: 0.6854 (mttt) REVERT: P 94 ASN cc_start: 0.7325 (t0) cc_final: 0.6590 (m110) REVERT: P 101 ARG cc_start: 0.7798 (mtp180) cc_final: 0.7526 (mmm160) REVERT: P 103 LYS cc_start: 0.8944 (tptp) cc_final: 0.8703 (tttp) REVERT: Q 322 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7521 (ttm110) REVERT: Q 386 ARG cc_start: 0.8947 (mtt180) cc_final: 0.8533 (mtt90) REVERT: Q 471 LYS cc_start: 0.7518 (mttt) cc_final: 0.6653 (tttt) REVERT: S 27 VAL cc_start: 0.8607 (t) cc_final: 0.8302 (m) REVERT: S 76 GLU cc_start: 0.7067 (tt0) cc_final: 0.6677 (pt0) REVERT: S 247 GLU cc_start: 0.8194 (tt0) cc_final: 0.7954 (tt0) REVERT: S 295 LEU cc_start: 0.7682 (tp) cc_final: 0.7368 (tp) REVERT: S 403 LYS cc_start: 0.8476 (tppt) cc_final: 0.8186 (mmtt) REVERT: S 422 ASN cc_start: 0.7960 (m-40) cc_final: 0.7608 (m-40) REVERT: T 101 ARG cc_start: 0.7988 (mtp180) cc_final: 0.6956 (mpt-90) REVERT: U 85 MET cc_start: 0.3228 (mtm) cc_final: 0.2795 (mtp) REVERT: U 213 HIS cc_start: 0.8622 (m170) cc_final: 0.8352 (m-70) REVERT: U 217 ARG cc_start: 0.7926 (mtt-85) cc_final: 0.7720 (mtt180) REVERT: U 362 MET cc_start: 0.7600 (mmp) cc_final: 0.7294 (mmm) REVERT: U 374 GLU cc_start: 0.6411 (pt0) cc_final: 0.6204 (mt-10) REVERT: U 386 ARG cc_start: 0.8666 (mtt180) cc_final: 0.8359 (mtt180) REVERT: U 403 LYS cc_start: 0.8614 (tppt) cc_final: 0.8148 (mmtt) REVERT: U 425 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7142 (mtm180) REVERT: U 471 LYS cc_start: 0.7099 (mttt) cc_final: 0.6867 (mttt) REVERT: V 94 ASN cc_start: 0.7325 (t0) cc_final: 0.6581 (m110) REVERT: V 101 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7524 (mmm160) REVERT: V 103 LYS cc_start: 0.8943 (tptp) cc_final: 0.8700 (tttp) REVERT: W 89 ARG cc_start: 0.6893 (mtm180) cc_final: 0.6684 (mtt180) REVERT: W 322 ARG cc_start: 0.7837 (mtp180) cc_final: 0.7499 (ttm110) REVERT: W 386 ARG cc_start: 0.8952 (mtt180) cc_final: 0.8539 (mtt90) REVERT: W 471 LYS cc_start: 0.7522 (mttt) cc_final: 0.6659 (tttt) outliers start: 64 outliers final: 40 residues processed: 792 average time/residue: 0.5689 time to fit residues: 695.1172 Evaluate side-chains 696 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 656 time to evaluate : 4.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain O residue 191 LEU Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 38 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 431 optimal weight: 7.9990 chunk 552 optimal weight: 3.9990 chunk 327 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 564 optimal weight: 4.9990 chunk 308 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 429 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN C 452 GLN E 303 GLN ** G 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 GLN I 452 GLN K 303 GLN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 340 GLN O 452 GLN Q 303 GLN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 340 GLN U 452 GLN W 303 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.146809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118738 restraints weight = 57376.627| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.55 r_work: 0.3105 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 48708 Z= 0.313 Angle : 0.560 4.536 65652 Z= 0.306 Chirality : 0.041 0.172 7092 Planarity : 0.004 0.041 8640 Dihedral : 5.003 18.959 6552 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.36 % Allowed : 9.45 % Favored : 88.19 % 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: 0.38 (0.11), residues: 5784 helix: 0.97 (0.10), residues: 2508 sheet: 0.61 (0.14), residues: 1116 loop : -0.72 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS S 92 PHE 0.012 0.002 PHE Q 173 TYR 0.016 0.002 TYR A 345 ARG 0.003 0.000 ARG I 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 702 time to evaluate : 4.397 Fit side-chains REVERT: A 27 VAL cc_start: 0.8555 (t) cc_final: 0.8242 (m) REVERT: A 295 LEU cc_start: 0.7880 (tp) cc_final: 0.7510 (tp) REVERT: A 403 LYS cc_start: 0.8532 (tppt) cc_final: 0.8203 (mmtt) REVERT: A 422 ASN cc_start: 0.8037 (m-40) cc_final: 0.7612 (m-40) REVERT: B 95 TYR cc_start: 0.6550 (OUTLIER) cc_final: 0.5510 (t80) REVERT: C 118 LYS cc_start: 0.7407 (mttt) cc_final: 0.6978 (ptmt) REVERT: C 213 HIS cc_start: 0.8663 (m170) cc_final: 0.8428 (m-70) REVERT: C 217 ARG cc_start: 0.7831 (mtt-85) cc_final: 0.7585 (mtt90) REVERT: C 362 MET cc_start: 0.7818 (mmp) cc_final: 0.7517 (mmm) REVERT: C 386 ARG cc_start: 0.8830 (mtt180) cc_final: 0.8569 (mtt90) REVERT: C 403 LYS cc_start: 0.8662 (tppt) cc_final: 0.8205 (mmtt) REVERT: C 425 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7124 (mtm180) REVERT: D 95 TYR cc_start: 0.6197 (OUTLIER) cc_final: 0.5369 (t80) REVERT: D 101 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7208 (tpt170) REVERT: D 103 LYS cc_start: 0.8931 (tptp) cc_final: 0.8693 (tttp) REVERT: E 198 LYS cc_start: 0.5520 (OUTLIER) cc_final: 0.5146 (pptt) REVERT: E 471 LYS cc_start: 0.7511 (mttt) cc_final: 0.6693 (tttt) REVERT: F 95 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.5545 (t80) REVERT: G 27 VAL cc_start: 0.8551 (t) cc_final: 0.8242 (m) REVERT: G 295 LEU cc_start: 0.7880 (tp) cc_final: 0.7513 (tp) REVERT: G 403 LYS cc_start: 0.8517 (tppt) cc_final: 0.8186 (mmtt) REVERT: G 422 ASN cc_start: 0.8047 (m-40) cc_final: 0.7622 (m-40) REVERT: H 95 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.5511 (t80) REVERT: I 118 LYS cc_start: 0.7411 (mttt) cc_final: 0.6971 (ptmt) REVERT: I 213 HIS cc_start: 0.8659 (m170) cc_final: 0.8426 (m-70) REVERT: I 217 ARG cc_start: 0.7831 (mtt-85) cc_final: 0.7591 (mtt90) REVERT: I 362 MET cc_start: 0.7770 (mmp) cc_final: 0.7468 (mmm) REVERT: I 386 ARG cc_start: 0.8820 (mtt180) cc_final: 0.8561 (mtt90) REVERT: I 403 LYS cc_start: 0.8655 (tppt) cc_final: 0.8196 (mmtt) REVERT: I 425 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7113 (mtm180) REVERT: I 471 LYS cc_start: 0.7166 (mttt) cc_final: 0.6964 (mttt) REVERT: J 95 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.5382 (t80) REVERT: J 101 ARG cc_start: 0.7779 (mtp180) cc_final: 0.7205 (tpt170) REVERT: J 103 LYS cc_start: 0.8929 (tptp) cc_final: 0.8689 (tttp) REVERT: K 198 LYS cc_start: 0.5517 (OUTLIER) cc_final: 0.5143 (pptt) REVERT: K 471 LYS cc_start: 0.7495 (mttt) cc_final: 0.6684 (tttt) REVERT: L 95 TYR cc_start: 0.6257 (OUTLIER) cc_final: 0.5549 (t80) REVERT: M 27 VAL cc_start: 0.8552 (t) cc_final: 0.8245 (m) REVERT: M 295 LEU cc_start: 0.7875 (tp) cc_final: 0.7509 (tp) REVERT: M 403 LYS cc_start: 0.8509 (tppt) cc_final: 0.8179 (mmtt) REVERT: M 422 ASN cc_start: 0.8049 (m-40) cc_final: 0.7634 (m-40) REVERT: N 95 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.5541 (t80) REVERT: O 118 LYS cc_start: 0.7425 (mttt) cc_final: 0.6987 (ptmt) REVERT: O 213 HIS cc_start: 0.8646 (m170) cc_final: 0.8411 (m-70) REVERT: O 217 ARG cc_start: 0.7853 (mtt-85) cc_final: 0.7603 (mtt90) REVERT: O 362 MET cc_start: 0.7802 (mmp) cc_final: 0.7496 (mmm) REVERT: O 386 ARG cc_start: 0.8831 (mtt180) cc_final: 0.8571 (mtt90) REVERT: O 403 LYS cc_start: 0.8656 (tppt) cc_final: 0.8194 (mmtt) REVERT: O 425 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7120 (mtm180) REVERT: O 471 LYS cc_start: 0.7151 (mttt) cc_final: 0.6948 (mttt) REVERT: P 95 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.5397 (t80) REVERT: P 101 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7190 (tpt170) REVERT: P 103 LYS cc_start: 0.8922 (tptp) cc_final: 0.8682 (tttp) REVERT: Q 198 LYS cc_start: 0.5506 (OUTLIER) cc_final: 0.5135 (pptt) REVERT: Q 471 LYS cc_start: 0.7501 (mttt) cc_final: 0.6681 (tttt) REVERT: R 95 TYR cc_start: 0.6267 (OUTLIER) cc_final: 0.5561 (t80) REVERT: S 27 VAL cc_start: 0.8560 (t) cc_final: 0.8250 (m) REVERT: S 295 LEU cc_start: 0.7876 (tp) cc_final: 0.7509 (tp) REVERT: S 403 LYS cc_start: 0.8515 (tppt) cc_final: 0.8187 (mmtt) REVERT: S 422 ASN cc_start: 0.8054 (m-40) cc_final: 0.7631 (m-40) REVERT: T 95 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.5534 (t80) REVERT: U 118 LYS cc_start: 0.7398 (mttt) cc_final: 0.6965 (ptmt) REVERT: