Starting phenix.real_space_refine on Thu Oct 10 06:54:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkb_19267/10_2024/8rkb_19267.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkb_19267/10_2024/8rkb_19267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkb_19267/10_2024/8rkb_19267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkb_19267/10_2024/8rkb_19267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkb_19267/10_2024/8rkb_19267.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rkb_19267/10_2024/8rkb_19267.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 144 5.16 5 C 31872 2.51 5 N 8988 2.21 5 O 9480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 50484 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3151 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 26, 'TRANS': 378} Chain: "B" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1056 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 130} Restraints were copied for chains: D, F, H, J, L, N, P, R, T, V, X, C, E, G, I, K, M, O, Q, S, U, W Time building chain proxies: 10.58, per 1000 atoms: 0.21 Number of scatterers: 50484 At special positions: 0 Unit cell: (167.554, 167.554, 164.219, 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 144 16.00 O 9480 8.00 N 8988 7.00 C 31872 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: 9.33 Conformation dependent library (CDL) restraints added in 4.8 seconds 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12120 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 48 sheets defined 58.1% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 removed outlier: 3.528A pdb=" N GLN A 16 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 19 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG A 24 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 31 Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 56 through 71 removed outlier: 4.330A pdb=" N GLN A 60 " --> pdb=" O ASN A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 87 removed outlier: 3.633A pdb=" N ILE A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Proline residue: A 212 - end of helix Processing helix chain 'A' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 302 Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 326 through 346 Processing helix chain 'A' and resid 346 through 355 removed outlier: 3.536A pdb=" N LEU A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Proline residue: A 385 - end of helix Processing helix chain 'A' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 23 removed outlier: 6.870A pdb=" N GLU B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN B 16 " --> pdb=" O GLN B 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 Processing helix chain 'B' and resid 64 through 79 Processing helix chain 'B' and resid 87 through 105 Processing helix chain 'C' and resid 13 through 19 removed outlier: 3.529A pdb=" N GLN C 16 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG C 18 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C 19 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG C 24 " --> pdb=" O GLN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 41 through 54 Processing helix chain 'C' and resid 56 through 71 removed outlier: 4.331A pdb=" N GLN C 60 " --> pdb=" O ASN C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 87 removed outlier: 3.633A pdb=" N ILE C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 200 through 203 Processing helix chain 'C' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP C 211 " --> pdb=" O ARG C 207 " (cutoff:3.500A) Proline residue: C 212 - end of helix Processing helix chain 'C' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 302 Processing helix chain 'C' and resid 317 through 324 Processing helix chain 'C' and resid 326 through 346 Processing helix chain 'C' and resid 346 through 355 removed outlier: 3.536A pdb=" N LEU C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 364 Processing helix chain 'C' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET C 380 " --> pdb=" O ASP C 376 " (cutoff:3.500A) Proline residue: C 385 - end of helix Processing helix chain 'C' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL C 399 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 23 removed outlier: 6.871A pdb=" N GLU D 15 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN D 16 " --> pdb=" O GLN D 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS D 17 " --> pdb=" O TYR D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 53 Processing helix chain 'D' and resid 64 through 79 Processing helix chain 'D' and resid 87 through 105 Processing helix chain 'E' and resid 13 through 19 removed outlier: 3.528A pdb=" N GLN E 16 " --> pdb=" O ARG E 13 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG E 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU E 19 " --> pdb=" O GLN E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG E 24 " --> pdb=" O GLN E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 41 through 54 Processing helix chain 'E' and resid 56 through 71 removed outlier: 4.330A pdb=" N GLN E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 87 removed outlier: 3.634A pdb=" N ILE E 85 " --> pdb=" O ARG E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP E 128 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 200 through 203 Processing helix chain 'E' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP E 211 " --> pdb=" O ARG E 207 " (cutoff:3.500A) Proline residue: E 212 - end of helix Processing helix chain 'E' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 302 Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 326 through 346 Processing helix chain 'E' and resid 346 through 355 removed outlier: 3.536A pdb=" N LEU E 350 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 364 Processing helix chain 'E' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Proline residue: E 385 - end of helix Processing helix chain 'E' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL E 399 " --> pdb=" O PRO E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 23 removed outlier: 6.870A pdb=" N GLU F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN F 16 " --> pdb=" O GLN F 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS F 17 " --> pdb=" O TYR F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 53 Processing helix chain 'F' and resid 64 through 79 Processing helix chain 'F' and resid 87 through 105 Processing helix chain 'G' and resid 13 through 19 removed outlier: 3.528A pdb=" N GLN G 16 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG G 18 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU G 19 " --> pdb=" O GLN G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG G 24 " --> pdb=" O GLN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 41 through 54 Processing helix chain 'G' and resid 56 through 71 removed outlier: 4.330A pdb=" N GLN G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 87 removed outlier: 3.633A pdb=" N ILE G 85 " --> pdb=" O ARG G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 133 Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'G' and resid 200 through 203 Processing helix chain 'G' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL G 208 " --> pdb=" O GLY G 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Proline residue: G 212 - end of helix Processing helix chain 'G' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY G 259 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 302 Processing helix chain 'G' and resid 317 through 324 Processing helix chain 'G' and resid 326 through 346 Processing helix chain 'G' and resid 346 through 355 removed outlier: 3.536A pdb=" N LEU G 350 " --> pdb=" O LEU G 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG G 355 " --> pdb=" O LEU G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 360 through 364 Processing helix chain 'G' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET G 380 " --> pdb=" O ASP G 376 " (cutoff:3.500A) Proline residue: G 385 - end of helix Processing helix chain 'G' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL G 399 " --> pdb=" O PRO G 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 23 removed outlier: 6.870A pdb=" N GLU H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN H 16 " --> pdb=" O GLN H 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS H 17 " --> pdb=" O TYR H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 53 Processing helix chain 'H' and resid 64 through 79 Processing helix chain 'H' and resid 87 through 105 Processing helix chain 'I' and resid 13 through 19 removed outlier: 3.529A pdb=" N GLN I 16 " --> pdb=" O ARG I 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG I 18 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU I 19 " --> pdb=" O GLN I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG I 24 " --> pdb=" O GLN I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 31 Processing helix chain 'I' and resid 41 through 54 Processing helix chain 'I' and resid 56 through 71 removed outlier: 4.331A pdb=" N GLN I 60 " --> pdb=" O ASN I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 87 removed outlier: 3.633A pdb=" N ILE I 85 " --> pdb=" O ARG I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 115 Processing helix chain 'I' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP I 128 " --> pdb=" O LEU I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 133 Processing helix chain 'I' and resid 157 through 159 No H-bonds generated for 'chain 'I' and resid 157 through 159' Processing helix chain 'I' and resid 200 through 203 Processing helix chain 'I' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL I 208 " --> pdb=" O GLY I 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP I 211 " --> pdb=" O ARG I 207 " (cutoff:3.500A) Proline residue: I 212 - end of helix Processing helix chain 'I' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY I 259 " --> pdb=" O VAL I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 302 Processing helix chain 'I' and resid 317 through 324 Processing helix chain 'I' and resid 326 through 346 Processing helix chain 'I' and resid 346 through 355 removed outlier: 3.536A pdb=" N LEU I 350 " --> pdb=" O LEU I 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG I 355 " --> pdb=" O LEU I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 364 Processing helix chain 'I' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET I 380 " --> pdb=" O ASP I 376 " (cutoff:3.500A) Proline residue: I 385 - end of helix Processing helix chain 'I' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL I 399 " --> pdb=" O PRO I 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 23 removed outlier: 6.871A pdb=" N GLU J 15 " --> pdb=" O GLU J 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN J 16 " --> pdb=" O GLN J 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS J 17 " --> pdb=" O TYR