Starting phenix.real_space_refine on Fri Dec 27 08:03:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vd8_43145/12_2024/8vd8_43145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vd8_43145/12_2024/8vd8_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_43145/12_2024/8vd8_43145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vd8_43145/12_2024/8vd8_43145.map" model { file = "/net/cci-nas-00/data/ceres_data/8vd8_43145/12_2024/8vd8_43145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vd8_43145/12_2024/8vd8_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 10.94, per 1000 atoms: 0.23 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: 8.97 Conformation dependent library (CDL) restraints added in 4.7 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: 4.35 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: 15.48 Time building geometry restraints manager: 10.50 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: 0.00 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: 0.510 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: 1.440 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 70.050 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.110 ------------------------------------------------------------------------------- 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 : 4.399 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: 0.5962 time to fit residues: 1016.3956 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 : 4.473 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 4.432 Fit side-chains REVERT: A 27 VAL cc_start: 0.8627 (t) cc_final: 0.8293 (m) REVERT: A 76 GLU cc_start: 0.6959 (tt0) cc_final: 0.6684 (pt0) REVERT: A 213 HIS cc_start: 0.8238 (m170) cc_final: 0.8019 (m170) REVERT: A 247 GLU cc_start: 0.8248 (tt0) cc_final: 0.8008 (tt0) REVERT: A 295 LEU cc_start: 0.7691 (tp) cc_final: 0.7397 (tp) REVERT: A 403 LYS cc_start: 0.8209 (tppt) cc_final: 0.7929 (mmtt) REVERT: A 422 ASN cc_start: 0.7789 (m-40) cc_final: 0.7455 (m-40) REVERT: B 101 ARG cc_start: 0.7796 (mtp180) cc_final: 0.6898 (mpt-90) REVERT: C 85 MET cc_start: 0.3145 (mtm) cc_final: 0.2735 (mtp) REVERT: C 208 ASP cc_start: 0.7579 (m-30) cc_final: 0.7363 (m-30) REVERT: C 213 HIS cc_start: 0.8533 (m170) cc_final: 0.8266 (m-70) REVERT: C 217 ARG cc_start: 0.7817 (mtt-85) cc_final: 0.7611 (mtt180) REVERT: C 362 MET cc_start: 0.7408 (mmp) cc_final: 0.7131 (mmm) REVERT: C 386 ARG cc_start: 0.8702 (mtt180) cc_final: 0.8435 (mtt180) REVERT: C 403 LYS cc_start: 0.8341 (tppt) cc_final: 0.7872 (mmtt) REVERT: C 425 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.6849 (mtm180) REVERT: C 471 LYS cc_start: 0.7162 (mttt) cc_final: 0.6916 (mttt) REVERT: D 94 ASN cc_start: 0.7407 (t0) cc_final: 0.6733 (m110) REVERT: D 101 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7326 (mmm160) REVERT: D 103 LYS cc_start: 0.8917 (tptp) cc_final: 0.8670 (tttp) REVERT: E 322 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7226 (ttm110) REVERT: E 386 ARG cc_start: 0.9016 (mtt180) cc_final: 0.8601 (mtt90) REVERT: E 471 LYS cc_start: 0.7504 (mttt) cc_final: 0.6707 (tttt) REVERT: G 27 VAL cc_start: 0.8631 (t) cc_final: 0.8298 (m) REVERT: G 76 GLU cc_start: 0.6952 (tt0) cc_final: 0.6677 (pt0) REVERT: G 213 HIS cc_start: 0.8240 (m170) cc_final: 0.8020 (m170) REVERT: G 247 GLU cc_start: 0.8244 (tt0) cc_final: 0.8004 (tt0) REVERT: G 295 LEU cc_start: 0.7690 (tp) cc_final: 0.7394 (tp) REVERT: G 403 LYS cc_start: 0.8214 (tppt) cc_final: 0.7930 (mmtt) REVERT: G 422 ASN cc_start: 0.7790 (m-40) cc_final: 0.7457 (m-40) REVERT: H 101 ARG cc_start: 0.7799 (mtp180) cc_final: 0.6898 (mpt-90) REVERT: I 85 MET cc_start: 0.3146 (mtm) cc_final: 0.2746 (mtp) REVERT: I 208 ASP cc_start: 0.7582 (m-30) cc_final: 0.7372 (m-30) REVERT: I 213 HIS cc_start: 0.8531 (m170) cc_final: 0.8264 (m-70) REVERT: I 217 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.7614 (mtt180) REVERT: I 362 MET cc_start: 0.7405 (mmp) cc_final: 0.7132 (mmm) REVERT: I 386 ARG cc_start: 0.8701 (mtt180) cc_final: 0.8436 (mtt180) REVERT: I 403 LYS cc_start: 0.8338 (tppt) cc_final: 0.7869 (mmtt) REVERT: I 425 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.6854 (mtm180) REVERT: I 471 LYS cc_start: 0.7161 (mttt) cc_final: 0.6913 (mttt) REVERT: J 94 ASN cc_start: 0.7404 (t0) cc_final: 0.6730 (m110) REVERT: J 101 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7326 (mmm160) REVERT: J 103 LYS cc_start: 0.8918 (tptp) cc_final: 0.8671 (tttp) REVERT: K 322 ARG cc_start: 0.7500 (mtp180) cc_final: 0.7224 (ttm110) REVERT: K 386 ARG cc_start: 0.9016 (mtt180) cc_final: 0.8603 (mtt90) REVERT: K 471 LYS cc_start: 0.7501 (mttt) cc_final: 0.6704 (tttt) REVERT: M 27 VAL cc_start: 0.8625 (t) cc_final: 0.8290 (m) REVERT: M 76 GLU cc_start: 0.6953 (tt0) cc_final: 0.6663 (pt0) REVERT: M 213 HIS cc_start: 0.8239 (m170) cc_final: 0.8019 (m170) REVERT: M 247 GLU cc_start: 0.8247 (tt0) cc_final: 0.8007 (tt0) REVERT: M 295 LEU cc_start: 0.7692 (tp) cc_final: 0.7397 (tp) REVERT: M 403 LYS cc_start: 0.8207 (tppt) cc_final: 0.7927 (mmtt) REVERT: M 422 ASN cc_start: 0.7791 (m-40) cc_final: 0.7456 (m-40) REVERT: N 101 ARG cc_start: 0.7797 (mtp180) cc_final: 0.6900 (mpt-90) REVERT: O 85 MET cc_start: 0.3141 (mtm) cc_final: 0.2740 (mtp) REVERT: O 208 ASP cc_start: 0.7580 (m-30) cc_final: 0.7370 (m-30) REVERT: O 213 HIS cc_start: 0.8529 (m170) cc_final: 0.8262 (m-70) REVERT: O 217 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7618 (mtt180) REVERT: O 362 MET cc_start: 0.7408 (mmp) cc_final: 0.7136 (mmm) REVERT: O 386 ARG cc_start: 0.8704 (mtt180) cc_final: 0.8442 (mtt180) REVERT: O 403 LYS cc_start: 0.8338 (tppt) cc_final: 0.7869 (mmtt) REVERT: O 425 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6849 (mtm180) REVERT: O 471 LYS cc_start: 0.7156 (mttt) cc_final: 0.6908 (mttt) REVERT: P 94 ASN cc_start: 0.7410 (t0) cc_final: 0.6735 (m110) REVERT: P 101 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7323 (mmm160) REVERT: P 103 LYS cc_start: 0.8917 (tptp) cc_final: 0.8671 (tttp) REVERT: Q 213 HIS cc_start: 0.8527 (m170) cc_final: 0.8325 (m170) REVERT: Q 322 ARG cc_start: 0.7494 (mtp180) cc_final: 0.7222 (ttm110) REVERT: Q 386 ARG cc_start: 0.9014 (mtt180) cc_final: 0.8599 (mtt90) REVERT: Q 471 LYS cc_start: 0.7499 (mttt) cc_final: 0.6707 (tttt) REVERT: S 27 VAL cc_start: 0.8627 (t) cc_final: 0.8295 (m) REVERT: S 76 GLU cc_start: 0.6956 (tt0) cc_final: 0.6663 (pt0) REVERT: S 213 HIS cc_start: 0.8240 (m170) cc_final: 0.8022 (m170) REVERT: S 247 GLU cc_start: 0.8246 (tt0) cc_final: 0.8004 (tt0) REVERT: S 295 LEU cc_start: 0.7692 (tp) cc_final: 0.7400 (tp) REVERT: S 403 LYS cc_start: 0.8208 (tppt) cc_final: 0.7928 (mmtt) REVERT: S 422 ASN cc_start: 0.7792 (m-40) cc_final: 0.7458 (m-40) REVERT: T 101 ARG cc_start: 0.7794 (mtp180) cc_final: 0.6894 (mpt-90) REVERT: U 85 MET cc_start: 0.3147 (mtm) cc_final: 0.2736 (mtp) REVERT: U 208 ASP cc_start: 0.7582 (m-30) cc_final: 0.7365 (m-30) REVERT: U 213 HIS cc_start: 0.8532 (m170) cc_final: 0.8262 (m-70) REVERT: U 217 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7617 (mtt180) REVERT: U 362 MET cc_start: 0.7408 (mmp) cc_final: 0.7132 (mmm) REVERT: U 386 ARG cc_start: 0.8705 (mtt180) cc_final: 0.8442 (mtt180) REVERT: U 403 LYS cc_start: 0.8338 (tppt) cc_final: 0.7871 (mmtt) REVERT: U 425 ARG cc_start: 0.7244 (mtm-85) cc_final: 0.6847 (mtm180) REVERT: U 471 LYS cc_start: 0.7160 (mttt) cc_final: 0.6911 (mttt) REVERT: V 94 ASN cc_start: 0.7407 (t0) cc_final: 0.6732 (m110) REVERT: V 101 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7322 (mmm160) REVERT: V 103 LYS cc_start: 0.8918 (tptp) cc_final: 0.8673 (tttp) REVERT: W 322 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7224 (ttm110) REVERT: W 386 ARG cc_start: 0.9015 (mtt180) cc_final: 0.8602 (mtt90) REVERT: W 471 LYS cc_start: 0.7501 (mttt) cc_final: 0.6706 (tttt) outliers start: 64 outliers final: 40 residues processed: 792 average time/residue: 0.5732 time to fit residues: 698.2989 Evaluate side-chains 694 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 654 time to evaluate : 4.510 ------------------------------------------------------------------------------- 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 290 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 435 optimal weight: 1.9990 chunk 356 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 524 optimal weight: 4.9990 chunk 566 optimal weight: 2.9990 chunk 466 optimal weight: 4.9990 chunk 519 optimal weight: 0.8980 chunk 178 optimal weight: 0.1980 chunk 420 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 48708 Z= 0.164 Angle : 0.467 4.403 65652 Z= 0.260 Chirality : 0.038 0.136 7092 Planarity : 0.004 0.036 8640 Dihedral : 4.600 17.679 6552 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.40 % Allowed : 9.52 % Favored : 89.08 % 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: 0.70 (0.11), residues: 5784 helix: 1.28 (0.10), residues: 2520 sheet: 0.79 (0.14), residues: 1116 loop : -0.62 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 92 PHE 0.010 0.001 PHE S 461 TYR 0.013 0.001 TYR C 345 ARG 0.004 0.000 ARG I 399 *********************** 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 