U 213 HIS cc_start: 0.8655 (m170) cc_final: 0.8416 (m-70) REVERT: U 217 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.7594 (mtt90) REVERT: U 362 MET cc_start: 0.7795 (mmp) cc_final: 0.7492 (mmm) REVERT: U 386 ARG cc_start: 0.8828 (mtt180) cc_final: 0.8571 (mtt90) REVERT: U 403 LYS cc_start: 0.8650 (tppt) cc_final: 0.8188 (mmtt) REVERT: U 425 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7127 (mtm180) REVERT: U 471 LYS cc_start: 0.7169 (mttt) cc_final: 0.6965 (mttt) REVERT: V 95 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.5385 (t80) REVERT: V 101 ARG cc_start: 0.7778 (mtp180) cc_final: 0.7203 (tpt170) REVERT: V 103 LYS cc_start: 0.8923 (tptp) cc_final: 0.8681 (tttp) REVERT: W 198 LYS cc_start: 0.5516 (OUTLIER) cc_final: 0.5137 (pptt) REVERT: W 471 LYS cc_start: 0.7507 (mttt) cc_final: 0.6695 (tttt) REVERT: X 95 TYR cc_start: 0.6270 (OUTLIER) cc_final: 0.5560 (t80) outliers start: 125 outliers final: 73 residues processed: 790 average time/residue: 0.5854 time to fit residues: 711.4332 Evaluate side-chains 710 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 621 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 198 LYS Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 414 SER Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 198 LYS Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 414 SER Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 199 THR Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 176 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 411 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 chunk 459 optimal weight: 6.9990 chunk 510 optimal weight: 8.9990 chunk 440 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 523 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN G 283 ASN ** G 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 452 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN M 283 ASN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN S 283 ASN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 452 GLN ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.148419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.120220 restraints weight = 57026.125| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.54 r_work: 0.3049 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 48708 Z= 0.221 Angle : 0.494 4.167 65652 Z= 0.271 Chirality : 0.039 0.138 7092 Planarity : 0.004 0.037 8640 Dihedral : 4.632 16.666 6552 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.23 % Allowed : 10.70 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5784 helix: 1.24 (0.10), residues: 2520 sheet: 0.55 (0.14), residues: 1116 loop : -0.68 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS S 92 PHE 0.011 0.002 PHE E 173 TYR 0.015 0.001 TYR O 345 ARG 0.008 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 683 time to evaluate : 4.136 Fit side-chains REVERT: A 27 VAL cc_start: 0.8406 (t) cc_final: 0.8064 (m) REVERT: A 295 LEU cc_start: 0.7860 (tp) cc_final: 0.7467 (tp) REVERT: A 403 LYS cc_start: 0.8465 (tppt) cc_final: 0.8016 (mmtt) REVERT: B 95 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.5585 (t80) REVERT: B 101 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7507 (mmp-170) REVERT: C 118 LYS cc_start: 0.7449 (mttt) cc_final: 0.6890 (ptmt) REVERT: C 170 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7979 (mtt) REVERT: C 213 HIS cc_start: 0.8633 (m170) cc_final: 0.8370 (m-70) REVERT: C 362 MET cc_start: 0.7920 (mmp) cc_final: 0.7671 (mmm) REVERT: C 386 ARG cc_start: 0.8825 (mtt180) cc_final: 0.8546 (mtt90) REVERT: C 403 LYS cc_start: 0.8627 (tppt) cc_final: 0.8190 (mmtt) REVERT: C 425 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.6964 (mtm180) REVERT: C 471 LYS cc_start: 0.7065 (mttt) cc_final: 0.6653 (mttt) REVERT: D 95 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.5389 (t80) REVERT: D 101 ARG cc_start: 0.7723 (mtp180) cc_final: 0.7161 (tpt170) REVERT: D 103 LYS cc_start: 0.8945 (tptp) cc_final: 0.8711 (tttp) REVERT: E 198 LYS cc_start: 0.5229 (OUTLIER) cc_final: 0.4831 (pptt) REVERT: E 208 ASP cc_start: 0.7620 (m-30) cc_final: 0.7357 (m-30) REVERT: E 471 LYS cc_start: 0.7214 (mttt) cc_final: 0.6588 (tttt) REVERT: F 95 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5555 (t80) REVERT: G 27 VAL cc_start: 0.8410 (t) cc_final: 0.8067 (m) REVERT: G 295 LEU cc_start: 0.7869 (tp) cc_final: 0.7478 (tp) REVERT: G 403 LYS cc_start: 0.8462 (tppt) cc_final: 0.8011 (mmtt) REVERT: H 95 TYR cc_start: 0.6575 (OUTLIER) cc_final: 0.5589 (t80) REVERT: I 118 LYS cc_start: 0.7446 (mttt) cc_final: 0.6885 (ptmt) REVERT: I 170 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7967 (mtt) REVERT: I 213 HIS cc_start: 0.8648 (m170) cc_final: 0.8382 (m-70) REVERT: I 362 MET cc_start: 0.7922 (mmp) cc_final: 0.7671 (mmm) REVERT: I 386 ARG cc_start: 0.8821 (mtt180) cc_final: 0.8540 (mtt90) REVERT: I 403 LYS cc_start: 0.8622 (tppt) cc_final: 0.8185 (mmtt) REVERT: I 425 ARG cc_start: 0.7543 (mtm-85) cc_final: 0.6956 (mtm180) REVERT: I 471 LYS cc_start: 0.7020 (mttt) cc_final: 0.6803 (mttt) REVERT: J 95 TYR cc_start: 0.6133 (OUTLIER) cc_final: 0.5378 (t80) REVERT: J 101 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7162 (tpt170) REVERT: J 103 LYS cc_start: 0.8950 (tptp) cc_final: 0.8719 (tttp) REVERT: K 198 LYS cc_start: 0.5223 (OUTLIER) cc_final: 0.4819 (pptt) REVERT: K 208 ASP cc_start: 0.7545 (m-30) cc_final: 0.7305 (m-30) REVERT: K 471 LYS cc_start: 0.7192 (mttt) cc_final: 0.6570 (tttt) REVERT: L 95 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.5584 (t80) REVERT: M 27 VAL cc_start: 0.8403 (t) cc_final: 0.8061 (m) REVERT: M 295 LEU cc_start: 0.7866 (tp) cc_final: 0.7475 (tp) REVERT: M 403 LYS cc_start: 0.8459 (tppt) cc_final: 0.8006 (mmtt) REVERT: N 95 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.5588 (t80) REVERT: O 118 LYS cc_start: 0.7444 (mttt) cc_final: 0.6883 (ptmt) REVERT: O 170 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7955 (mtt) REVERT: O 213 HIS cc_start: 0.8647 (m170) cc_final: 0.8376 (m-70) REVERT: O 362 MET cc_start: 0.7915 (mmp) cc_final: 0.7673 (mmm) REVERT: O 386 ARG cc_start: 0.8829 (mtt180) cc_final: 0.8551 (mtt90) REVERT: O 403 LYS cc_start: 0.8618 (tppt) cc_final: 0.8181 (mmtt) REVERT: O 425 ARG cc_start: 0.7571 (mtm-85) cc_final: 0.6973 (mtm180) REVERT: O 471 LYS cc_start: 0.7008 (mttt) cc_final: 0.6784 (mttt) REVERT: P 95 TYR cc_start: 0.6135 (OUTLIER) cc_final: 0.5379 (t80) REVERT: P 101 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7152 (tpt170) REVERT: P 103 LYS cc_start: 0.8942 (tptp) cc_final: 0.8711 (tttp) REVERT: Q 198 LYS cc_start: 0.5219 (OUTLIER) cc_final: 0.4823 (pptt) REVERT: Q 208 ASP cc_start: 0.7554 (m-30) cc_final: 0.7313 (m-30) REVERT: Q 471 LYS cc_start: 0.7199 (mttt) cc_final: 0.6580 (tttt) REVERT: R 95 TYR cc_start: 0.6272 (OUTLIER) cc_final: 0.5576 (t80) REVERT: S 27 VAL cc_start: 0.8404 (t) cc_final: 0.8061 (m) REVERT: S 295 LEU cc_start: 0.7858 (tp) cc_final: 0.7466 (tp) REVERT: S 403 LYS cc_start: 0.8461 (tppt) cc_final: 0.8009 (mmtt) REVERT: T 95 TYR cc_start: 0.6570 (OUTLIER) cc_final: 0.5578 (t80) REVERT: U 118 LYS cc_start: 0.7450 (mttt) cc_final: 0.6888 (ptmt) REVERT: U 170 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7979 (mtt) REVERT: U 213 HIS cc_start: 0.8638 (m170) cc_final: 0.8371 (m-70) REVERT: U 362 MET cc_start: 0.7919 (mmp) cc_final: 0.7676 (mmm) REVERT: U 386 ARG cc_start: 0.8827 (mtt180) cc_final: 0.8552 (mtt90) REVERT: U 403 LYS cc_start: 0.8620 (tppt) cc_final: 0.8183 (mmtt) REVERT: U 425 ARG cc_start: 0.7570 (mtm-85) cc_final: 0.6975 (mtm180) REVERT: U 471 LYS cc_start: 0.7015 (mttt) cc_final: 0.6785 (mttt) REVERT: V 95 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.5379 (t80) REVERT: V 101 ARG cc_start: 0.7721 (mtp180) cc_final: 0.7159 (tpt170) REVERT: V 103 LYS cc_start: 0.8950 (tptp) cc_final: 0.8718 (tttp) REVERT: W 198 LYS cc_start: 0.5220 (OUTLIER) cc_final: 0.4826 (pptt) REVERT: W 208 ASP cc_start: 0.7631 (m-30) cc_final: 0.7366 (m-30) REVERT: W 471 LYS cc_start: 0.7190 (mttt) cc_final: 0.6574 (tttt) REVERT: X 95 TYR cc_start: 0.6250 (OUTLIER) cc_final: 0.5553 (t80) outliers start: 118 outliers final: 76 residues processed: 763 average time/residue: 0.5740 time to fit residues: 676.9387 Evaluate side-chains 717 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 621 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 198 LYS Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 414 SER Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 198 LYS Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 414 SER Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 199 THR Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 440 LEU Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 209 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 479 optimal weight: 2.9990 chunk 451 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN E 303 GLN ** G 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN S 283 ASN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.146642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.118450 restraints weight = 57179.573| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.55 r_work: 0.3110 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 48708 Z= 0.326 Angle : 0.550 5.146 65652 Z= 0.296 Chirality : 0.041 0.154 7092 Planarity : 0.004 0.045 8640 Dihedral : 4.787 17.033 6552 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.02 % Allowed : 11.70 % Favored : 85.28 % 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: 0.54 (0.11), residues: 5784 helix: 1.22 (0.10), residues: 2484 sheet: 0.43 (0.14), residues: 1116 loop : -0.61 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS S 92 PHE 0.014 0.002 PHE E 173 TYR 0.014 0.002 TYR A 345 ARG 0.008 0.000 ARG I 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 631 time to evaluate : 4.329 Fit side-chains REVERT: A 27 VAL cc_start: 0.8478 (t) cc_final: 0.8193 (m) REVERT: A 295 LEU cc_start: 0.7892 (tp) cc_final: 0.7546 (tp) REVERT: A 403 LYS cc_start: 0.8550 (tppt) cc_final: 0.8070 (mmtt) REVERT: B 95 TYR cc_start: 0.6517 (OUTLIER) cc_final: 0.5416 (t80) REVERT: C 118 LYS cc_start: 0.7520 (mttt) cc_final: 0.7013 (ptmt) REVERT: C 170 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8102 (mtt) REVERT: C 213 HIS cc_start: 0.8592 (m170) cc_final: 0.8388 (m-70) REVERT: C 386 ARG cc_start: 0.8889 (mtt180) cc_final: 0.8617 (mtt90) REVERT: C 403 LYS cc_start: 0.8724 (tppt) cc_final: 0.8276 (mmtt) REVERT: C 425 ARG cc_start: 0.7581 (mtm-85) cc_final: 0.7083 (mtm180) REVERT: C 471 LYS cc_start: 0.7280 (mttt) cc_final: 0.6941 (mttt) REVERT: D 95 TYR cc_start: 0.6149 (OUTLIER) cc_final: 0.5463 (t80) REVERT: D 101 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7176 (tpt170) REVERT: D 103 LYS cc_start: 0.8950 (tptp) cc_final: 0.8744 (tttp) REVERT: E 198 LYS cc_start: 0.5271 (OUTLIER) cc_final: 0.5029 (ptpt) REVERT: E 303 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8527 (tm130) REVERT: E 471 LYS cc_start: 0.7361 (mttt) cc_final: 0.6754 (tttt) REVERT: E 475 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6764 (t0) REVERT: F 95 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5430 (t80) REVERT: G 27 VAL cc_start: 0.8469 (t) cc_final: 0.8187 (m) REVERT: G 295 LEU cc_start: 0.7882 (tp) cc_final: 0.7537 (tp) REVERT: G 403 LYS cc_start: 0.8536 (tppt) cc_final: 0.8057 (mmtt) REVERT: H 95 TYR cc_start: 0.6530 (OUTLIER) cc_final: 0.5439 (t80) REVERT: I 118 LYS cc_start: 0.7520 (mttt) cc_final: 0.7012 (ptmt) REVERT: I 170 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8100 (mtt) REVERT: I 213 HIS cc_start: 0.8613 (m170) cc_final: 0.8412 (m-70) REVERT: I 386 ARG cc_start: 0.8883 (mtt180) cc_final: 0.8612 (mtt90) REVERT: I 403 LYS cc_start: 0.8727 (tppt) cc_final: 0.8280 (mmtt) REVERT: I 425 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7068 (mtm180) REVERT: J 95 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.5478 (t80) REVERT: J 101 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7175 (tpt170) REVERT: J 103 LYS cc_start: 0.8950 (tptp) cc_final: 0.8746 (tttp) REVERT: K 198 LYS cc_start: 0.5276 (OUTLIER) cc_final: 0.5031 (ptpt) REVERT: K 208 ASP cc_start: 0.7730 (m-30) cc_final: 0.7522 (m-30) REVERT: K 303 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8528 (tm130) REVERT: K 471 LYS cc_start: 0.7353 (mttt) cc_final: 0.6748 (tttt) REVERT: K 475 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6771 (t0) REVERT: L 95 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5406 (t80) REVERT: M 27 VAL cc_start: 0.8462 (t) cc_final: 0.8181 (m) REVERT: M 295 LEU cc_start: 0.7884 (tp) cc_final: 0.7540 (tp) REVERT: M 403 LYS cc_start: 0.8540 (tppt) cc_final: 0.8056 (mmtt) REVERT: N 95 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.5445 (t80) REVERT: O 118 LYS cc_start: 0.7512 (mttt) cc_final: 0.7011 (ptmt) REVERT: O 170 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8025 (mtt) REVERT: O 386 ARG cc_start: 0.8893 (mtt180) cc_final: 0.8620 (mtt90) REVERT: O 403 LYS cc_start: 0.8721 (tppt) cc_final: 0.8272 (mmtt) REVERT: O 425 ARG cc_start: 0.7594 (mtm-85) cc_final: 0.7081 (mtm180) REVERT: P 95 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.5494 (t80) REVERT: P 101 ARG cc_start: 0.7769 (mtp180) cc_final: 0.7163 (tpt170) REVERT: P 103 LYS cc_start: 0.8941 (tptp) cc_final: 0.8736 (tttp) REVERT: Q 198 LYS cc_start: 0.5274 (OUTLIER) cc_final: 0.5032 (ptpt) REVERT: Q 208 ASP cc_start: 0.7743 (m-30) cc_final: 0.7538 (m-30) REVERT: Q 303 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8524 (tm130) REVERT: Q 425 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7230 (mtm180) REVERT: Q 471 LYS cc_start: 0.7352 (mttt) cc_final: 0.6747 (tttt) REVERT: Q 475 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6747 (t0) REVERT: R 95 TYR cc_start: 0.6220 (OUTLIER) cc_final: 0.5435 (t80) REVERT: S 27 VAL cc_start: 0.8469 (t) cc_final: 0.8184 (m) REVERT: S 295 LEU cc_start: 0.7889 (tp) cc_final: 0.7545 (tp) REVERT: S 403 LYS cc_start: 0.8542 (tppt) cc_final: 0.8061 (mmtt) REVERT: T 95 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.5412 (t80) REVERT: U 118 LYS cc_start: 0.7516 (mttt) cc_final: 0.7002 (ptmt) REVERT: U 170 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8077 (mtt) REVERT: U 213 HIS cc_start: 0.8579 (m170) cc_final: 0.8378 (m-70) REVERT: U 386 ARG cc_start: 0.8894 (mtt180) cc_final: 0.8625 (mtt90) REVERT: U 403 LYS cc_start: 0.8721 (tppt) cc_final: 0.8265 (mmtt) REVERT: U 425 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7086 (mtm180) REVERT: V 95 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.5479 (t80) REVERT: V 101 ARG cc_start: 0.7764 (mtp180) cc_final: 0.7170 (tpt170) REVERT: V 103 LYS cc_start: 0.8947 (tptp) cc_final: 0.8744 (tttp) REVERT: W 198 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.5037 (ptpt) REVERT: W 303 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8517 (tm130) REVERT: W 471 LYS cc_start: 0.7345 (mttt) cc_final: 0.6751 (tttt) REVERT: W 475 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6755 (t0) REVERT: X 95 TYR cc_start: 0.6215 (OUTLIER) cc_final: 0.5431 (t80) outliers start: 160 outliers final: 120 residues processed: 723 average time/residue: 0.5755 time to fit residues: 641.5048 Evaluate side-chains 758 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 610 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 303 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 198 LYS Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 286 MET Chi-restraints excluded: chain K residue 303 GLN Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 ASN Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 18 ASN Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 191 LEU Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 414 SER Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 191 LEU Chi-restraints excluded: chain Q residue 198 LYS Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 286 MET Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain Q residue 475 