J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 53 Processing helix chain 'J' and resid 64 through 79 Processing helix chain 'J' and resid 87 through 105 Processing helix chain 'K' and resid 13 through 19 removed outlier: 3.528A pdb=" N GLN K 16 " --> pdb=" O ARG K 13 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG K 18 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU K 19 " --> pdb=" O GLN K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG K 24 " --> pdb=" O GLN K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 31 Processing helix chain 'K' and resid 41 through 54 Processing helix chain 'K' and resid 56 through 71 removed outlier: 4.330A pdb=" N GLN K 60 " --> pdb=" O ASN K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 87 removed outlier: 3.634A pdb=" N ILE K 85 " --> pdb=" O ARG K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 115 Processing helix chain 'K' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 133 Processing helix chain 'K' and resid 157 through 159 No H-bonds generated for 'chain 'K' and resid 157 through 159' Processing helix chain 'K' and resid 200 through 203 Processing helix chain 'K' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL K 208 " --> pdb=" O GLY K 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP K 211 " --> pdb=" O ARG K 207 " (cutoff:3.500A) Proline residue: K 212 - end of helix Processing helix chain 'K' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY K 259 " --> pdb=" O VAL K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 302 Processing helix chain 'K' and resid 317 through 324 Processing helix chain 'K' and resid 326 through 346 Processing helix chain 'K' and resid 346 through 355 removed outlier: 3.536A pdb=" N LEU K 350 " --> pdb=" O LEU K 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG K 355 " --> pdb=" O LEU K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 364 Processing helix chain 'K' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET K 380 " --> pdb=" O ASP K 376 " (cutoff:3.500A) Proline residue: K 385 - end of helix Processing helix chain 'K' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL K 399 " --> pdb=" O PRO K 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 23 removed outlier: 6.870A pdb=" N GLU L 15 " --> pdb=" O GLU L 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN L 16 " --> pdb=" O GLN L 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS L 17 " --> pdb=" O TYR L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 53 Processing helix chain 'L' and resid 64 through 79 Processing helix chain 'L' and resid 87 through 105 Processing helix chain 'M' and resid 13 through 19 removed outlier: 3.528A pdb=" N GLN M 16 " --> pdb=" O ARG M 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG M 18 " --> pdb=" O GLN M 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU M 19 " --> pdb=" O GLN M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG M 24 " --> pdb=" O GLN M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 31 Processing helix chain 'M' and resid 41 through 54 Processing helix chain 'M' and resid 56 through 71 removed outlier: 4.330A pdb=" N GLN M 60 " --> pdb=" O ASN M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 87 removed outlier: 3.633A pdb=" N ILE M 85 " --> pdb=" O ARG M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 115 Processing helix chain 'M' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP M 128 " --> pdb=" O LEU M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 133 Processing helix chain 'M' and resid 157 through 159 No H-bonds generated for 'chain 'M' and resid 157 through 159' Processing helix chain 'M' and resid 200 through 203 Processing helix chain 'M' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL M 208 " --> pdb=" O GLY M 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP M 211 " --> pdb=" O ARG M 207 " (cutoff:3.500A) Proline residue: M 212 - end of helix Processing helix chain 'M' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY M 259 " --> pdb=" O VAL M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 302 Processing helix chain 'M' and resid 317 through 324 Processing helix chain 'M' and resid 326 through 346 Processing helix chain 'M' and resid 346 through 355 removed outlier: 3.536A pdb=" N LEU M 350 " --> pdb=" O LEU M 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG M 355 " --> pdb=" O LEU M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 360 through 364 Processing helix chain 'M' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET M 380 " --> pdb=" O ASP M 376 " (cutoff:3.500A) Proline residue: M 385 - end of helix Processing helix chain 'M' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL M 399 " --> pdb=" O PRO M 395 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 23 removed outlier: 6.870A pdb=" N GLU N 15 " --> pdb=" O GLU N 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN N 16 " --> pdb=" O GLN N 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS N 17 " --> pdb=" O TYR N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 53 Processing helix chain 'N' and resid 64 through 79 Processing helix chain 'N' and resid 87 through 105 Processing helix chain 'O' and resid 13 through 19 removed outlier: 3.529A pdb=" N GLN O 16 " --> pdb=" O ARG O 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG O 18 " --> pdb=" O GLN O 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU O 19 " --> pdb=" O GLN O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG O 24 " --> pdb=" O GLN O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 31 Processing helix chain 'O' and resid 41 through 54 Processing helix chain 'O' and resid 56 through 71 removed outlier: 4.331A pdb=" N GLN O 60 " --> pdb=" O ASN O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 87 removed outlier: 3.633A pdb=" N ILE O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 115 Processing helix chain 'O' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP O 128 " --> pdb=" O LEU O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 133 Processing helix chain 'O' and resid 157 through 159 No H-bonds generated for 'chain 'O' and resid 157 through 159' Processing helix chain 'O' and resid 200 through 203 Processing helix chain 'O' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL O 208 " --> pdb=" O GLY O 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP O 211 " --> pdb=" O ARG O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix Processing helix chain 'O' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY O 259 " --> pdb=" O VAL O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 282 through 302 Processing helix chain 'O' and resid 317 through 324 Processing helix chain 'O' and resid 326 through 346 Processing helix chain 'O' and resid 346 through 355 removed outlier: 3.536A pdb=" N LEU O 350 " --> pdb=" O LEU O 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG O 355 " --> pdb=" O LEU O 351 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 364 Processing helix chain 'O' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET O 380 " --> pdb=" O ASP O 376 " (cutoff:3.500A) Proline residue: O 385 - end of helix Processing helix chain 'O' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL O 399 " --> pdb=" O PRO O 395 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 23 removed outlier: 6.871A pdb=" N GLU P 15 " --> pdb=" O GLU P 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN P 16 " --> pdb=" O GLN P 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS P 17 " --> pdb=" O TYR P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 53 Processing helix chain 'P' and resid 64 through 79 Processing helix chain 'P' and resid 87 through 105 Processing helix chain 'Q' and resid 13 through 19 removed outlier: 3.529A pdb=" N GLN Q 16 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG Q 18 " --> pdb=" O GLN Q 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU Q 19 " --> pdb=" O GLN Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG Q 24 " --> pdb=" O GLN Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 31 Processing helix chain 'Q' and resid 41 through 54 Processing helix chain 'Q' and resid 56 through 71 removed outlier: 4.330A pdb=" N GLN Q 60 " --> pdb=" O ASN Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 87 removed outlier: 3.634A pdb=" N ILE Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 115 Processing helix chain 'Q' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP Q 128 " --> pdb=" O LEU Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 133 Processing helix chain 'Q' and resid 157 through 159 No H-bonds generated for 'chain 'Q' and resid 157 through 159' Processing helix chain 'Q' and resid 200 through 203 Processing helix chain 'Q' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL Q 208 " --> pdb=" O GLY Q 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP Q 211 " --> pdb=" O ARG Q 207 " (cutoff:3.500A) Proline residue: Q 212 - end of helix Processing helix chain 'Q' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY Q 259 " --> pdb=" O VAL Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 282 through 302 Processing helix chain 'Q' and resid 317 through 324 Processing helix chain 'Q' and resid 326 through 346 Processing helix chain 'Q' and resid 346 through 355 removed outlier: 3.537A pdb=" N LEU Q 350 " --> pdb=" O LEU Q 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG Q 355 " --> pdb=" O LEU Q 351 " (cutoff:3.500A) Processing helix chain 'Q' and resid 360 through 364 Processing helix chain 'Q' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET Q 380 " --> pdb=" O ASP Q 376 " (cutoff:3.500A) Proline residue: Q 385 - end of helix Processing helix chain 'Q' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL Q 399 " --> pdb=" O PRO Q 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 23 removed outlier: 6.870A pdb=" N GLU R 15 " --> pdb=" O GLU R 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN R 16 " --> pdb=" O GLN R 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS R 17 " --> pdb=" O TYR R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 53 Processing helix chain 'R' and resid 64 through 79 Processing helix chain 'R' and resid 87 through 105 Processing helix chain 'S' and resid 13 through 19 removed outlier: 3.528A pdb=" N GLN S 16 " --> pdb=" O ARG S 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG S 18 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU S 19 " --> pdb=" O GLN S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG S 24 " --> pdb=" O GLN S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 31 Processing helix chain 'S' and resid 41 through 54 Processing helix chain 'S' and resid 56 through 71 removed outlier: 4.330A pdb=" N GLN S 60 " --> pdb=" O ASN S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 87 removed outlier: 3.633A pdb=" N ILE S 85 " --> pdb=" O ARG S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 115 