875 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 801 time to evaluate : 4.928 Fit side-chains REVERT: A 27 VAL cc_start: 0.8363 (t) cc_final: 0.8047 (m) REVERT: A 213 HIS cc_start: 0.8206 (m170) cc_final: 0.7980 (m-70) REVERT: A 295 LEU cc_start: 0.7755 (tp) cc_final: 0.7423 (tp) REVERT: A 403 LYS cc_start: 0.8189 (tppt) cc_final: 0.7722 (mmtt) REVERT: B 95 TYR cc_start: 0.6601 (OUTLIER) cc_final: 0.5693 (t80) REVERT: C 47 LYS cc_start: 0.8028 (mttt) cc_final: 0.7713 (mmtt) REVERT: C 118 LYS cc_start: 0.7328 (mttt) cc_final: 0.6943 (ptmt) REVERT: C 213 HIS cc_start: 0.8552 (m170) cc_final: 0.8292 (m-70) REVERT: C 362 MET cc_start: 0.7461 (mmp) cc_final: 0.7206 (mmm) REVERT: C 386 ARG cc_start: 0.8811 (mtt180) cc_final: 0.8485 (mtt90) REVERT: C 403 LYS cc_start: 0.8307 (tppt) cc_final: 0.7863 (mmtt) REVERT: C 425 ARG cc_start: 0.7174 (mtm-85) cc_final: 0.6648 (mtm180) REVERT: C 468 GLU cc_start: 0.8054 (tp30) cc_final: 0.7754 (tp30) REVERT: C 478 GLU cc_start: 0.6003 (mp0) cc_final: 0.5127 (tt0) REVERT: D 94 ASN cc_start: 0.7360 (t0) cc_final: 0.6694 (m110) REVERT: D 95 TYR cc_start: 0.5973 (OUTLIER) cc_final: 0.5145 (t80) REVERT: D 101 ARG cc_start: 0.7482 (mtp180) cc_final: 0.6939 (tpt170) REVERT: D 103 LYS cc_start: 0.8886 (tptp) cc_final: 0.8648 (tttp) REVERT: E 198 LYS cc_start: 0.5584 (OUTLIER) cc_final: 0.5238 (pptt) REVERT: E 386 ARG cc_start: 0.9025 (mtt180) cc_final: 0.8616 (mtt90) REVERT: G 27 VAL cc_start: 0.8368 (t) cc_final: 0.8052 (m) REVERT: G 213 HIS cc_start: 0.8209 (m170) cc_final: 0.7981 (m-70) REVERT: G 295 LEU cc_start: 0.7752 (tp) cc_final: 0.7422 (tp) REVERT: G 340 GLN cc_start: 0.8554 (tt0) cc_final: 0.8038 (mt0) REVERT: G 403 LYS cc_start: 0.8193 (tppt) cc_final: 0.7721 (mmtt) REVERT: H 95 TYR cc_start: 0.6601 (OUTLIER) cc_final: 0.5692 (t80) REVERT: I 47 LYS cc_start: 0.8026 (mttt) cc_final: 0.7714 (mmtt) REVERT: I 118 LYS cc_start: 0.7326 (mttt) cc_final: 0.6943 (ptmt) REVERT: I 213 HIS cc_start: 0.8552 (m170) cc_final: 0.8293 (m-70) REVERT: I 362 MET cc_start: 0.7460 (mmp) cc_final: 0.7206 (mmm) REVERT: I 386 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8485 (mtt90) REVERT: I 403 LYS cc_start: 0.8299 (tppt) cc_final: 0.7858 (mmtt) REVERT: I 425 ARG cc_start: 0.7174 (mtm-85) cc_final: 0.6649 (mtm180) REVERT: I 468 GLU cc_start: 0.8052 (tp30) cc_final: 0.7752 (tp30) REVERT: I 478 GLU cc_start: 0.5995 (mp0) cc_final: 0.5122 (tt0) REVERT: J 94 ASN cc_start: 0.7359 (t0) cc_final: 0.6690 (m110) REVERT: J 95 TYR cc_start: 0.5974 (OUTLIER) cc_final: 0.5149 (t80) REVERT: J 101 ARG cc_start: 0.7481 (mtp180) cc_final: 0.6939 (tpt170) REVERT: J 103 LYS cc_start: 0.8886 (tptp) cc_final: 0.8648 (tttp) REVERT: K 198 LYS cc_start: 0.5574 (OUTLIER) cc_final: 0.5230 (pptt) REVERT: K 386 ARG cc_start: 0.9025 (mtt180) cc_final: 0.8612 (mtt90) REVERT: M 27 VAL cc_start: 0.8359 (t) cc_final: 0.8043 (m) REVERT: M 213 HIS cc_start: 0.8208 (m170) cc_final: 0.7980 (m-70) REVERT: M 295 LEU cc_start: 0.7754 (tp) cc_final: 0.7423 (tp) REVERT: M 340 GLN cc_start: 0.8555 (tt0) cc_final: 0.8038 (mt0) REVERT: M 403 LYS cc_start: 0.8189 (tppt) cc_final: 0.7722 (mmtt) REVERT: N 95 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.5694 (t80) REVERT: O 47 LYS cc_start: 0.8026 (mttt) cc_final: 0.7716 (mmtt) REVERT: O 118 LYS cc_start: 0.7331 (mttt) cc_final: 0.6946 (ptmt) REVERT: O 213 HIS cc_start: 0.8550 (m170) cc_final: 0.8291 (m-70) REVERT: O 362 MET cc_start: 0.7462 (mmp) cc_final: 0.7209 (mmm) REVERT: O 386 ARG cc_start: 0.8809 (mtt180) cc_final: 0.8486 (mtt90) REVERT: O 403 LYS cc_start: 0.8297 (tppt) cc_final: 0.7856 (mmtt) REVERT: O 425 ARG cc_start: 0.7172 (mtm-85) cc_final: 0.6649 (mtm180) REVERT: O 468 GLU cc_start: 0.8046 (tp30) cc_final: 0.7753 (tp30) REVERT: O 478 GLU cc_start: 0.6001 (mp0) cc_final: 0.5119 (tt0) REVERT: P 94 ASN cc_start: 0.7361 (t0) cc_final: 0.6696 (m110) REVERT: P 95 TYR cc_start: 0.5974 (OUTLIER) cc_final: 0.5155 (t80) REVERT: P 101 ARG cc_start: 0.7479 (mtp180) cc_final: 0.6937 (tpt170) REVERT: P 103 LYS cc_start: 0.8887 (tptp) cc_final: 0.8649 (tttp) REVERT: Q 198 LYS cc_start: 0.5576 (OUTLIER) cc_final: 0.5231 (pptt) REVERT: Q 213 HIS cc_start: 0.8507 (m170) cc_final: 0.8296 (m170) REVERT: Q 386 ARG cc_start: 0.9022 (mtt180) cc_final: 0.8609 (mtt90) REVERT: S 27 VAL cc_start: 0.8365 (t) cc_final: 0.8048 (m) REVERT: S 213 HIS cc_start: 0.8203 (m170) cc_final: 0.7979 (m-70) REVERT: S 295 LEU cc_start: 0.7756 (tp) cc_final: 0.7426 (tp) REVERT: S 340 GLN cc_start: 0.8557 (tt0) cc_final: 0.8039 (mt0) REVERT: S 403 LYS cc_start: 0.8188 (tppt) cc_final: 0.7723 (mmtt) REVERT: T 95 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.5691 (t80) REVERT: U 47 LYS cc_start: 0.8028 (mttt) cc_final: 0.7712 (mmtt) REVERT: U 118 LYS cc_start: 0.7331 (mttt) cc_final: 0.6945 (ptmt) REVERT: U 213 HIS cc_start: 0.8554 (m170) cc_final: 0.8293 (m-70) REVERT: U 362 MET cc_start: 0.7460 (mmp) cc_final: 0.7205 (mmm) REVERT: U 386 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8486 (mtt90) REVERT: U 403 LYS cc_start: 0.8299 (tppt) cc_final: 0.7857 (mmtt) REVERT: U 425 ARG cc_start: 0.7171 (mtm-85) cc_final: 0.6647 (mtm180) REVERT: U 468 GLU cc_start: 0.8048 (tp30) cc_final: 0.7750 (tp30) REVERT: U 478 GLU cc_start: 0.5998 (mp0) cc_final: 0.5121 (tt0) REVERT: V 94 ASN cc_start: 0.7361 (t0) cc_final: 0.6695 (m110) REVERT: V 95 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.5152 (t80) REVERT: V 101 ARG cc_start: 0.7482 (mtp180) cc_final: 0.6943 (tpt170) REVERT: V 103 LYS cc_start: 0.8888 (tptp) cc_final: 0.8650 (tttp) REVERT: W 198 LYS cc_start: 0.5579 (OUTLIER) cc_final: 0.5232 (pptt) REVERT: W 386 ARG cc_start: 0.9024 (mtt180) cc_final: 0.8617 (mtt90) outliers start: 74 outliers final: 38 residues processed: 839 average time/residue: 0.5900 time to fit residues: 758.2710 Evaluate side-chains 700 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 650 time to evaluate : 4.428 ------------------------------------------------------------------------------- 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 B residue 95 TYR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU 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 204 VAL Chi-restraints excluded: chain E residue 324 THR 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 324 THR Chi-restraints excluded: chain I residue 325 GLU 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 204 VAL Chi-restraints excluded: chain K residue 324 THR 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 324 THR Chi-restraints excluded: chain O residue 325 GLU 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 204 VAL Chi-restraints excluded: chain Q residue 324 THR 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 T residue 95 TYR Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU 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 204 VAL Chi-restraints excluded: chain W residue 324 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 0.9990 chunk 393 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 351 optimal weight: 1.9990 chunk 525 optimal weight: 3.9990 chunk 556 optimal weight: 0.2980 chunk 274 optimal weight: 0.2980 chunk 498 optimal weight: 0.0980 chunk 150 optimal weight: 7.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 303 GLN A 452 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN E 303 GLN G 73 ASN G 303 GLN G 340 GLN G 452 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 ASN K 303 GLN M 73 ASN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 340 GLN M 452 GLN ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN Q 303 GLN S 73 ASN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 340 GLN S 452 GLN ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN W 303 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 48708 Z= 0.120 Angle : 0.423 4.646 65652 Z= 0.233 Chirality : 0.036 0.135 7092 Planarity : 0.003 0.035 8640 Dihedral : 4.141 16.294 6552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.51 % Allowed : 11.32 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.11), residues: 5784 helix: 1.66 (0.10), residues: 2520 sheet: 0.80 (0.14), residues: 1116 loop : -0.53 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS U 238 PHE 0.010 0.001 PHE A 461 TYR 0.014 0.001 TYR S 378 ARG 0.003 0.000 ARG O 399 *********************** 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 807 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 727 time to evaluate : 4.455 Fit side-chains REVERT: A 27 VAL cc_start: 0.8222 (t) cc_final: 0.7988 (m) REVERT: A 213 HIS cc_start: 0.8302 (m170) cc_final: 0.8100 (m-70) REVERT: A 216 TYR cc_start: 0.8790 (m-80) cc_final: 0.8503 (m-80) REVERT: A 295 LEU cc_start: 0.7742 (tp) cc_final: 0.7446 (tp) REVERT: A 403 LYS cc_start: 0.8180 (tppt) cc_final: 0.7731 (mmtt) REVERT: A 463 GLN cc_start: 0.5867 (mm110) cc_final: 0.5547 (mt0) REVERT: B 95 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.5701 (t80) REVERT: B 101 ARG cc_start: 0.7755 (mtp180) cc_final: 0.7393 (mmp-170) REVERT: C 47 LYS cc_start: 0.7989 (mttt) cc_final: 0.7680 (mmtt) REVERT: C 116 ASP cc_start: 0.4085 (m-30) cc_final: 0.3761 (m-30) REVERT: C 118 