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 18 ASN Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 294 ASN Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 18 ASN Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 414 SER Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 286 MET Chi-restraints excluded: chain W residue 303 GLN Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 440 LEU Chi-restraints excluded: chain W residue 475 ASP Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 110 optimal weight: 8.9990 chunk 529 optimal weight: 9.9990 chunk 444 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 354 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 428 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 410 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 559 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** G 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN S 283 ASN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN W 303 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.147247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118981 restraints weight = 57160.621| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.56 r_work: 0.3032 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 48708 Z= 0.274 Angle : 0.519 5.178 65652 Z= 0.281 Chirality : 0.040 0.140 7092 Planarity : 0.004 0.048 8640 Dihedral : 4.657 16.686 6552 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.23 % Allowed : 11.89 % Favored : 84.88 % 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: 5784 helix: 1.26 (0.10), residues: 2496 sheet: 0.39 (0.14), residues: 1116 loop : -0.57 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 92 PHE 0.013 0.002 PHE K 173 TYR 0.014 0.002 TYR A 345 ARG 0.010 0.000 ARG O 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 639 time to evaluate : 4.153 Fit side-chains REVERT: A 27 VAL cc_start: 0.8400 (t) cc_final: 0.8079 (m) REVERT: A 295 LEU cc_start: 0.7888 (tp) cc_final: 0.7536 (tp) REVERT: A 403 LYS cc_start: 0.8471 (tppt) cc_final: 0.8002 (mmtt) REVERT: B 95 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.5450 (t80) REVERT: B 101 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7498 (mmp-170) REVERT: C 80 ARG cc_start: 0.4694 (OUTLIER) cc_final: 0.4334 (ptm-80) REVERT: C 118 LYS cc_start: 0.7373 (mttt) cc_final: 0.6807 (ptmt) REVERT: C 170 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8044 (mtt) REVERT: C 213 HIS cc_start: 0.8578 (m170) cc_final: 0.8341 (m-70) REVERT: C 301 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.7085 (ttp-110) REVERT: C 365 ASP cc_start: 0.6273 (t0) cc_final: 0.5990 (t0) REVERT: C 386 ARG cc_start: 0.8885 (mtt180) cc_final: 0.8618 (mtt180) REVERT: C 403 LYS cc_start: 0.8686 (tppt) cc_final: 0.8185 (mmtt) REVERT: C 425 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.6983 (mtm180) REVERT: C 471 LYS cc_start: 0.7033 (mttt) cc_final: 0.6690 (mttt) REVERT: D 95 TYR cc_start: 0.6094 (OUTLIER) cc_final: 0.5473 (t80) REVERT: D 101 ARG cc_start: 0.7750 (mtp180) cc_final: 0.7161 (tpt170) REVERT: D 103 LYS cc_start: 0.8951 (tptp) cc_final: 0.8745 (tttp) REVERT: E 198 LYS cc_start: 0.5268 (OUTLIER) cc_final: 0.5027 (ptpt) REVERT: E 471 LYS cc_start: 0.7263 (mttt) cc_final: 0.6674 (tttt) REVERT: E 475 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6764 (t0) REVERT: F 95 TYR cc_start: 0.6155 (OUTLIER) cc_final: 0.5388 (t80) REVERT: G 27 VAL cc_start: 0.8399 (t) cc_final: 0.8078 (m) REVERT: G 295 LEU cc_start: 0.7890 (tp) cc_final: 0.7541 (tp) REVERT: G 403 LYS cc_start: 0.8456 (tppt) cc_final: 0.7990 (mmtt) REVERT: H 95 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5456 (t80) REVERT: H 101 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7488 (mmp-170) REVERT: I 80 ARG cc_start: 0.4674 (OUTLIER) cc_final: 0.4320 (ptm-80) REVERT: I 118 LYS cc_start: 0.7351 (mttt) cc_final: 0.6787 (ptmt) REVERT: I 170 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8025 (mtt) REVERT: I 213 HIS cc_start: 0.8596 (m170) cc_final: 0.8355 (m-70) REVERT: I 301 ARG cc_start: 0.7318 (mtm-85) cc_final: 0.7098 (ttp-110) REVERT: I 365 ASP cc_start: 0.6273 (t0) cc_final: 0.5955 (t0) REVERT: I 386 ARG cc_start: 0.8879 (mtt180) cc_final: 0.8617 (mtt180) REVERT: I 403 LYS cc_start: 0.8682 (tppt) cc_final: 0.8185 (mmtt) REVERT: I 425 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.6983 (mtm180) REVERT: I 471 LYS cc_start: 0.7253 (mtpp) cc_final: 0.6630 (mttt) REVERT: J 95 TYR cc_start: 0.6099 (OUTLIER) cc_final: 0.5477 (t80) REVERT: J 101 ARG cc_start: 0.7751 (mtp180) cc_final: 0.7158 (tpt170) REVERT: J 103 LYS cc_start: 0.8951 (tptp) cc_final: 0.8745 (tttp) REVERT: K 198 LYS cc_start: 0.5260 (OUTLIER) cc_final: 0.5020 (ptpt) REVERT: K 208 ASP cc_start: 0.7619 (m-30) cc_final: 0.7356 (m-30) REVERT: K 471 LYS cc_start: 0.7249 (mttt) cc_final: 0.6661 (tttt) REVERT: K 475 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6762 (t0) REVERT: L 95 TYR cc_start: 0.6155 (OUTLIER) cc_final: 0.5385 (t80) REVERT: M 27 VAL cc_start: 0.8398 (t) cc_final: 0.8079 (m) REVERT: M 295 LEU cc_start: 0.7882 (tp) cc_final: 0.7532 (tp) REVERT: M 403 LYS cc_start: 0.8462 (tppt) cc_final: 0.7991 (mmtt) REVERT: N 95 TYR cc_start: 0.6535 (OUTLIER) cc_final: 0.5464 (t80) REVERT: N 101 ARG cc_start: 0.7881 (mtp180) cc_final: 0.7493 (mmp-170) REVERT: O 80 ARG cc_start: 0.4666 (OUTLIER) cc_final: 0.4313 (ptm-80) REVERT: O 118 LYS cc_start: 0.7370 (mttt) cc_final: 0.6807 (ptmt) REVERT: O 170 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8012 (mtt) REVERT: O 301 ARG cc_start: 0.7306 (mtm-85) cc_final: 0.7085 (ttp-110) REVERT: O 365 ASP cc_start: 0.6272 (t0) cc_final: 0.5971 (t0) REVERT: O 386 ARG cc_start: 0.8888 (mtt180) cc_final: 0.8627 (mtt180) REVERT: O 403 LYS cc_start: 0.8674 (tppt) cc_final: 0.8174 (mmtt) REVERT: O 425 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.6985 (mtm180) REVERT: O 471 LYS cc_start: 0.7253 (mtpp) cc_final: 0.6623 (mttt) REVERT: P 95 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.5492 (t80) REVERT: P 101 ARG cc_start: 0.7751 (mtp180) cc_final: 0.7151 (tpt170) REVERT: P 103 LYS cc_start: 0.8945 (tptp) cc_final: 0.8742 (tttp) REVERT: Q 198 LYS cc_start: 0.5259 (OUTLIER) cc_final: 0.5021 (ptpt) REVERT: Q 208 ASP cc_start: 0.7635 (m-30) cc_final: 0.7371 (m-30) REVERT: Q 471 LYS cc_start: 0.7254 (mttt) cc_final: 0.6668 (tttt) REVERT: Q 475 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6760 (t0) REVERT: R 95 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5395 (t80) REVERT: S 27 VAL cc_start: 0.8404 (t) cc_final: 0.8082 (m) REVERT: S 295 LEU cc_start: 0.7890 (tp) cc_final: 0.7540 (tp) REVERT: S 403 LYS cc_start: 0.8467 (tppt) cc_final: 0.7996 (mmtt) REVERT: T 95 TYR cc_start: 0.6522 (OUTLIER) cc_final: 0.5438 (t80) REVERT: T 101 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7490 (mmp-170) REVERT: U 80 ARG cc_start: 0.4678 (OUTLIER) cc_final: 0.4324 (ptm-80) REVERT: U 118 LYS cc_start: 0.7374 (mttt) cc_final: 0.6809 (ptmt) REVERT: U 170 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8025 (mtt) REVERT: U 213 HIS cc_start: 0.8583 (m170) cc_final: 0.8346 (m-70) REVERT: U 301 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.7088 (ttp-110) REVERT: U 365 ASP cc_start: 0.6281 (t0) cc_final: 0.5998 (t0) REVERT: U 386 ARG cc_start: 0.8891 (mtt180) cc_final: 0.8628 (mtt180) REVERT: U 403 LYS cc_start: 0.8679 (tppt) cc_final: 0.8176 (mmtt) REVERT: U 425 ARG cc_start: 0.7543 (mtm-85) cc_final: 0.6985 (mtm180) REVERT: U 471 LYS cc_start: 0.7267 (mtpp) cc_final: 0.6636 (mttt) REVERT: V 95 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.5472 (t80) REVERT: V 101 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7166 (tpt170) REVERT: V 103 LYS cc_start: 0.8950 (tptp) cc_final: 0.8745 (tttp) REVERT: W 198 LYS cc_start: 0.5256 (OUTLIER) cc_final: 0.5018 (ptpt) REVERT: W 471 LYS cc_start: 0.7249 (mttt) cc_final: 0.6669 (tttt) REVERT: W 475 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6760 (t0) REVERT: X 95 TYR cc_start: 0.6152 (OUTLIER) cc_final: 0.5396 (t80) outliers