LYS cc_start: 0.7378 (mttt) cc_final: 0.6913 (ptmt) REVERT: C 189 ARG cc_start: 0.7795 (mtp-110) cc_final: 0.7538 (mtp85) REVERT: C 213 HIS cc_start: 0.8535 (m170) cc_final: 0.8284 (m-70) REVERT: C 362 MET cc_start: 0.7445 (mmp) cc_final: 0.7228 (mmm) REVERT: C 386 ARG cc_start: 0.8835 (mtt180) cc_final: 0.8489 (mtt90) REVERT: C 403 LYS cc_start: 0.8312 (tppt) cc_final: 0.7903 (mmtt) REVERT: C 425 ARG cc_start: 0.7233 (mtm-85) cc_final: 0.6831 (mtm180) REVERT: D 95 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.5328 (t80) REVERT: D 101 ARG cc_start: 0.7459 (mtp180) cc_final: 0.6915 (tpt170) REVERT: E 198 LYS cc_start: 0.5372 (OUTLIER) cc_final: 0.5085 (ptpt) REVERT: E 386 ARG cc_start: 0.8984 (mtt180) cc_final: 0.8665 (mtt90) REVERT: E 411 ASN cc_start: 0.7262 (m110) cc_final: 0.6902 (m-40) REVERT: E 437 ILE cc_start: 0.9066 (mm) cc_final: 0.8665 (mt) REVERT: G 27 VAL cc_start: 0.8223 (t) cc_final: 0.7986 (m) REVERT: G 213 HIS cc_start: 0.8305 (m170) cc_final: 0.8101 (m-70) REVERT: G 216 TYR cc_start: 0.8790 (m-80) cc_final: 0.8507 (m-80) REVERT: G 295 LEU cc_start: 0.7742 (tp) cc_final: 0.7448 (tp) REVERT: G 340 GLN cc_start: 0.8540 (tt0) cc_final: 0.8062 (mt0) REVERT: G 403 LYS cc_start: 0.8184 (tppt) cc_final: 0.7733 (mmtt) REVERT: H 95 TYR cc_start: 0.6621 (OUTLIER) cc_final: 0.5699 (t80) REVERT: H 101 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7392 (mmp-170) REVERT: I 47 LYS cc_start: 0.7989 (mttt) cc_final: 0.7678 (mmtt) REVERT: I 116 ASP cc_start: 0.4083 (m-30) cc_final: 0.3774 (m-30) REVERT: I 118 LYS cc_start: 0.7381 (mttt) cc_final: 0.6913 (ptmt) REVERT: I 189 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7541 (mtp85) REVERT: I 213 HIS cc_start: 0.8538 (m170) cc_final: 0.8284 (m-70) REVERT: I 362 MET cc_start: 0.7442 (mmp) cc_final: 0.7227 (mmm) REVERT: I 386 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8492 (mtt90) REVERT: I 403 LYS cc_start: 0.8308 (tppt) cc_final: 0.7897 (mmtt) REVERT: I 425 ARG cc_start: 0.7230 (mtm-85) cc_final: 0.6853 (mtm180) REVERT: J 95 TYR cc_start: 0.6114 (OUTLIER) cc_final: 0.5328 (t80) REVERT: J 101 ARG cc_start: 0.7456 (mtp180) cc_final: 0.6915 (tpt170) REVERT: K 198 LYS cc_start: 0.5373 (OUTLIER) cc_final: 0.5083 (ptpt) REVERT: K 386 ARG cc_start: 0.8983 (mtt180) cc_final: 0.8662 (mtt90) REVERT: K 411 ASN cc_start: 0.7264 (m110) cc_final: 0.6903 (m-40) REVERT: K 437 ILE cc_start: 0.9066 (mm) cc_final: 0.8667 (mt) REVERT: M 27 VAL cc_start: 0.8218 (t) cc_final: 0.7981 (m) REVERT: M 213 HIS cc_start: 0.8305 (m170) cc_final: 0.8103 (m-70) REVERT: M 216 TYR cc_start: 0.8787 (m-80) cc_final: 0.8504 (m-80) REVERT: M 295 LEU cc_start: 0.7744 (tp) cc_final: 0.7448 (tp) REVERT: M 340 GLN cc_start: 0.8539 (tt0) cc_final: 0.8061 (mt0) REVERT: M 403 LYS cc_start: 0.8180 (tppt) cc_final: 0.7728 (mmtt) REVERT: M 463 GLN cc_start: 0.5863 (mm110) cc_final: 0.5547 (mt0) REVERT: N 95 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.5697 (t80) REVERT: N 101 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7395 (mmp-170) REVERT: O 47 LYS cc_start: 0.7991 (mttt) cc_final: 0.7680 (mmtt) REVERT: O 116 ASP cc_start: 0.4084 (m-30) cc_final: 0.3773 (m-30) REVERT: O 118 LYS cc_start: 0.7380 (mttt) cc_final: 0.6908 (ptmt) REVERT: O 189 ARG cc_start: 0.7802 (mtp-110) cc_final: 0.7545 (mtp85) REVERT: O 213 HIS cc_start: 0.8538 (m170) cc_final: 0.8284 (m-70) REVERT: O 362 MET cc_start: 0.7444 (mmp) cc_final: 0.7229 (mmm) REVERT: O 386 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8495 (mtt90) REVERT: O 403 LYS cc_start: 0.8308 (tppt) cc_final: 0.7897 (mmtt) REVERT: O 425 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6855 (mtm180) REVERT: P 95 TYR cc_start: 0.6114 (OUTLIER) cc_final: 0.5330 (t80) REVERT: P 101 ARG cc_start: 0.7456 (mtp180) cc_final: 0.6915 (tpt170) REVERT: Q 198 LYS cc_start: 0.5372 (OUTLIER) cc_final: 0.5084 (ptpt) REVERT: Q 386 ARG cc_start: 0.8983 (mtt180) cc_final: 0.8663 (mtt90) REVERT: Q 411 ASN cc_start: 0.7269 (m110) cc_final: 0.6904 (m-40) REVERT: Q 437 ILE cc_start: 0.9066 (mm) cc_final: 0.8665 (mt) REVERT: S 27 VAL cc_start: 0.8222 (t) cc_final: 0.7987 (m) REVERT: S 213 HIS cc_start: 0.8300 (m170) cc_final: 0.8100 (m-70) REVERT: S 216 TYR cc_start: 0.8789 (m-80) cc_final: 0.8509 (m-80) REVERT: S 295 LEU cc_start: 0.7742 (tp) cc_final: 0.7445 (tp) REVERT: S 340 GLN cc_start: 0.8538 (tt0) cc_final: 0.8062 (mt0) REVERT: S 403 LYS cc_start: 0.8175 (tppt) cc_final: 0.7725 (mmtt) REVERT: S 463 GLN cc_start: 0.5865 (mm110) cc_final: 0.5550 (mt0) REVERT: T 95 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.5699 (t80) REVERT: T 101 ARG cc_start: 0.7754 (mtp180) cc_final: 0.7393 (mmp-170) REVERT: U 47 LYS cc_start: 0.7985 (mttt) cc_final: 0.7679 (mmtt) REVERT: U 116 ASP cc_start: 0.4083 (m-30) cc_final: 0.3760 (m-30) REVERT: U 118 LYS cc_start: 0.7379 (mttt) cc_final: 0.6911 (ptmt) REVERT: U 189 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7537 (mtp85) REVERT: U 213 HIS cc_start: 0.8536 (m170) cc_final: 0.8281 (m-70) REVERT: U 362 MET cc_start: 0.7444 (mmp) cc_final: 0.7222 (mmm) REVERT: U 386 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8492 (mtt90) REVERT: U 403 LYS cc_start: 0.8307 (tppt) cc_final: 0.7898 (mmtt) REVERT: U 425 ARG cc_start: 0.7223 (mtm-85) cc_final: 0.6811 (mtm180) REVERT: V 95 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.5328 (t80) REVERT: V 101 ARG cc_start: 0.7459 (mtp180) cc_final: 0.6916 (tpt170) REVERT: W 198 LYS cc_start: 0.5368 (OUTLIER) cc_final: 0.5083 (ptpt) REVERT: W 386 ARG cc_start: 0.8983 (mtt180) cc_final: 0.8666 (mtt90) REVERT: W 411 ASN cc_start: 0.7261 (m110) cc_final: 0.6896 (m-40) outliers start: 80 outliers final: 41 residues processed: 777 average time/residue: 0.5568 time to fit residues: 672.6997 Evaluate side-chains 719 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 666 time to evaluate : 4.393 ------------------------------------------------------------------------------- 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 228 LEU Chi-restraints excluded: chain C residue 325 GLU 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 198 LYS Chi-restraints excluded: chain E residue 204 VAL 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 228 LEU Chi-restraints excluded: chain I residue 325 GLU 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 198 LYS Chi-restraints excluded: chain K residue 204 VAL 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 228 LEU Chi-restraints excluded: chain O residue 325 GLU 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 152 GLU Chi-restraints excluded: chain Q residue 198 LYS Chi-restraints excluded: chain Q residue 204 VAL 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 228 LEU Chi-restraints excluded: chain U residue 325 GLU 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 198 LYS Chi-restraints excluded: chain W residue 204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 2.9990 chunk 316 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 414 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 475 optimal weight: 0.9980 chunk 384 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 284 optimal weight: 0.8980 chunk 499 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** 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 41 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 48708 Z= 0.219 Angle : 0.480 5.663 65652 Z= 0.260 Chirality : 0.038 0.138 7092 Planarity : 0.003 0.030 8640 Dihedral : 4.300 15.427 6552 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.42 % Allowed : 12.13 % Favored : 85.45 % 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: 0.91 (0.11), residues: 5784 helix: 1.60 (0.10), residues: 2520 sheet: 0.70 (0.14), residues: 1116 loop : -0.60 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 238 PHE 0.012 0.002 PHE E 173 TYR 0.014 0.001 TYR C 345 ARG 0.007 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 783 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 655 time to evaluate : 4.434 Fit side-chains REVERT: A 27 VAL cc_start: 0.8364 (t) cc_final: 0.8057 (m) REVERT: A 213 HIS cc_start: 0.8272 (m170) cc_final: 0.8042 (m-70) REVERT: A 216 TYR cc_start: 0.8847 (m-80) cc_final: 0.8549 (m-80) REVERT: A 243 MET cc_start: 0.7938 (tmm) cc_final: 0.7546 (tmm) REVERT: A 295 LEU cc_start: 0.7773 (tp) cc_final: 0.7454 (tp) REVERT: A 403 LYS cc_start: 0.8187 (tppt) cc_final: 0.7710 (mmtt) REVERT: B 95 TYR cc_start: 0.6581 (OUTLIER) cc_final: 0.5584 (t80) REVERT: C 213 HIS cc_start: 0.8529 (m170) cc_final: 0.8287 (m-70) REVERT: C 386 ARG cc_start: 0.8818 (mtt180) cc_final: 0.8506 (mtt90) REVERT: C 403 LYS cc_start: 0.8365 (tppt) cc_final: 0.7935 (mmtt) REVERT: C 425 ARG cc_start: 0.7192 (mtm-85) cc_final: 0.6624 (mtm180) REVERT: D 95 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.5381 (t80) REVERT: D 101 ARG cc_start: 0.7467 (mtp180) cc_final: 0.6965 (tpt170) REVERT: E 208 ASP cc_start: 0.7571 (m-30) cc_final: 0.7356 (m-30) REVERT: E 386 ARG cc_start: 0.9041 (mtt180) cc_final: 0.8689 (mtt90) REVERT: E 437 ILE cc_start: 0.9131 (mm) cc_final: 0.8720 (mt) REVERT: F 95 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.5415 (t80) REVERT: G 27 VAL cc_start: 0.8369 (t) cc_final: 0.8062 (m) REVERT: G 213 HIS cc_start: 0.8276 (m170) cc_final: 0.8043 (m-70) REVERT: G 216 TYR cc_start: 0.8848 (m-80) cc_final: 0.8552 (m-80) REVERT: G 243 MET cc_start: 0.7935 (tmm) cc_final: 0.7541 (tmm) REVERT: G 295 LEU cc_start: 0.7771 (tp) cc_final: 0.7452 (tp) REVERT: G 403 LYS cc_start: 0.8192 (tppt) cc_final: 0.7712 (mmtt) REVERT: H 95 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.5582 (t80) REVERT: I 213 HIS cc_start: 0.8528 (m170) cc_final: 0.8286 (m-70) REVERT: I 386 ARG cc_start: 0.8818 (mtt180) cc_final: 0.8505 (mtt90) REVERT: I 403 LYS cc_start: 0.8358 (tppt) cc_final: 0.7931 (mmtt) REVERT: I 425 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6630 (mtm180) REVERT: J 95 TYR cc_start: 0.6190 (OUTLIER) cc_final: 0.5380 (t80) REVERT: J 101 ARG cc_start: 0.7466 (mtp180) cc_final: 0.6964 (tpt170) REVERT: K 386 ARG cc_start: 0.9041 (mtt180) cc_final: 0.8687 (mtt90) REVERT: K 437 ILE cc_start: 0.9129 (mm) cc_final: 0.8720 (mt) REVERT: L 95 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5418 (t80) REVERT: M 27 VAL cc_start: 0.8362 (t) cc_final: 0.8054 (m) REVERT: M 213 HIS cc_start: 0.8276 (m170) cc_final: 0.8042 (m-70) REVERT: M 216 TYR cc_start: 0.8892 (m-80) cc_final: 0.8563 (m-80) REVERT: M 243 MET cc_start: 0.7940 (tmm) cc_final: 0.7546 (tmm) REVERT: M 295 LEU cc_start: 0.7771 (tp) cc_final: 0.7452 (tp) REVERT: M 403 LYS cc_start: 0.8188 (tppt) cc_final: 0.7706 (mmtt) REVERT: N 95 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.5580 (t80) REVERT: O 213 HIS cc_start: 0.8528 (m170) cc_final: 0.8285 (m-70) REVERT: O 376 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7268 (mmm) REVERT: O 386 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8509 (mtt90) REVERT: O 403 LYS cc_start: 0.8356 (tppt) cc_final: 0.7927 (mmtt) REVERT: O 425 ARG cc_start: 0.7195 (mtm-85) cc_final: 0.6627 (mtm180) REVERT: P 95 TYR cc_start: 0.6188 (OUTLIER) cc_final: 0.5383 (t80) REVERT: P 101 ARG cc_start: 0.7466 (mtp180) cc_final: 0.6964 (tpt170) REVERT: Q 386 ARG cc_start: 0.9040 (mtt180) cc_final: 0.8686 (mtt90) REVERT: Q 437 ILE cc_start: 0.9129 (mm) cc_final: 0.8717 (mt) REVERT: R 95 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.5415 (t80) REVERT: S 27 VAL cc_start: 0.8368 (t) cc_final: 0.8058 (m) REVERT: S 213 HIS cc_start: 0.8270 (m170) cc_final: 0.8041 (m-70) REVERT: S 216 TYR cc_start: 0.8892 (m-80) cc_final: 0.8562 (m-80) REVERT: S 243 MET cc_start: 0.7938 (tmm) cc_final: 0.7546 (tmm) REVERT: S 295 LEU cc_start: 0.7772 (tp) cc_final: 0.7454 (tp) REVERT: S 403 LYS cc_start: 0.8183 (tppt) cc_final: 0.7698 (mmtt) REVERT: T 95 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.5582 (t80) REVERT: U 213 HIS cc_start: 0.8528 (m170) cc_final: 0.8284 (m-70) REVERT: U 376 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7271 (mmm) REVERT: U 386 ARG cc_start: 0.8818 (mtt180) cc_final: 0.8509 (mtt90) REVERT: U 403 LYS cc_start: 0.8363 (tppt) cc_final: 0.7932 (mmtt) REVERT: U 425 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6623 (mtm180) REVERT: V 95 TYR cc_start: 0.6189 (OUTLIER) cc_final: 0.5385 (t80) REVERT: V 101 ARG cc_start: 0.7468 (mtp180) cc_final: 0.6963 (tpt170) REVERT: W 208 ASP cc_start: 0.7569 (m-30) cc_final: 0.7354 (m-30) REVERT: W 386 ARG cc_start: 0.9040 (mtt180) cc_final: 0.8689 (mtt90) REVERT: X 95 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.5415 (t80) outliers start: 128 outliers final: 92 residues processed: 731 average time/residue: 0.5665 time to fit residues: 641.9466 Evaluate side-chains 711 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 605 time to evaluate : 5.252 ------------------------------------------------------------------------------- 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 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 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 27 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU 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 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 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 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 27 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU 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 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 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 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 376 MET 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 27 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU 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 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 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 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 376 MET 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 27 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU 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 X residue 95 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 9.9990 chunk 501 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 326 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 557 optimal weight: 8.9990 chunk 462 optimal weight: 8.9990 chunk 258 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 292 optimal weight: 0.4980 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN E 303 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 452 GLN Q 303 GLN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 452 GLN W 303 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 48708 Z= 0.331 Angle : 0.553 5.382 65652 Z= 0.296 Chirality : 0.041 0.150 7092 Planarity : 0.004 0.033 8640 Dihedral : 4.651 17.222 6552 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.89 % Allowed : 12.26 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.66 (0.11), residues: 5784 helix: 1.32 (0.10), residues: 2520 sheet: 0.56 (0.14), residues: 1092 loop : -0.61 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 238 PHE 0.014 0.002 PHE E 173 TYR 0.014 0.002 TYR O 337 ARG 0.007 0.000 ARG C 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 775 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 622 time to evaluate : 4.503 Fit side-chains REVERT: A 27 VAL cc_start: 0.8439 (t) cc_final: 0.8207 (m) REVERT: A 182 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7516 (ttt180) REVERT: A 213 HIS cc_start: 0.8237 (m170) cc_final: 0.8017 (m-70) REVERT: A 295 LEU cc_start: 0.7928 (tp) cc_final: 0.7600 (tp) REVERT: A 403 LYS cc_start: 0.8248 (tppt) cc_final: 0.7753 (mmtt) REVERT: B 95 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5368 (t80) REVERT: C 118 LYS cc_start: 0.7303 (mttt) cc_final: 0.6958 (ptmt) REVERT: C 170 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7868 (mtt) REVERT: C 213 HIS cc_start: 0.8517 (m170) cc_final: 0.8282 (m-70) REVERT: C 386 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8536 (mtt90) REVERT: C 403 LYS cc_start: 0.8425 (tppt) cc_final: 0.7958 (mmtt) REVERT: C 425 ARG cc_start: 0.7232 (mtm-85) cc_final: 0.6767 (mtm180) REVERT: D 95 TYR cc_start: 0.6141 (OUTLIER) cc_final: 0.5453 (t80) REVERT: D 101 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7021 (tpt170) REVERT: E 208 ASP cc_start: 0.7665 (m-30) cc_final: 0.7448 (m-30) REVERT: E 386 ARG cc_start: 0.9028 (mtt180) cc_final: 0.8698 (mtt90) REVERT: E 475 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6835 (t0) REVERT: F 95 TYR cc_start: 0.6171 (OUTLIER) cc_final: 0.5405 (t80) REVERT: G 27 VAL cc_start: 0.8441 (t) cc_final: 0.8210 (m) REVERT: G 182 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7513 (ttt180) REVERT: G 213 HIS cc_start: 0.8241 (m170) cc_final: 0.8019 (m-70) REVERT: G 295 LEU cc_start: 0.7927 (tp) cc_final: 0.7602 (tp) REVERT: G 403 LYS cc_start: 0.8252 (tppt) cc_final: 0.7753 (mmtt) REVERT: H 95 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.5364 (t80) REVERT: I 118 LYS cc_start: 0.7308 (mttt) cc_final: 0.6961 (ptmt) REVERT: I 170 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7867 (mtt) REVERT: I 213 HIS cc_start: 0.8516 (m170) cc_final: 0.8282 (m-70) REVERT: I 386 ARG cc_start: 0.8823 (mtt180) cc_final: 0.8534 (mtt90) REVERT: I 403 LYS cc_start: 0.8419 (tppt) cc_final: 0.7952 (mmtt) REVERT: I 425 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6774 (mtm180) REVERT: J 95 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5451 (t80) REVERT: J 101 ARG cc_start: 0.7638 (mtp180) cc_final: 0.7018 (tpt170) REVERT: K 208 ASP cc_start: 0.7585 (m-30) cc_final: 0.7341 (m-30) REVERT: K 386 ARG cc_start: 0.9029 (mtt180) cc_final: 0.8701 (mtt90) REVERT: K 425 ARG cc_start: 0.7364 (mtm-85) cc_final: 0.6896 (mtm180) REVERT: K 475 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6838 (t0) REVERT: L 95 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.5403 (t80) REVERT: M 27 VAL cc_start: 0.8436 (t) cc_final: 0.8203 (m) REVERT: M 182 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7514 (ttt180) REVERT: M 213 HIS cc_start: 0.8238 (m170) cc_final: 0.8015 (m-70) REVERT: M 247 GLU cc_start: 0.8308 (tt0) cc_final: 0.8105 (tt0) REVERT: M 295 LEU cc_start: 0.7870 (tp) cc_final: 0.7545 (tp) REVERT: M 403 LYS cc_start: 0.8250 (tppt) cc_final: 0.7754 (mmtt) REVERT: N 95 TYR cc_start: 0.6520 (OUTLIER) cc_final: 0.5366 (t80) REVERT: O 118 LYS cc_start: 0.7307 (mttt) cc_final: 0.6959 (ptmt) REVERT: O 170 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7870 (mtt) REVERT: O 213 HIS cc_start: 0.8516 (m170) cc_final: 0.8279 (m-70) REVERT: O 386 ARG cc_start: 0.8811 (mtt180) cc_final: 0.8540 (mtt90) REVERT: O 403 LYS cc_start: 0.8416 (tppt) cc_final: 0.7949 (mmtt) REVERT: O 425 ARG cc_start: 0.7234 (mtm-85) cc_final: 0.6766 (mtm180) REVERT: P 95 TYR cc_start: 0.6133 (OUTLIER) cc_final: 0.5454 (t80) REVERT: P 101 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7020 (tpt170) REVERT: Q 154 MET cc_start: 0.9100 (ttm) cc_final: 0.8772 (mtp) REVERT: Q 208 ASP cc_start: 0.7587 (m-30) cc_final: 0.7347 (m-30) REVERT: Q 386 ARG cc_start: 0.9027 (mtt180) cc_final: 0.8696 (mtt90) REVERT: Q 475 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6838 (t0) REVERT: R 95 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5404 (t80) REVERT: S 27 VAL cc_start: 0.8440 (t) cc_final: 0.8205 (m) REVERT: S 182 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7521 (ttt180) REVERT: S 213 HIS cc_start: 0.8235 (m170) cc_final: 0.8016 (m-70) REVERT: S 295 LEU cc_start: 0.7929 (tp) cc_final: 0.7606 (tp) REVERT: S 403 LYS cc_start: 0.8239 (tppt) cc_final: 0.7740 (mmtt) REVERT: T 95 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5367 (t80) REVERT: U 118 LYS cc_start: 0.7304 (mttt) cc_final: 0.6957 (ptmt) REVERT: U 170 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7870 (mtt) REVERT: U 213 HIS cc_start: 0.8517 (m170) cc_final: 0.8281 (m-70) REVERT: U 386 ARG cc_start: 0.8812 (mtt180) cc_final: 0.8541 (mtt90) REVERT: U 403 LYS cc_start: 0.8424 (tppt) cc_final: 0.7954 (mmtt) REVERT: U 425 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6766 (mtm180) REVERT: V 95 TYR cc_start: 0.6135 (OUTLIER) cc_final: 0.5454 (t80) REVERT: V 101 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7019 (tpt170) REVERT: W 208 ASP cc_start: 0.7659 (m-30) cc_final: 0.7444 (m-30) REVERT: W 386 ARG cc_start: 0.9028 (mtt180) cc_final: 0.8699 (mtt90) REVERT: W 475 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6837 (t0) REVERT: X 95 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5402 (t80) outliers start: 153 outliers final: 99 residues processed: 710 average time/residue: 0.5540 time to fit residues: 613.2805 Evaluate side-chains 709 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 586 time to evaluate : 4.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 182 ARG 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 355 MET 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 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 27 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 438 GLU 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 133 VAL Chi-restraints excluded: chain G residue 182 ARG 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 18 ASN 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 95 TYR Chi-restraints excluded: chain K residue 27 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 K residue 438 GLU 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 133 VAL Chi-restraints excluded: chain M residue 182 ARG 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 18 ASN 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 95 TYR Chi-restraints excluded: chain Q residue 27 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 Q residue 438 GLU 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 133 VAL Chi-restraints excluded: chain S residue 182 ARG 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 18 ASN 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 95 TYR Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 438 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 317 optimal weight: 0.9990 chunk 406 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 chunk 469 optimal weight: 1.9990 chunk 311 optimal weight: 7.9990 chunk 555 optimal weight: 2.9990 chunk 347 optimal weight: 7.9990 chunk 338 optimal weight: 0.6980 chunk 256 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN M 283 ASN M 303 GLN ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 48708 Z= 0.132 Angle : 0.441 5.487 65652 Z= 0.241 Chirality : 0.037 0.131 7092 Planarity : 0.003 0.035 8640 Dihedral : 4.156 16.495 6552 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.21 % Allowed : 13.59 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.11), residues: 5784 helix: 1.64 (0.10), residues: 2520 sheet: 0.53 (0.14), residues: 1116 loop : -0.53 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 92 PHE 0.010 0.001 PHE U 173 TYR 0.014 0.001 TYR E 378 ARG 0.004 0.000 ARG K 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 768 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 651 time to evaluate : 4.486 Fit side-chains REVERT: A 27 VAL cc_start: 0.8173 (t) cc_final: 0.7964 (m) REVERT: A 182 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7660 (ttm170) REVERT: A 213 HIS cc_start: 0.8268 (m170) cc_final: 0.8065 (m-70) REVERT: A 216 TYR cc_start: 0.8877 (m-80) cc_final: 0.8640 (m-80) REVERT: A 295 LEU cc_start: 0.7876 (tp) cc_final: 0.7565 (tp) REVERT: A 322 ARG cc_start: 0.7261 (mtp85) cc_final: 0.7058 (ttm110) REVERT: A 403 LYS cc_start: 0.8155 (tppt) cc_final: 0.7703 (mmtt) REVERT: A 471 LYS cc_start: 0.7488 (mtpp) cc_final: 0.7088 (mtpt) REVERT: B 95 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5362 (t80) REVERT: B 101 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7190 (mmp-170) REVERT: C 118 LYS cc_start: 0.7326 (mttt) cc_final: 0.6969 (ptmt) REVERT: C 170 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7970 (mtt) REVERT: C 213 HIS cc_start: 0.8494 (m170) cc_final: 0.8260 (m-70) REVERT: C 403 LYS cc_start: 0.8421 (tppt) cc_final: 0.7993 (mmtt) REVERT: C 425 ARG cc_start: 0.7156 (mtm-85) cc_final: 0.6616 (mtm180) REVERT: D 95 TYR cc_start: 0.6124 (OUTLIER) cc_final: 0.5360 (t80) REVERT: D 101 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7044 (tpt170) REVERT: E 208 ASP cc_start: 0.7546 (m-30) cc_final: 0.7345 (m-30) REVERT: E 386 ARG cc_start: 0.8991 (mtt180) cc_final: 0.8671 (mtt90) REVERT: E 411 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.6964 (m-40) REVERT: F 95 TYR cc_start: 0.6132 (OUTLIER) cc_final: 0.5402 (t80) REVERT: G 27 VAL cc_start: 0.8179 (t) cc_final: 0.7968 (m) REVERT: G 182 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7659 (ttm170) REVERT: G 213 HIS cc_start: 0.8271 (m170) cc_final: 0.8065 (m-70) REVERT: G 216 TYR cc_start: 0.8875 (m-80) cc_final: 0.8642 (m-80) REVERT: G 295 LEU cc_start: 0.7877 (tp) cc_final: 0.7575 (tp) REVERT: G 322 ARG cc_start: 0.7262 (mtp85) cc_final: 0.7061 (ttm110) REVERT: G 403 LYS cc_start: 0.8158 (tppt) cc_final: 0.7700 (mmtt) REVERT: G 471 LYS cc_start: 0.7491 (mtpp) cc_final: 0.7091 (mtpt) REVERT: H 95 TYR cc_start: 0.6401 (OUTLIER) cc_final: 0.5362 (t80) REVERT: H 101 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7136 (mmp-170) REVERT: I 118 LYS cc_start: 0.7335 (mttt) cc_final: 0.6972 (ptmt) REVERT: I 170 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7969 (mtt) REVERT: I 213 HIS cc_start: 0.8492 (m170) cc_final: 0.8260 (m-70) REVERT: I 403 LYS cc_start: 0.8414 (tppt) cc_final: 0.7990 (mmtt) REVERT: I 425 ARG cc_start: 0.7159 (mtm-85) cc_final: 0.6616 (mtm180) REVERT: J 95 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.5356 (t80) REVERT: J 101 ARG cc_start: 0.7558 (mtp180) cc_final: 0.7041 (tpt170) REVERT: K 208 ASP cc_start: 0.7482 (m-30) cc_final: 0.7242 (m-30) REVERT: K 386 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8670 (mtt90) REVERT: K 411 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.6963 (m-40) REVERT: L 95 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5398 (t80) REVERT: M 27 VAL cc_start: 0.8179 (t) cc_final: 0.7968 (m) REVERT: M 182 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7658 (ttm170) REVERT: M 213 HIS cc_start: 0.8272 (m170) cc_final: 0.8066 (m-70) REVERT: M 216 TYR cc_start: 0.8876 (m-80) cc_final: 0.8645 (m-80) REVERT: M 295 LEU cc_start: 0.7871 (tp) cc_final: 0.7569 (tp) REVERT: M 303 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8693 (pp30) REVERT: M 403 LYS cc_start: 0.8155 (tppt) cc_final: 0.7696 (mmtt) REVERT: M 471 LYS cc_start: 0.7487 (mtpp) cc_final: 0.7084 (mtpt) REVERT: N 95 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5359 (t80) REVERT: N 101 ARG cc_start: 0.7665 (mtp180) cc_final: 0.7137 (mmp-170) REVERT: O 118 LYS cc_start: 0.7330 (mttt) cc_final: 0.6969 (ptmt) REVERT: O 170 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7971 (mtt) REVERT: O 213 HIS cc_start: 0.8493 (m170) cc_final: 0.8258 (m-70) REVERT: O 386 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8622 (mtt180) REVERT: O 403 LYS cc_start: 0.8410 (tppt) cc_final: 0.7987 (mmtt) REVERT: O 425 ARG cc_start: 0.7160 (mtm-85) cc_final: 0.6618 (mtm180) REVERT: P 95 TYR cc_start: 0.6118 (OUTLIER) cc_final: 0.5360 (t80) REVERT: P 101 ARG cc_start: 0.7562 (mtp180) cc_final: 0.7044 (tpt170) REVERT: Q 154 MET cc_start: 0.9017 (ttm) cc_final: 0.8427 (mtp) REVERT: Q 208 ASP