start: 171 outliers final: 131 residues processed: 747 average time/residue: 0.5733 time to fit residues: 659.6592 Evaluate side-chains 777 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 618 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 198 LYS Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 286 MET Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 ASN Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 18 ASN Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 414 SER Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 191 LEU Chi-restraints excluded: chain Q residue 198 LYS Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain Q residue 475 ASP Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 18 ASN Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 294 ASN Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 18 ASN Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 414 SER Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 286 MET Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 440 LEU Chi-restraints excluded: chain W residue 475 ASP Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 418 optimal weight: 5.9990 chunk 545 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 446 optimal weight: 0.9990 chunk 569 optimal weight: 5.9990 chunk 463 optimal weight: 3.9990 chunk 455 optimal weight: 6.9990 chunk 457 optimal weight: 2.9990 chunk 347 optimal weight: 8.9990 chunk 315 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** G 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN S 73 ASN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.147657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119395 restraints weight = 57284.612| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.55 r_work: 0.3133 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 48708 Z= 0.260 Angle : 0.513 5.743 65652 Z= 0.276 Chirality : 0.039 0.137 7092 Planarity : 0.004 0.053 8640 Dihedral : 4.588 16.278 6552 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.40 % Allowed : 12.38 % Favored : 84.22 % 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: 0.53 (0.11), residues: 5784 helix: 1.26 (0.10), residues: 2520 sheet: 0.34 (0.14), residues: 1116 loop : -0.64 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS M 92 PHE 0.012 0.002 PHE Q 173 TYR 0.013 0.002 TYR S 378 ARG 0.011 0.000 ARG I 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 634 time to evaluate : 4.210 Fit side-chains REVERT: A 27 VAL cc_start: 0.8370 (t) cc_final: 0.8080 (m) REVERT: A 295 LEU cc_start: 0.7890 (tp) cc_final: 0.7547 (tp) REVERT: A 403 LYS cc_start: 0.8507 (tppt) cc_final: 0.8035 (mmtt) REVERT: B 95 TYR cc_start: 0.6520 (OUTLIER) cc_final: 0.5412 (t80) REVERT: B 101 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7557 (mmp-170) REVERT: C 80 ARG cc_start: 0.4936 (OUTLIER) cc_final: 0.4537 (ptm-80) REVERT: C 118 LYS cc_start: 0.7433 (mttt) cc_final: 0.6928 (ptmt) REVERT: C 170 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7996 (mtt) REVERT: C 301 ARG cc_start: 0.7330 (mtm-85) cc_final: 0.7127 (ttp-110) REVERT: C 365 ASP cc_start: 0.6371 (t0) cc_final: 0.6069 (t0) REVERT: C 386 ARG cc_start: 0.8894 (mtt180) cc_final: 0.8631 (mtt180) REVERT: C 403 LYS cc_start: 0.8761 (tppt) cc_final: 0.8289 (mmtt) REVERT: C 425 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7054 (mtm180) REVERT: C 471 LYS cc_start: 0.7175 (mttt) cc_final: 0.6809 (mttt) REVERT: D 95 TYR cc_start: 0.6135 (OUTLIER) cc_final: 0.5478 (t80) REVERT: D 101 ARG cc_start: 0.7786 (mtp180) cc_final: 0.7162 (tpt170) REVERT: D 103 LYS cc_start: 0.8938 (tptp) cc_final: 0.8736 (tttp) REVERT: E 198 LYS cc_start: 0.5325 (OUTLIER) cc_final: 0.5084 (ptpt) REVERT: E 471 LYS cc_start: 0.7352 (mttt) cc_final: 0.6758 (tttt) REVERT: F 95 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.5350 (t80) REVERT: G 295 LEU cc_start: 0.7889 (tp) cc_final: 0.7545 (tp) REVERT: G 403 LYS cc_start: 0.8493 (tppt) cc_final: 0.8025 (mmtt) REVERT: H 95 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.5418 (t80) REVERT: H 101 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7543 (mmp-170) REVERT: I 80 ARG cc_start: 0.4927 (OUTLIER) cc_final: 0.4525 (ptm-80) REVERT: I 118 LYS cc_start: 0.7426 (mttt) cc_final: 0.6925 (ptmt) REVERT: I 170 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7976 (mtt) REVERT: I 213 HIS cc_start: 0.8594 (m170) cc_final: 0.8391 (m-70) REVERT: I 365 ASP cc_start: 0.6385 (t0) cc_final: 0.6039 (t0) REVERT: I 386 ARG cc_start: 0.8888 (mtt180) cc_final: 0.8629 (mtt180) REVERT: I 403 LYS cc_start: 0.8760 (tppt) cc_final: 0.8290 (mmtt) REVERT: I 425 ARG cc_start: 0.7520 (mtm-85) cc_final: 0.7002 (mtm180) REVERT: I 471 LYS cc_start: 0.7403 (mtpp) cc_final: 0.6762 (mttt) REVERT: J 95 TYR cc_start: 0.6142 (OUTLIER) cc_final: 0.5483 (t80) REVERT: J 101 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7168 (tpt170) REVERT: K 198 LYS cc_start: 0.5313 (OUTLIER) cc_final: 0.5075 (ptpt) REVERT: K 208 ASP cc_start: 0.7634 (m-30) cc_final: 0.7420 (m-30) REVERT: K 471 LYS cc_start: 0.7339 (mttt) cc_final: 0.6747 (tttt) REVERT: K 475 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6857 (t0) REVERT: L 95 TYR cc_start: 0.6087 (OUTLIER) cc_final: 0.5329 (t80) REVERT: M 295 LEU cc_start: 0.7890 (tp) cc_final: 0.7546 (tp) REVERT: M 403 LYS cc_start: 0.8497 (tppt) cc_final: 0.8020 (mmtt) REVERT: N 95 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.5421 (t80) REVERT: N 101 ARG cc_start: 0.7922 (mtp180) cc_final: 0.7543 (mmp-170) REVERT: O 80 ARG cc_start: 0.4906 (OUTLIER) cc_final: 0.4500 (ptm-80) REVERT: O 118 LYS cc_start: 0.7440 (mttt) cc_final: 0.6938 (ptmt) REVERT: O 170 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7955 (mtt) REVERT: O 365 ASP cc_start: 0.6376 (t0) cc_final: 0.6048 (t0) REVERT: O 386 ARG cc_start: 0.8900 (mtt180) cc_final: 0.8640 (mtt180) REVERT: O 403 LYS cc_start: 0.8762 (tppt) cc_final: 0.8285 (mmtt) REVERT: O 425 ARG cc_start: 0.7556 (mtm-85) cc_final: 0.7052 (mtm180) REVERT: O 471 LYS cc_start: 0.7399 (mtpp) cc_final: 0.6754 (mttt) REVERT: P 95 TYR cc_start: 0.6154 (OUTLIER) cc_final: 0.5502 (t80) REVERT: P 101 ARG cc_start: 0.7787 (mtp180) cc_final: 0.7155 (tpt170) REVERT: Q 198 LYS cc_start: 0.5321 (OUTLIER) cc_final: 0.5083 (ptpt) REVERT: Q 208 ASP cc_start: 0.7650 (m-30) cc_final: 0.7436 (m-30) REVERT: Q 471 LYS cc_start: 0.7338 (mttt) cc_final: 0.6745 (tttt) REVERT: Q 475 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6852 (t0) REVERT: R 95 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.5340 (t80) REVERT: S 27 VAL cc_start: 0.8373 (t) cc_final: 0.8081 (m) REVERT: S 295 LEU cc_start: 0.7898 (tp) cc_final: 0.7554 (tp) REVERT: S 403 LYS cc_start: 0.8498 (tppt) cc_final: 0.8025 (mmtt) REVERT: T 95 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5401 (t80) REVERT: T 101 ARG cc_start: 0.7922 (mtp180) cc_final: 0.7543 (mmp-170) REVERT: U 80 ARG cc_start: 0.4942 (OUTLIER) cc_final: 0.4534 (ptm-80) REVERT: U 118 LYS cc_start: 0.7440 (mttt) cc_final: 0.6931 (ptmt) REVERT: U 170 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.7966 (mtt) REVERT: U 213 HIS cc_start: 0.8569 (m170) cc_final: 0.8368 (m-70) REVERT: U 301 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.7120 (ttp-110) REVERT: U 365 ASP cc_start: 0.6380 (t0) cc_final: 0.6064 (t0) REVERT: U 386 ARG cc_start: 0.8900 (mtt180) cc_final: 0.8638 (mtt180) REVERT: U 403 LYS cc_start: 0.8753 (tppt) cc_final: 0.8277 (mmtt) REVERT: U 425 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.7058 (mtm180) REVERT: U 471 LYS cc_start: 0.7401 (mtpp) cc_final: 0.6754 (mttt) REVERT: V 95 TYR cc_start: 0.6141 (OUTLIER) cc_final: 0.5484 (t80) REVERT: V 101 ARG cc_start: 0.7790 (mtp180) cc_final: 0.7170 (tpt170) REVERT: V 103 LYS cc_start: 0.8941 (tptp) cc_final: 0.8740 (tttp) REVERT: W 198 LYS cc_start: 0.5321 (OUTLIER) cc_final: 0.5083 (ptpt) REVERT: W 471 LYS cc_start: 0.7340 (mttt) cc_final: 0.6751 (tttt) REVERT: W 475 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6847 (t0) REVERT: X 95 