cc_start: 0.7479 (m-30) cc_final: 0.7243 (m-30) REVERT: Q 386 ARG cc_start: 0.8986 (mtt180) cc_final: 0.8631 (mtt90) REVERT: Q 411 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.6967 (m-40) REVERT: R 95 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.5401 (t80) REVERT: S 27 VAL cc_start: 0.8177 (t) cc_final: 0.7964 (m) REVERT: S 182 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7669 (ttm170) REVERT: S 213 HIS cc_start: 0.8264 (m170) cc_final: 0.8062 (m-70) REVERT: S 216 TYR cc_start: 0.8879 (m-80) cc_final: 0.8647 (m-80) REVERT: S 295 LEU cc_start: 0.7872 (tp) cc_final: 0.7571 (tp) REVERT: S 303 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8700 (pp30) REVERT: S 403 LYS cc_start: 0.8156 (tppt) cc_final: 0.7697 (mmtt) REVERT: S 471 LYS cc_start: 0.7483 (mtpp) cc_final: 0.7082 (mtpt) REVERT: T 95 TYR cc_start: 0.6400 (OUTLIER) cc_final: 0.5359 (t80) REVERT: T 101 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7133 (mmp-170) REVERT: U 118 LYS cc_start: 0.7325 (mttt) cc_final: 0.6967 (ptmt) REVERT: U 170 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7970 (mtt) REVERT: U 213 HIS cc_start: 0.8494 (m170) cc_final: 0.8259 (m-70) REVERT: U 386 ARG cc_start: 0.8837 (mtt180) cc_final: 0.8622 (mtt180) REVERT: U 403 LYS cc_start: 0.8417 (tppt) cc_final: 0.7990 (mmtt) REVERT: U 425 ARG cc_start: 0.7158 (mtm-85) cc_final: 0.6617 (mtm180) REVERT: V 95 TYR cc_start: 0.6120 (OUTLIER) cc_final: 0.5361 (t80) REVERT: V 101 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7042 (tpt170) REVERT: W 386 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8637 (mtt90) REVERT: W 411 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.6959 (m-40) REVERT: X 95 TYR cc_start: 0.6133 (OUTLIER) cc_final: 0.5401 (t80) outliers start: 117 outliers final: 69 residues processed: 711 average time/residue: 0.5713 time to fit residues: 629.3789 Evaluate side-chains 726 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 631 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ARG 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 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 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 27 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 182 ARG Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR 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 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 27 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 411 ASN Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 182 ARG 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 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 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 27 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 324 THR Chi-restraints excluded: chain Q residue 411 ASN Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 182 ARG 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 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 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 27 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 243 MET Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 411 ASN 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 343 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 331 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 352 optimal weight: 8.9990 chunk 378 optimal weight: 7.9990 chunk 274 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 436 optimal weight: 3.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN E 303 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 GLN K 303 GLN M 283 ASN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 452 GLN Q 303 GLN S 283 ASN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 452 GLN W 303 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 48708 Z= 0.288 Angle : 0.534 8.435 65652 Z= 0.283 Chirality : 0.040 0.134 7092 Planarity : 0.004 0.056 8640 Dihedral : 4.439 15.986 6552 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.61 % Allowed : 13.40 % Favored : 83.99 % 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: 0.62 (0.11), residues: 5784 helix: 1.36 (0.10), residues: 2556 sheet: 0.38 (0.13), residues: 1116 loop : -0.68 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 92 PHE 0.013 0.002 PHE W 173 TYR 0.013 0.002 TYR S 378 ARG 0.012 0.000 ARG M 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 757 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 619 time to evaluate : 4.515 Fit side-chains REVERT: A 182 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7507 (ttt180) REVERT: A 213 HIS cc_start: 0.8240 (m170) cc_final: 0.8009 (m-70) REVERT: A 295 LEU cc_start: 0.7920 (tp) cc_final: 0.7590 (tp) REVERT: A 403 LYS cc_start: 0.8185 (tppt) cc_final: 0.7727 (mmtt) REVERT: B 95 TYR cc_start: 0.6489 (OUTLIER) cc_final: 0.5376 (t80) REVERT: C 118 LYS cc_start: 0.7308 (mttt) cc_final: 0.6987 (ptmt) REVERT: C 170 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8095 (mtt) REVERT: C 213 HIS cc_start: 0.8513 (m170) cc_final: 0.8277 (m-70) REVERT: C 403 LYS cc_start: 0.8423 (tppt) cc_final: 0.7979 (mmtt) REVERT: C 425 ARG cc_start: 0.7177 (mtm-85) cc_final: 0.6638 (mtm180) REVERT: D 95 TYR cc_start: 0.6124 (OUTLIER) cc_final: 0.5461 (t80) REVERT: D 101 ARG cc_start: 0.7638 (mtp180) cc_final: 0.7051 (tpt170) REVERT: E 208 ASP cc_start: 0.7569 (m-30) cc_final: 0.7364 (m-30) REVERT: E 386 ARG cc_start: 0.9031 (mtt180) cc_final: 0.8688 (mtt90) REVERT: F 95 TYR cc_start: 0.6164 (OUTLIER) cc_final: 0.5413 (t80) REVERT: G 182 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7505 (ttt180) REVERT: G 213 HIS cc_start: 0.8243 (m170) cc_final: 0.8013 (m-70) REVERT: G 295 LEU cc_start: 0.7943 (tp) cc_final: 0.7620 (tp) REVERT: G 403 LYS cc_start: 0.8192 (tppt) cc_final: 0.7727 (mmtt) REVERT: H 95 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.5372 (t80) REVERT: I 118 LYS cc_start: 0.7311 (mttt) cc_final: 0.6990 (ptmt) REVERT: I 170 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8093 (mtt) REVERT: I 213 HIS cc_start: 0.8514 (m170) cc_final: 0.8276 (m-70) REVERT: I 403 LYS cc_start: 0.8416 (tppt) cc_final: 0.7970 (mmtt) REVERT: I 425 ARG cc_start: 0.7178 (mtm-85) cc_final: 0.6642 (mtm180) REVERT: J 95 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.5457 (t80) REVERT: J 101 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7048 (tpt170) REVERT: K 208 ASP cc_start: 0.7550 (m-30) cc_final: 0.7303 (m-30) REVERT: K 386 ARG cc_start: 0.9032 (mtt180) cc_final: 0.8687 (mtt90) REVERT: L 95 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.5410 (t80) REVERT: M 182 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7498 (ttt180) REVERT: M 213 HIS cc_start: 0.8242 (m170) cc_final: 0.8010 (m-70) REVERT: M 295 LEU cc_start: 0.7892 (tp) cc_final: 0.7574 (tp) REVERT: M 403 LYS cc_start: 0.8188 (tppt) cc_final: 0.7725 (mmtt) REVERT: N 95 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.5374 (t80) REVERT: O 118 LYS cc_start: 0.7310 (mttt) cc_final: 0.6985 (ptmt) REVERT: O 170 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8094 (mtt) REVERT: O 213 HIS cc_start: 0.8515 (m170) cc_final: 0.8278 (m-70) REVERT: O 386 ARG cc_start: 0.8889 (mtt180) cc_final: 0.8601 (mtt90) REVERT: O 403 LYS cc_start: 0.8415 (tppt) cc_final: 0.7968 (mmtt) REVERT: O 425 ARG cc_start: 0.7174 (mtm-85) cc_final: 0.6635 (mtm180) REVERT: P 95 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5456 (t80) REVERT: P 101 ARG cc_start: 0.7634 (mtp180) cc_final: 0.7048 (tpt170) REVERT: Q 154 MET cc_start: 0.9078 (ttm) cc_final: 0.8723 (mtp) REVERT: Q 386 ARG cc_start: 0.9033 (mtt180) cc_final: 0.8687 (mtt90) REVERT: R 95 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.5410 (t80) REVERT: S 182 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7512 (ttt180) REVERT: S 213 HIS cc_start: 0.8237 (m170) cc_final: 0.8007 (m-70) REVERT: S 295 LEU cc_start: 0.7895 (tp) cc_final: 0.7575 (tp) REVERT: S 403 LYS cc_start: 0.8183 (tppt) cc_final: 0.7717 (mmtt) REVERT: T 95 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.5374 (t80) REVERT: U 118 LYS cc_start: 0.7306 (mttt) cc_final: 0.6983 (ptmt) REVERT: U 170 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8092 (mtt) REVERT: U 213 HIS cc_start: 0.8517 (m170) cc_final: 0.8279 (m-70) REVERT: U 386 ARG cc_start: 0.8890 (mtt180) cc_final: 0.8599 (mtt90) REVERT: U 403 LYS cc_start: 0.8418 (tppt) cc_final: 0.7981 (mmtt) REVERT: U 425 ARG cc_start: 0.7175 (mtm-85) cc_final: 0.6638 (mtm180) REVERT: V 95 TYR cc_start: 0.6118 (OUTLIER) cc_final: 0.5461 (t80) REVERT: V 101 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7048 (tpt170) REVERT: W 386 ARG cc_start: 0.9033 (mtt180) cc_final: 0.8690 (mtt90) REVERT: X 95 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.5411 (t80) outliers start: 138 outliers final: 107 residues processed: 697 average time/residue: 0.5818 time to fit residues: 622.6873 Evaluate side-chains 732 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 605 time to evaluate : 4.462 ------------------------------------------------------------------------------- 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 182 ARG 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 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 386 ARG 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 27 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 LEU 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 182 ARG 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 18 ASN 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 386 ARG 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 27 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 411 ASN Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 440 LEU 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 182 ARG 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 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 95 TYR Chi-restraints excluded: chain Q residue 27 VAL 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 324 THR Chi-restraints excluded: chain Q residue 411 ASN Chi-restraints excluded: chain Q residue 438 GLU Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 182 ARG 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 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 27 VAL Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 411 ASN Chi-restraints excluded: chain W residue 438 GLU Chi-restraints excluded: chain W residue 440 LEU 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 505 optimal weight: 9.9990 chunk 531 optimal weight: 6.9990 chunk 485 optimal weight: 1.9990 chunk 517 optimal weight: 0.9980 chunk 311 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 406 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 467 optimal weight: 30.0000 chunk 489 optimal weight: 6.9990 chunk 515 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN G 283 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3494 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= 0.186 Angle : 0.482 8.610 65652 Z= 0.258 Chirality : 0.038 0.129 7092 Planarity : 0.003 0.058 8640 Dihedral : 4.230 15.767 6552 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.57 % Allowed : 13.76 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.11), residues: 5784 helix: 1.49 (0.10), residues: 2556 sheet: 0.41 (0.14), residues: 1116 loop : -0.64 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 238 PHE 0.011 0.001 PHE W 173 TYR 0.015 0.001 TYR K 378 ARG 0.014 0.000 ARG M 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 771 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 635 time to evaluate : 5.036 Fit side-chains REVERT: A 70 LYS cc_start: 0.8698 (mtpt) cc_final: 0.8427 (mttp) REVERT: A 182 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7502 (ttt180) REVERT: A 213 HIS cc_start: 0.8263 (m170) cc_final: 0.8052 (m-70) REVERT: A 216 TYR cc_start: 0.8905 (m-80) cc_final: 0.8594 (m-80) REVERT: A 228 LEU cc_start: 0.8671 (mt) cc_final: 0.8440 (mt) REVERT: A 295 LEU cc_start: 0.7903 (tp) cc_final: 0.7579 (tp) REVERT: A 403 LYS cc_start: 0.8162 (tppt) cc_final: 0.7708 (mmtt) REVERT: B 95 TYR cc_start: 0.6427 (OUTLIER) cc_final: 0.5370 (t80) REVERT: B 101 ARG cc_start: 0.7712 (mtp180) cc_final: 0.7220 (mmp-170) REVERT: C 118 LYS cc_start: 0.7302 (mttt) cc_final: 0.7015 (ptmt) REVERT: C 170 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7915 (mtt) REVERT: C 403 LYS cc_start: 0.8370 (tppt) cc_final: 0.7937 (mmtt) REVERT: C 425 ARG cc_start: 0.7185 (mtm-85) cc_final: 0.6691 (mtm180) REVERT: C 468 GLU cc_start: 0.8267 (tp30) cc_final: 0.8042 (tp30) REVERT: D 95 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.5544 (t80) REVERT: D 101 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7063 (tpt170) REVERT: E 154 MET cc_start: 0.9107 (ttm) cc_final: 0.8582 (mtp) REVERT: E 208 ASP cc_start: 0.7486 (m-30) cc_final: 0.7262 (m-30) REVERT: E 386 ARG cc_start: 0.8994 (mtt180) cc_final: 0.8646 (mtt90) REVERT: F 95 TYR cc_start: 0.6134 (OUTLIER) cc_final: 0.5409 (t80) REVERT: G 70 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8427 (mttp) REVERT: G 182 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7502 (ttt180) REVERT: G 213 HIS cc_start: 0.8264 (m170) cc_final: 0.8055 (m-70) REVERT: G 216 TYR cc_start: 0.8903 (m-80) cc_final: 0.8596 (m-80) REVERT: G 228 LEU cc_start: 0.8674 (mt) cc_final: 0.8440 (mt) REVERT: G 295 LEU cc_start: 0.7896 (tp) cc_final: 0.7585 (tp) REVERT: G 403 LYS cc_start: 0.8166 (tppt) cc_final: 0.7708 (mmtt) REVERT: H 95 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.5370 (t80) REVERT: H 101 ARG cc_start: 0.7663 (mtp180) cc_final: 0.7170 (mmp-170) REVERT: I 118 LYS cc_start: 0.7308 (mttt) cc_final: 0.7016 (ptmt) REVERT: I 170 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7913 (mtt) REVERT: I 403 LYS cc_start: 0.8366 (tppt) cc_final: 0.7932 (mmtt) REVERT: I 425 ARG cc_start: 0.7186 (mtm-85) cc_final: 0.6695 (mtm180) REVERT: I 468 GLU cc_start: 0.8265 (tp30) cc_final: 0.8039 (tp30) REVERT: J 95 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5536 (t80) REVERT: J 101 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7059 (tpt170) REVERT: K 154 MET cc_start: 0.9079 (ttm) cc_final: 0.8545 (mtp) REVERT: K 386 ARG cc_start: 0.8992 (mtt180) cc_final: 0.8645 (mtt90) REVERT: L 95 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5409 (t80) REVERT: M 70 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8429 (mttp) REVERT: M 182 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7498 (ttt180) REVERT: M 213 HIS cc_start: 0.8266 (m170) cc_final: 0.8054 (m-70) REVERT: M 216 TYR cc_start: 0.8904 (m-80) cc_final: 0.8656 (m-80) REVERT: M 228 LEU cc_start: 0.8672 (mt) cc_final: 0.8442 (mt) REVERT: M 295 LEU cc_start: 0.7908 (tp) cc_final: 0.7597 (tp) REVERT: M 403 LYS cc_start: 0.8163 (tppt) cc_final: 0.7703 (mmtt) REVERT: N 95 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5365 (t80) REVERT: N 101 ARG cc_start: 0.7660 (mtp180) cc_final: 0.7167 (mmp-170) REVERT: O 118 LYS cc_start: 0.7308 (mttt) cc_final: 0.7014 (ptmt) REVERT: O 170 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7914 (mtt) REVERT: O 386 ARG cc_start: 0.8902 (mtt180) cc_final: 0.8699 (mtt180) REVERT: O 403 LYS cc_start: 0.8360 (tppt) cc_final: 0.7928 (mmtt) REVERT: O 425 ARG cc_start: 0.7184 (mtm-85) cc_final: 0.6693 (mtm180) REVERT: O 468 GLU cc_start: 0.8266 (tp30) cc_final: 0.8042 (tp30) REVERT: P 95 TYR cc_start: 0.6157 (OUTLIER) cc_final: 0.5538 (t80) REVERT: P 101 ARG cc_start: 0.7628 (mtp180) cc_final: 0.7058 (tpt170) REVERT: Q 386 ARG cc_start: 0.8993 (mtt180) cc_final: 0.8641 (mtt90) REVERT: R 95 TYR cc_start: 0.6134 (OUTLIER) cc_final: 0.5405 (t80) REVERT: S 70 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8430 (mttp) REVERT: S 182 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7507 (ttt180) REVERT: S 213 HIS cc_start: 0.8257 (m170) cc_final: 0.8049 (m-70) REVERT: S 216 TYR cc_start: 0.8906 (m-80) cc_final: 0.8657 (m-80) REVERT: S 228 LEU cc_start: 0.8668 (mt) cc_final: 0.8438 (mt) REVERT: S 295 LEU cc_start: 0.7910 (tp) cc_final: 0.7599 (tp) REVERT: S 403 LYS cc_start: 0.8160 (tppt) cc_final: 0.7698 (mmtt) REVERT: T 95 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.5366 (t80) REVERT: T 101 ARG cc_start: 0.7657 (mtp180) cc_final: 0.7165 (mmp-170) REVERT: U 118 LYS cc_start: 0.7277 (mttt) cc_final: 0.6981 (ptmt) REVERT: U 170 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7911 (mtt) REVERT: U 386 ARG cc_start: 0.8904 (mtt180) cc_final: 0.8699 (mtt180) REVERT: U 403 LYS cc_start: 0.8427 (tppt) cc_final: 0.8012 (mmtt) REVERT: U 425 ARG cc_start: 0.7181 (mtm-85) cc_final: 0.6692 (mtm180) REVERT: U 468 GLU cc_start: 0.8265 (tp30) cc_final: 0.8043 (tp30) REVERT: V 95 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5543 (t80) REVERT: V 101 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7059 (tpt170) REVERT: W 154 MET cc_start: 0.9105 (ttm) cc_final: 0.8582 (mtp) REVERT: W 386 ARG cc_start: 0.8997 (mtt180) cc_final: 0.8646 (mtt90) REVERT: X 95 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5408 (t80) outliers start: 136 outliers final: 96 residues processed: 717 average time/residue: 0.5706 time to fit residues: 633.1537 Evaluate side-chains 744 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 628 time to evaluate : 4.458 ------------------------------------------------------------------------------- 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 182 ARG 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 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 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 27 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 456 MET 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 182 ARG 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 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 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 27 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain K residue 456 MET 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 182 ARG 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 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 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 27 VAL 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 324 THR Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain Q residue 456 MET Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 182 ARG 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 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 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 27 VAL Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 204 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 0.9990 chunk 547 optimal weight: 10.0000 chunk 333 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 380 optimal weight: 0.9980 chunk 573 optimal weight: 6.9990 chunk 528 optimal weight: 10.0000 chunk 456 optimal weight: 7.9990 chunk 47 optimal weight: 0.0970 chunk 352 optimal weight: 8.9990 chunk 280 optimal weight: 8.