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.5361 (t80) outliers start: 180 outliers final: 134 residues processed: 746 average time/residue: 0.5806 time to fit residues: 664.9063 Evaluate side-chains 776 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 615 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 198 LYS Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 ASN Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 18 ASN Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 191 LEU Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 414 SER Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 191 LEU Chi-restraints excluded: chain Q residue 198 LYS Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 414 SER Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain Q residue 475 ASP Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 18 ASN Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 294 ASN Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 18 ASN Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 414 SER Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 414 SER Chi-restraints excluded: chain W residue 440 LEU Chi-restraints excluded: chain W residue 475 ASP Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 304 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 493 optimal weight: 5.9990 chunk 573 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 426 optimal weight: 6.9990 chunk 437 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 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 283 ASN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** G 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN M 283 ASN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN S 283 ASN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.146600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118351 restraints weight = 57215.159| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.55 r_work: 0.3089 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 48708 Z= 0.327 Angle : 0.558 8.106 65652 Z= 0.297 Chirality : 0.041 0.151 7092 Planarity : 0.004 0.056 8640 Dihedral : 4.699 16.574 6552 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.57 % Allowed : 12.38 % Favored : 84.05 % 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: 0.51 (0.11), residues: 5784 helix: 1.22 (0.10), residues: 2484 sheet: 0.27 (0.14), residues: 1116 loop : -0.55 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS S 92 PHE 0.014 0.002 PHE K 173 TYR 0.014 0.002 TYR Q 334 ARG 0.012 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 631 time to evaluate : 4.161 Fit side-chains REVERT: A 295 LEU cc_start: 0.7995 (tp) cc_final: 0.7625 (tp) REVERT: A 403 LYS cc_start: 0.8591 (tppt) cc_final: 0.8115 (mmtt) REVERT: B 95 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.5427 (t80) REVERT: B 101 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7594 (mmp-170) REVERT: C 80 ARG cc_start: 0.5055 (OUTLIER) cc_final: 0.4607 (ptm-80) REVERT: C 118 LYS cc_start: 0.7478 (mttt) cc_final: 0.6941 (ptmt) REVERT: C 170 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8108 (mtt) REVERT: C 301 ARG cc_start: 0.7381 (mtm-85) cc_final: 0.7180 (ttp-110) REVERT: C 365 ASP cc_start: 0.6450 (t0) cc_final: 0.5997 (t0) REVERT: C 386 ARG cc_start: 0.8919 (mtt180) cc_final: 0.8677 (mtt90) REVERT: C 403 LYS cc_start: 0.8825 (tppt) cc_final: 0.8350 (mmtt) REVERT: C 425 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7197 (mtm180) REVERT: C 471 LYS cc_start: 0.7238 (mttt) cc_final: 0.6873 (mttt) REVERT: D 95 TYR cc_start: 0.6009 (OUTLIER) cc_final: 0.5349 (t80) REVERT: D 101 ARG cc_start: 0.7826 (mtp180) cc_final: 0.7246 (tpt170) REVERT: E 471 LYS cc_start: 0.7419 (mttt) cc_final: 0.6786 (tttt) REVERT: F 95 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.5458 (t80) REVERT: G 295 LEU cc_start: 0.7994 (tp) cc_final: 0.7623 (tp) REVERT: G 403 LYS cc_start: 0.8571 (tppt) cc_final: 0.8098 (mmtt) REVERT: H 95 TYR cc_start: 0.6523 (OUTLIER) cc_final: 0.5396 (t80) REVERT: H 101 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7575 (mmp-170) REVERT: I 80 ARG cc_start: 0.5060 (OUTLIER) cc_final: 0.4599 (ptm-80) REVERT: I 118 LYS cc_start: 0.7452 (mttt) cc_final: 0.6912 (ptmt) REVERT: I 170 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8078 (mtt) REVERT: I 365 ASP cc_start: 0.6442 (t0) cc_final: 0.5963 (t0) REVERT: I 386 ARG cc_start: 0.8912 (mtt180) cc_final: 0.8673 (mtt90) REVERT: I 403 LYS cc_start: 0.8826 (tppt) cc_final: 0.8352 (mmtt) REVERT: I 425 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7145 (mtm180) REVERT: J 95 TYR cc_start: 0.6009 (OUTLIER) cc_final: 0.5350 (t80) REVERT: J 101 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7234 (tpt170) REVERT: K 208 ASP cc_start: 0.7745 (m-30) cc_final: 0.7538 (m-30) REVERT: K 471 LYS cc_start: 0.7391 (mttt) cc_final: 0.6764 (tttt) REVERT: K 475 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6861 (t0) REVERT: L 95 TYR cc_start: 0.6241 (OUTLIER) cc_final: 0.5463 (t80) REVERT: M 295 LEU cc_start: 0.7998 (tp) cc_final: 0.7627 (tp) REVERT: M 403 LYS cc_start: 0.8574 (tppt) cc_final: 0.8093 (mmtt) REVERT: N 95 TYR cc_start: 0.6537 (OUTLIER) cc_final: 0.5424 (t80) REVERT: N 101 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7572 (mmp-170) REVERT: O 80 ARG cc_start: 0.5045 (OUTLIER) cc_final: 0.4581 (ptm-80) REVERT: O 118 LYS cc_start: 0.7476 (mttt) cc_final: 0.6936 (ptmt) REVERT: O 170 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8047 (mtt) REVERT: O 365 ASP cc_start: 0.6446 (t0) cc_final: 0.5960 (t0) REVERT: O 386 ARG cc_start: 0.8915 (mtt180) cc_final: 0.8674 (mtt90) REVERT: O 403 LYS cc_start: 0.8829 (tppt) cc_final: 0.8354 (mmtt) REVERT: O 425 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7144 (mtm180) REVERT: P 95 TYR cc_start: 0.6019 (OUTLIER) cc_final: 0.5378 (t80) REVERT: P 101 ARG cc_start: 0.7809 (mtp180) cc_final: 0.7234 (tpt170) REVERT: Q 208 ASP cc_start: 0.7764 (m-30) cc_final: 0.7563 (m-30) REVERT: Q 471 LYS cc_start: 0.7395 (mttt) cc_final: 0.6763 (tttt) REVERT: Q 475 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6847 (t0) REVERT: R 95 TYR cc_start: 0.6248 (OUTLIER) cc_final: 0.5475 (t80) REVERT: S 295 LEU cc_start: 0.7997 (tp) cc_final: 0.7628 (tp) REVERT: S 403 LYS cc_start: 0.8581 (tppt) cc_final: 0.8105 (mmtt) REVERT: T 95 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5408 (t80) REVERT: T 101 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7584 (mmp-170) REVERT: U 80 ARG cc_start: 0.5074 (OUTLIER) cc_final: 0.4607 (ptm-80) REVERT: U 118 LYS cc_start: 0.7480 (mttt) cc_final: 0.6933 (ptmt) REVERT: U 170 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8077 (mtt) REVERT: U 301 ARG cc_start: 0.7373 (mtm-85) cc_final: 0.7171 (ttp-110) REVERT: U 365 ASP cc_start: 0.6453 (t0) cc_final: 0.5998 (t0) REVERT: U 386 ARG cc_start: 0.8918 (mtt180) cc_final: 0.8678 (mtt90) REVERT: U 403 LYS cc_start: 0.8819 (tppt) cc_final: 0.8340 (mmtt) REVERT: U 425 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7148 (mtm180) REVERT: V 95 TYR cc_start: 0.6009 (OUTLIER) cc_final: 0.5341 (t80) REVERT: V 101 ARG cc_start: 0.7834 (mtp180) cc_final: 0.7247 (tpt170) REVERT: W 471 LYS cc_start: 0.7401 (mttt) cc_final: 0.6788 (tttt) REVERT: W 475 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6844 (t0) REVERT: X 95 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.5460 (t80) outliers start: 189 outliers final: 147 residues processed: 742 average time/residue: 0.5651 time to fit residues: 654.1586 Evaluate side-chains 776 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 606 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 198 LYS Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 286 MET Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 ASN Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 191 LEU Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 414 SER Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 18 ASN Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 191 LEU Chi-restraints excluded: chain Q residue 198 LYS Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 286 MET Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 414 SER Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain Q residue 475 ASP Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 18 ASN Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 294 ASN Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 414 SER Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 286 MET Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 414 SER Chi-restraints excluded: chain W residue 440 LEU Chi-restraints excluded: chain W residue 475 ASP Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 57 optimal weight: 0.9990 chunk 561 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 429 optimal weight: 8.9990 chunk 201 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 278 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 92 HIS A 283 ASN A 303 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN G 73 ASN G 92 HIS G 303 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN M 73 ASN M 92 HIS M 283 ASN M 303 GLN ** O 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN S 92 HIS S 283 ASN S 303 GLN ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121193 restraints weight = 56806.874| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.57 r_work: 0.3064 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 48708 Z= 0.168 Angle : 0.471 8.272 65652 Z= 0.254 Chirality : 0.037 0.132 7092 Planarity : 0.004 0.058 8640 Dihedral : 4.306 15.131 6552 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.49 % Allowed : 13.62 % Favored : 83.88 % 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: 0.75 (0.11), residues: 5784 helix: 1.46 (0.10), residues: 2520 sheet: 0.52 (0.14), residues: 1044 loop : -0.56 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 238 PHE 0.010 0.001 PHE O 173 TYR 0.015 0.001 TYR M 378 ARG 0.014 0.000 ARG U 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 657 time to evaluate : 4.134 Fit side-chains REVERT: A 216 TYR cc_start: 0.8999 (m-80) cc_final: 0.8641 (m-80) REVERT: A 295 LEU cc_start: 0.7888 (tp) cc_final: 0.7538 (tp) REVERT: A 303 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8569 (pp30) REVERT: A 403 LYS cc_start: 0.8418 (tppt) cc_final: 0.7964 (mmtt) REVERT: B 95 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.5453 (t80) REVERT: B 101 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7499 (mmp-170) REVERT: C 47 LYS cc_start: 0.8154 (mttt) cc_final: 0.7681 (mmtt) REVERT: C 118 LYS cc_start: 0.7303 (mttt) cc_final: 0.6795 (ptmt) REVERT: C 170 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8016 (mtt) REVERT: C 301 ARG cc_start: 0.7280 (mtm-85) cc_final: 0.7079 (ttp-110) REVERT: C 365 ASP cc_start: 0.6050 (t0) cc_final: 0.5728 (t0) REVERT: C 386 ARG cc_start: 0.8898 (mtt180) cc_final: 0.8648 (mtt90) REVERT: C 403 LYS cc_start: 0.8640 (tppt) cc_final: 0.8162 (mmtt) REVERT: C 425 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.6857 (mtm180) REVERT: C 471 LYS cc_start: 0.7040 (mttt) cc_final: 0.6784 (mttt) REVERT: D 95 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.5674 (t80) REVERT: D 101 ARG cc_start: 0.7660 (mtp180) cc_final: 0.7029 (tpt170) REVERT: E 198 LYS cc_start: 0.5166 (OUTLIER) cc_final: 0.4944 (ptpt) REVERT: E 471 LYS cc_start: 0.7334 (mttt) cc_final: 0.6754 (tttt) REVERT: F 95 TYR cc_start: 0.6134 (OUTLIER) cc_final: 0.5415 (t80) REVERT: G 216 TYR cc_start: 0.9007 (m-80) cc_final: 0.8650 (m-80) REVERT: G 295 LEU cc_start: 0.7889 (tp) cc_final: 0.7546 (tp) REVERT: G 303 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8567 (pp30) REVERT: G 403 LYS cc_start: 0.8406 (tppt) cc_final: 0.7956 (mmtt) REVERT: H 95 TYR cc_start: 0.6446 (OUTLIER) cc_final: 0.5427 (t80) REVERT: H 101 ARG cc_start: 0.7854 (mtp180) cc_final: 0.7497 (mmp-170) REVERT: I 47 LYS cc_start: 0.8146 (mttt) cc_final: 0.7673 (mmtt) REVERT: I 118 LYS cc_start: 0.7301 (mttt) cc_final: 0.6797 (ptmt) REVERT: I 170 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8003 (mtt) REVERT: I 365 ASP cc_start: 0.6043 (t0) cc_final: 0.5712 (t0) REVERT: I 386 ARG cc_start: 0.8890 (mtt180) cc_final: 0.8641 (mtt90) REVERT: I 403 LYS cc_start: 0.8629 (tppt) cc_final: 0.8155 (mmtt) REVERT: I 425 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.6848 (mtm180) REVERT: I 471 LYS cc_start: 0.7146 (mtpp) cc_final: 0.6856 (mtmm) REVERT: J 95 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.5662 (t80) REVERT: J 101 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7165 (tpt170) REVERT: K 198 LYS cc_start: 0.5178 (OUTLIER) cc_final: 0.4953 (ptpt) REVERT: K 208 ASP cc_start: 0.7628 (m-30) cc_final: 0.7359 (m-30) REVERT: K 471 LYS cc_start: 0.7264 (mttt) cc_final: 0.6673 (tttt) REVERT: L 95 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.5413 (t80) REVERT: M 216 TYR cc_start: 0.9007 (m-80) cc_final: 0.8653 (m-80) REVERT: M 295 LEU cc_start: 0.7885 (tp) cc_final: 0.7545 (tp) REVERT: M 303 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8563 (pp30) REVERT: M 403 LYS cc_start: 0.8408 (tppt) cc_final: 0.7956 (mmtt) REVERT: N 95 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.5434 (t80) REVERT: N 101 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7482 (mmp-170) REVERT: O 47 LYS cc_start: 0.8144 (mttt) cc_final: 0.7669 (mmtt) REVERT: O 80 ARG cc_start: 0.4715 (OUTLIER) cc_final: 0.4506 (ptm-80) REVERT: O 118 LYS cc_start: 0.7315 (mttt) cc_final: 0.6813 (ptmt) REVERT: O 170 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.7990 (mtt) REVERT: O 365 ASP cc_start: 0.6025 (t0) cc_final: 0.5724 (t0) REVERT: O 386 ARG cc_start: 0.8897 (mtt180) cc_final: 0.8646 (mtt90) REVERT: O 403 LYS cc_start: 0.8627 (tppt) cc_final: 0.8147 (mmtt) REVERT: O 425 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.6870 (mtm180) REVERT: O 471 LYS cc_start: 0.7135 (mtpp) cc_final: 0.6841 (mtmm) REVERT: P 95 TYR cc_start: 0.6225 (OUTLIER) cc_final: 0.5673 (t80) REVERT: P 101 ARG cc_start: 0.7751 (mtp180) cc_final: 0.7162 (tpt170) REVERT: Q 198 LYS cc_start: 0.5178 (OUTLIER) cc_final: 0.4952 (ptpt) REVERT: Q 208 ASP cc_start: 0.7651 (m-30) cc_final: 0.7380 (m-30) REVERT: Q 471 LYS cc_start: 0.7265 (mttt) cc_final: 0.6674 (tttt) REVERT: R 95 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.5424 (t80) REVERT: S 216 TYR cc_start: 0.9011 (m-80) cc_final: 0.8658 (m-80) REVERT: S 295 LEU cc_start: 0.7892 (tp) cc_final: 0.7544 (tp) REVERT: S 303 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8571 (pp30) REVERT: S 403 LYS cc_start: 0.8409 (tppt) cc_final: 0.7950 (mmtt) REVERT: T 95 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.5426 (t80) REVERT: T 101 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7491 (mmp-170) REVERT: U 47 LYS cc_start: 0.8147 (mttt) cc_final: 0.7674 (mmtt) REVERT: U 118 LYS cc_start: 0.7311 (mttt) cc_final: 0.6809 (ptmt) REVERT: U 170 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7996 (mtt) REVERT: U 301 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.7068 (ttp-110) REVERT: U 365 ASP cc_start: 0.6046 (t0) cc_final: 0.5733 (t0) REVERT: U 386 ARG cc_start: 0.8899 (mtt180) cc_final: 0.8648 (mtt90) REVERT: U 403 LYS cc_start: 0.8631 (tppt) cc_final: 0.8151 (mmtt) REVERT: U 425 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.6865 (mtm180) REVERT: U 471 LYS cc_start: 0.7153 (mtpp) cc_final: 0.6855 (mtmm) REVERT: V 95 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5678 (t80) REVERT: V 101 ARG cc_start: 0.7651 (mtp180) cc_final: 0.7016 (tpt170) REVERT: W 198 LYS cc_start: 0.5168 (OUTLIER) cc_final: 0.4946 (ptpt) REVERT: W 471 LYS cc_start: 0.7254 (mttt) cc_final: 0.6670 (tttt) REVERT: X 95 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5429 (t80) outliers start: 132 outliers final: 84 residues processed: 739 average time/residue: 0.5693 time to fit residues: 651.6530 Evaluate side-chains 727 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 618 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 198 