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 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** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 48708 Z= 0.264 Angle : 0.527 8.554 65652 Z= 0.280 Chirality : 0.039 0.132 7092 Planarity : 0.004 0.062 8640 Dihedral : 4.386 16.119 6552 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.29 % Allowed : 13.91 % Favored : 83.81 % 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: 0.61 (0.11), residues: 5784 helix: 1.36 (0.10), residues: 2556 sheet: 0.33 (0.14), residues: 1116 loop : -0.65 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS S 238 PHE 0.013 0.002 PHE E 173 TYR 0.014 0.002 TYR S 378 ARG 0.014 0.000 ARG M 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 743 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 622 time to evaluate : 4.501 Fit side-chains REVERT: A 70 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8428 (mttp) REVERT: A 182 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7514 (ttt180) REVERT: A 213 HIS cc_start: 0.8219 (m170) cc_final: 0.7986 (m-70) REVERT: A 295 LEU cc_start: 0.7913 (tp) cc_final: 0.7582 (tp) REVERT: A 403 LYS cc_start: 0.8177 (tppt) cc_final: 0.7719 (mmtt) REVERT: B 95 TYR cc_start: 0.6468 (OUTLIER) cc_final: 0.5373 (t80) REVERT: B 101 ARG cc_start: 0.7685 (mtp180) cc_final: 0.7204 (mmp-170) REVERT: C 118 LYS cc_start: 0.7330 (mttt) cc_final: 0.7027 (ptmt) REVERT: C 170 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7920 (mtt) REVERT: C 403 LYS cc_start: 0.8416 (tppt) cc_final: 0.7970 (mmtt) REVERT: C 425 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6687 (mtm180) REVERT: D 95 TYR cc_start: 0.6108 (OUTLIER) cc_final: 0.5458 (t80) REVERT: D 101 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7040 (tpt170) REVERT: E 208 ASP cc_start: 0.7567 (m-30) cc_final: 0.7363 (m-30) REVERT: E 386 ARG cc_start: 0.9032 (mtt180) cc_final: 0.8687 (mtt90) REVERT: F 95 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.5420 (t80) REVERT: G 70 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8426 (mttp) REVERT: G 182 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7510 (ttt180) REVERT: G 213 HIS cc_start: 0.8223 (m170) cc_final: 0.7989 (m-70) REVERT: G 295 LEU cc_start: 0.7938 (tp) cc_final: 0.7612 (tp) REVERT: G 403 LYS cc_start: 0.8175 (tppt) cc_final: 0.7720 (mmtt) REVERT: H 95 TYR cc_start: 0.6468 (OUTLIER) cc_final: 0.5369 (t80) REVERT: H 101 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7199 (mmp-170) REVERT: I 118 LYS cc_start: 0.7335 (mttt) cc_final: 0.7030 (ptmt) REVERT: I 170 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7920 (mtt) REVERT: I 403 LYS cc_start: 0.8408 (tppt) cc_final: 0.7963 (mmtt) REVERT: I 425 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6689 (mtm180) REVERT: J 95 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5454 (t80) REVERT: J 101 ARG cc_start: 0.7635 (mtp180) cc_final: 0.7039 (tpt170) REVERT: K 208 ASP cc_start: 0.7554 (m-30) cc_final: 0.7307 (m-30) REVERT: K 386 ARG cc_start: 0.9032 (mtt180) cc_final: 0.8686 (mtt90) REVERT: L 95 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5419 (t80) REVERT: M 70 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8432 (mttp) REVERT: M 182 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7506 (ttt180) REVERT: M 213 HIS cc_start: 0.8220 (m170) cc_final: 0.7986 (m-70) REVERT: M 295 LEU cc_start: 0.7892 (tp) cc_final: 0.7574 (tp) REVERT: M 403 LYS cc_start: 0.8180 (tppt) cc_final: 0.7719 (mmtt) REVERT: N 95 TYR cc_start: 0.6464 (OUTLIER) cc_final: 0.5370 (t80) REVERT: N 101 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7197 (mmp-170) REVERT: O 118 LYS cc_start: 0.7334 (mttt) cc_final: 0.7027 (ptmt) REVERT: O 170 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7921 (mtt) REVERT: O 386 ARG cc_start: 0.8880 (mtt180) cc_final: 0.8660 (mtt180) REVERT: O 403 LYS cc_start: 0.8407 (tppt) cc_final: 0.7960 (mmtt) REVERT: O 425 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6688 (mtm180) REVERT: P 95 TYR cc_start: 0.6100 (OUTLIER) cc_final: 0.5455 (t80) REVERT: P 101 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7042 (tpt170) REVERT: Q 154 MET cc_start: 0.9084 (ttm) cc_final: 0.8803 (mtp) REVERT: Q 208 ASP cc_start: 0.7547 (m-30) cc_final: 0.7305 (m-30) REVERT: Q 386 ARG cc_start: 0.9033 (mtt180) cc_final: 0.8683 (mtt90) REVERT: R 95 TYR cc_start: 0.6164 (OUTLIER) cc_final: 0.5416 (t80) REVERT: S 70 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8429 (mttp) REVERT: S 182 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7519 (ttt180) REVERT: S 213 HIS cc_start: 0.8216 (m170) cc_final: 0.7983 (m-70) REVERT: S 295 LEU cc_start: 0.7898 (tp) cc_final: 0.7578 (tp) REVERT: S 403 LYS cc_start: 0.8174 (tppt) cc_final: 0.7711 (mmtt) REVERT: T 95 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5369 (t80) REVERT: T 101 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7196 (mmp-170) REVERT: U 118 LYS cc_start: 0.7328 (mttt) cc_final: 0.7023 (ptmt) REVERT: U 170 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7920 (mtt) REVERT: U 386 ARG cc_start: 0.8880 (mtt180) cc_final: 0.8661 (mtt180) REVERT: U 403 LYS cc_start: 0.8412 (tppt) cc_final: 0.7963 (mmtt) REVERT: U 425 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6689 (mtm180) REVERT: V 95 TYR cc_start: 0.6105 (OUTLIER) cc_final: 0.5459 (t80) REVERT: V 101 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7038 (tpt170) REVERT: W 386 ARG cc_start: 0.9032 (mtt180) cc_final: 0.8684 (mtt90) REVERT: X 95 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.5418 (t80) outliers start: 121 outliers final: 96 residues processed: 694 average time/residue: 0.5664 time to fit residues: 608.3711 Evaluate side-chains 735 residues out of total 5292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 619 time to evaluate : 4.488 ------------------------------------------------------------------------------- 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 182 ARG 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 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 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 27 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 456 MET 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 182 ARG 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 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 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 27 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain K residue 456 MET 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 182 ARG 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 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 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 27 VAL 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 324 THR Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain Q residue 456 MET Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 182 ARG 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 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 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 27 VAL Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 204 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 5.9990 chunk 486 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 421 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 457 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 469 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 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 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 = 0.3552 r_free = 0.3552 target = 0.140856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109562 restraints weight = 58306.370| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.80 r_work: 0.2987 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 48708 Z= 0.274 Angle : 0.529 8.325 65652 Z= 0.282 Chirality : 0.040 0.132 7092 Planarity : 0.004 0.063 8640 Dihedral : 4.419 16.250 6552 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.55 % Allowed : 13.79 % Favored : 83.65 % 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: 0.55 (0.11), residues: 5784 helix: 1.30 (0.10), residues: 2556 sheet: 0.29 (0.13), residues: 1116 loop : -0.66 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS S 92 PHE 0.013 0.002 PHE E 173 TYR 0.012 0.002 TYR K 334 ARG 0.014 0.000 ARG S 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10711.44 seconds wall clock time: 188 minutes 33.32 seconds (11313.32 seconds total)