LYS Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 414 SER Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 303 GLN Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 18 ASN Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 198 LYS Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 18 ASN Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 438 GLU Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 311 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 430 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 384 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** G 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.148603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120366 restraints weight = 57202.051| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.57 r_work: 0.3114 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 48708 Z= 0.220 Angle : 0.502 8.716 65652 Z= 0.268 Chirality : 0.038 0.130 7092 Planarity : 0.004 0.046 8640 Dihedral : 4.342 15.164 6552 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.19 % Allowed : 14.34 % Favored : 83.47 % 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: 0.63 (0.11), residues: 5784 helix: 1.36 (0.10), residues: 2556 sheet: 0.48 (0.14), residues: 1044 loop : -0.69 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS U 238 PHE 0.012 0.001 PHE E 173 TYR 0.012 0.001 TYR U 345 ARG 0.012 0.000 ARG C 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 613 time to evaluate : 4.154 Fit side-chains REVERT: A 295 LEU cc_start: 0.7981 (tp) cc_final: 0.7609 (tp) REVERT: A 403 LYS cc_start: 0.8546 (tppt) cc_final: 0.8085 (mmtt) REVERT: B 95 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.5448 (t80) REVERT: B 101 ARG cc_start: 0.7897 (mtp180) cc_final: 0.7537 (mmp-170) REVERT: C 75 VAL cc_start: 0.8257 (m) cc_final: 0.8046 (m) REVERT: C 118 LYS cc_start: 0.7443 (mttt) cc_final: 0.6932 (ptmt) REVERT: C 170 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8043 (mtt) REVERT: C 365 ASP cc_start: 0.6330 (t0) cc_final: 0.5828 (t0) REVERT: C 386 ARG cc_start: 0.8953 (mtt180) cc_final: 0.8706 (mtt90) REVERT: C 403 LYS cc_start: 0.8771 (tppt) cc_final: 0.8325 (mmtt) REVERT: C 425 ARG cc_start: 0.7650 (mtm-85) cc_final: 0.7055 (mtm180) REVERT: C 471 LYS cc_start: 0.7196 (mttt) cc_final: 0.6965 (mttt) REVERT: D 95 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.5603 (t80) REVERT: D 101 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7188 (tpt170) REVERT: E 198 LYS cc_start: 0.5150 (OUTLIER) cc_final: 0.4933 (ptpt) REVERT: E 471 LYS cc_start: 0.7398 (mttt) cc_final: 0.6771 (tttt) REVERT: F 95 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.5466 (t80) REVERT: G 295 LEU cc_start: 0.7982 (tp) cc_final: 0.7610 (tp) REVERT: G 403 LYS cc_start: 0.8540 (tppt) cc_final: 0.8084 (mmtt) REVERT: H 95 TYR cc_start: 0.6482 (OUTLIER) cc_final: 0.5428 (t80) REVERT: H 101 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7522 (mmp-170) REVERT: I 75 VAL cc_start: 0.8259 (m) cc_final: 0.8052 (m) REVERT: I 118 LYS cc_start: 0.7429 (mttt) cc_final: 0.6924 (ptmt) REVERT: I 170 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8019 (mtt) REVERT: I 365 ASP cc_start: 0.6284 (t0) cc_final: 0.5729 (t0) REVERT: I 386 ARG cc_start: 0.8943 (mtt180) cc_final: 0.8699 (mtt90) REVERT: I 403 LYS cc_start: 0.8767 (tppt) cc_final: 0.8321 (mmtt) REVERT: I 425 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7062 (mtm180) REVERT: I 471 LYS cc_start: 0.7232 (mtpp) cc_final: 0.7003 (mtmm) REVERT: J 95 TYR cc_start: 0.6220 (OUTLIER) cc_final: 0.5622 (t80) REVERT: J 101 ARG cc_start: 0.7819 (mtp180) cc_final: 0.7279 (tpt170) REVERT: K 208 ASP cc_start: 0.7754 (m-30) cc_final: 0.7545 (m-30) REVERT: K 471 LYS cc_start: 0.7389 (mttt) cc_final: 0.6746 (tttt) REVERT: L 95 TYR cc_start: 0.6241 (OUTLIER) cc_final: 0.5459 (t80) REVERT: M 295 LEU cc_start: 0.7988 (tp) cc_final: 0.7610 (tp) REVERT: M 403 LYS cc_start: 0.8540 (tppt) cc_final: 0.8075 (mmtt) REVERT: N 95 TYR cc_start: 0.6472 (OUTLIER) cc_final: 0.5431 (t80) REVERT: N 101 ARG cc_start: 0.7882 (mtp180) cc_final: 0.7524 (mmp-170) REVERT: O 75 VAL cc_start: 0.8247 (m) cc_final: 0.8036 (m) REVERT: O 80 ARG cc_start: 0.4956 (OUTLIER) cc_final: 0.4710 (ptm-80) REVERT: O 118 LYS cc_start: 0.7444 (mttt) cc_final: 0.6932 (ptmt) REVERT: O 170 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8010 (mtt) REVERT: O 365 ASP cc_start: 0.6271 (t0) cc_final: 0.5767 (t0) REVERT: O 386 ARG cc_start: 0.8954 (mtt180) cc_final: 0.8706 (mtt90) REVERT: O 403 LYS cc_start: 0.8774 (tppt) cc_final: 0.8326 (mmtt) REVERT: O 425 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7128 (mtm180) REVERT: O 471 LYS cc_start: 0.7225 (mtpp) cc_final: 0.6986 (mtmm) REVERT: P 95 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.5629 (t80) REVERT: P 101 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7291 (tpt170) REVERT: Q 208 ASP cc_start: 0.7768 (m-30) cc_final: 0.7559 (m-30) REVERT: Q 471 LYS cc_start: 0.7371 (mttt) cc_final: 0.6730 (tttt) REVERT: R 95 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5480 (t80) REVERT: S 295 LEU cc_start: 0.7986 (tp) cc_final: 0.7612 (tp) REVERT: S 403 LYS cc_start: 0.8530 (tppt) cc_final: 0.8063 (mmtt) REVERT: T 95 TYR cc_start: 0.6458 (OUTLIER) cc_final: 0.5409 (t80) REVERT: T 101 ARG cc_start: 0.7893 (mtp180) cc_final: 0.7534 (mmp-170) REVERT: U 75 VAL cc_start: 0.8255 (m) cc_final: 0.8043 (m) REVERT: U 118 LYS cc_start: 0.7448 (mttt) cc_final: 0.6934 (ptmt) REVERT: U 170 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8025 (mtt) REVERT: U 365 ASP cc_start: 0.6338 (t0) cc_final: 0.5845 (t0) REVERT: U 386 ARG cc_start: 0.8955 (mtt180) cc_final: 0.8708 (mtt90) REVERT: U 403 LYS cc_start: 0.8769 (tppt) cc_final: 0.8320 (mmtt) REVERT: U 425 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7124 (mtm180) REVERT: U 471 LYS cc_start: 0.7243 (mtpp) cc_final: 0.7007 (mtmm) REVERT: V 95 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5627 (t80) REVERT: V 101 ARG cc_start: 0.7761 (mtp180) cc_final: 0.7170 (tpt170) REVERT: W 198 LYS cc_start: 0.5155 (OUTLIER) cc_final: 0.4937 (ptpt) REVERT: W 471 LYS cc_start: 0.7394 (mttt) cc_final: 0.6757 (tttt) REVERT: X 95 TYR cc_start: 0.6251 (OUTLIER) cc_final: 0.5479 (t80) outliers start: 116 outliers final: 83 residues processed: 678 average time/residue: 0.5882 time to fit residues: 614.2527 Evaluate side-chains 704 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 602 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 18 ASN Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 18 ASN Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 438 GLU Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 122 optimal weight: 0.6980 chunk 379 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 421 optimal weight: 5.9990 chunk 529 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 178 optimal weight: 0.0980 chunk 199 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN G 303 GLN ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN M 303 GLN ** O 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN S 303 GLN ** U 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.151237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122605 restraints weight = 56385.138| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.51 r_work: 0.3102 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 48708 Z= 0.162 Angle : 0.468 8.574 65652 Z= 0.250 Chirality : 0.037 0.127 7092 Planarity : 0.004 0.051 8640 Dihedral : 4.173 14.428 6552 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.17 % Allowed : 14.44 % Favored : 83.39 % 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: 0.76 (0.11), residues: 5784 helix: 1.50 (0.10), residues: 2556 sheet: 0.54 (0.14), residues: 1044 loop : -0.67 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS U 238 PHE 0.010 0.001 PHE O 173 TYR 0.015 0.001 TYR Q 378 ARG 0.012 0.000 ARG I 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21629.91 seconds wall clock time: 372 minutes 23.90 seconds (22343.90 seconds total)