Processing helix chain 'S' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP S 128 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 133 Processing helix chain 'S' and resid 157 through 159 No H-bonds generated for 'chain 'S' and resid 157 through 159' Processing helix chain 'S' and resid 200 through 203 Processing helix chain 'S' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL S 208 " --> pdb=" O GLY S 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP S 211 " --> pdb=" O ARG S 207 " (cutoff:3.500A) Proline residue: S 212 - end of helix Processing helix chain 'S' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY S 259 " --> pdb=" O VAL S 255 " (cutoff:3.500A) Processing helix chain 'S' and resid 282 through 302 Processing helix chain 'S' and resid 317 through 324 Processing helix chain 'S' and resid 326 through 346 Processing helix chain 'S' and resid 346 through 355 removed outlier: 3.536A pdb=" N LEU S 350 " --> pdb=" O LEU S 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG S 355 " --> pdb=" O LEU S 351 " (cutoff:3.500A) Processing helix chain 'S' and resid 360 through 364 Processing helix chain 'S' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET S 380 " --> pdb=" O ASP S 376 " (cutoff:3.500A) Proline residue: S 385 - end of helix Processing helix chain 'S' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL S 399 " --> pdb=" O PRO S 395 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 23 removed outlier: 6.870A pdb=" N GLU T 15 " --> pdb=" O GLU T 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS T 17 " --> pdb=" O TYR T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 33 through 53 Processing helix chain 'T' and resid 64 through 79 Processing helix chain 'T' and resid 87 through 105 Processing helix chain 'U' and resid 13 through 19 removed outlier: 3.529A pdb=" N GLN U 16 " --> pdb=" O ARG U 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG U 18 " --> pdb=" O GLN U 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU U 19 " --> pdb=" O GLN U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG U 24 " --> pdb=" O GLN U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 27 through 31 Processing helix chain 'U' and resid 41 through 54 Processing helix chain 'U' and resid 56 through 71 removed outlier: 4.331A pdb=" N GLN U 60 " --> pdb=" O ASN U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 87 removed outlier: 3.633A pdb=" N ILE U 85 " --> pdb=" O ARG U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 99 through 115 Processing helix chain 'U' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP U 128 " --> pdb=" O LEU U 124 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 133 Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 200 through 203 Processing helix chain 'U' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL U 208 " --> pdb=" O GLY U 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP U 211 " --> pdb=" O ARG U 207 " (cutoff:3.500A) Proline residue: U 212 - end of helix Processing helix chain 'U' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY U 259 " --> pdb=" O VAL U 255 " (cutoff:3.500A) Processing helix chain 'U' and resid 282 through 302 Processing helix chain 'U' and resid 317 through 324 Processing helix chain 'U' and resid 326 through 346 Processing helix chain 'U' and resid 346 through 355 removed outlier: 3.536A pdb=" N LEU U 350 " --> pdb=" O LEU U 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG U 355 " --> pdb=" O LEU U 351 " (cutoff:3.500A) Processing helix chain 'U' and resid 360 through 364 Processing helix chain 'U' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET U 380 " --> pdb=" O ASP U 376 " (cutoff:3.500A) Proline residue: U 385 - end of helix Processing helix chain 'U' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL U 399 " --> pdb=" O PRO U 395 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 23 removed outlier: 6.871A pdb=" N GLU V 15 " --> pdb=" O GLU V 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS V 17 " --> pdb=" O TYR V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 53 Processing helix chain 'V' and resid 64 through 79 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'W' and resid 13 through 19 removed outlier: 3.528A pdb=" N GLN W 16 " --> pdb=" O ARG W 13 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG W 18 " --> pdb=" O GLN W 15 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU W 19 " --> pdb=" O GLN W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 25 removed outlier: 3.887A pdb=" N ARG W 24 " --> pdb=" O GLN W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 31 Processing helix chain 'W' and resid 41 through 54 Processing helix chain 'W' and resid 56 through 71 removed outlier: 4.330A pdb=" N GLN W 60 " --> pdb=" O ASN W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 87 removed outlier: 3.634A pdb=" N ILE W 85 " --> pdb=" O ARG W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 99 through 115 Processing helix chain 'W' and resid 118 through 128 removed outlier: 3.518A pdb=" N ASP W 128 " --> pdb=" O LEU W 124 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 133 Processing helix chain 'W' and resid 157 through 159 No H-bonds generated for 'chain 'W' and resid 157 through 159' Processing helix chain 'W' and resid 200 through 203 Processing helix chain 'W' and resid 204 through 230 removed outlier: 3.989A pdb=" N VAL W 208 " --> pdb=" O GLY W 204 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP W 211 " --> pdb=" O ARG W 207 " (cutoff:3.500A) Proline residue: W 212 - end of helix Processing helix chain 'W' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY W 259 " --> pdb=" O VAL W 255 " (cutoff:3.500A) Processing helix chain 'W' and resid 282 through 302 Processing helix chain 'W' and resid 317 through 324 Processing helix chain 'W' and resid 326 through 346 Processing helix chain 'W' and resid 346 through 355 removed outlier: 3.536A pdb=" N LEU W 350 " --> pdb=" O LEU W 346 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG W 355 " --> pdb=" O LEU W 351 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 364 Processing helix chain 'W' and resid 376 through 391 removed outlier: 3.530A pdb=" N MET W 380 " --> pdb=" O ASP W 376 " (cutoff:3.500A) Proline residue: W 385 - end of helix Processing helix chain 'W' and resid 395 through 404 removed outlier: 3.777A pdb=" N VAL W 399 " --> pdb=" O PRO W 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 23 removed outlier: 6.870A pdb=" N GLU X 15 " --> pdb=" O GLU X 11 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N GLN X 16 " --> pdb=" O GLN X 12 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS X 17 " --> pdb=" O TYR X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 53 Processing helix chain 'X' and resid 64 through 79 Processing helix chain 'X' and resid 87 through 105 Processing sheet with id=1, first strand: chain 'A' and resid 90 through 93 Processing sheet with id=2, first strand: chain 'A' and resid 148 through 156 removed outlier: 6.622A pdb=" N GLU A 140 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE A 153 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU A 138 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS A 155 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS A 136 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 161 through 164 removed outlier: 6.208A pdb=" N GLU A 170 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 234 through 238 Processing sheet with id=5, first strand: chain 'C' and resid 90 through 93 Processing sheet with id=6, first strand: chain 'C' and resid 148 through 156 removed outlier: 6.622A pdb=" N GLU C 140 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE C 153 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU C 138 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS C 155 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS C 136 " --> pdb=" O HIS C 155 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.209A pdb=" N GLU C 170 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 234 through 238 Processing sheet with id=9, first strand: chain 'E' and resid 90 through 93 Processing sheet with id=10, first strand: chain 'E' and resid 148 through 156 removed outlier: 6.623A pdb=" N GLU E 140 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE E 153 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU E 138 " --> pdb=" O PHE E 153 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N HIS E 155 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS E 136 " --> pdb=" O HIS E 155 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'E' and resid 161 through 164 removed outlier: 6.208A pdb=" N GLU E 170 " --> pdb=" O ASN E 164 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'E' and resid 234 through 238 Processing sheet with id=13, first strand: chain 'G' and resid 90 through 93 Processing sheet with id=14, first strand: chain 'G' and resid 148 through 156 removed outlier: 6.622A pdb=" N GLU G 140 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE G 153 " --> pdb=" O GLU G 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU G 138 " --> pdb=" O PHE G 153 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS G 155 " --> pdb=" O CYS G 136 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS G 136 " --> pdb=" O HIS G 155 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'G' and resid 161 through 164 removed outlier: 6.208A pdb=" N GLU G 170 " --> pdb=" O ASN G 164 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'G' and resid 234 through 238 Processing sheet with id=17, first strand: chain 'I' and resid 90 through 93 Processing sheet with id=18, first strand: chain 'I' and resid 148 through 156 removed outlier: 6.622A pdb=" N GLU I 140 " --> pdb=" O LEU I 151 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE I 153 " --> pdb=" O GLU I 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU I 138 " --> pdb=" O PHE I 153 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS I 155 " --> pdb=" O CYS I 136 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS I 136 " --> pdb=" O HIS I 155 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'I' and resid 161 through 164 removed outlier: 6.209A pdb=" N GLU I 170 " --> pdb=" O ASN I 164 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'I' and resid 234 through 238 Processing sheet with id=21, first strand: chain 'K' and resid 90 through 93 Processing sheet with id=22, first strand: chain 'K' and resid 148 through 156 removed outlier: 6.623A pdb=" N GLU K 140 " --> pdb=" O LEU K 151 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE K 153 " --> pdb=" O GLU K 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU K 138 " --> pdb=" O PHE K 153 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N HIS K 155 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS K 136 " --> pdb=" O HIS K 155 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'K' and resid 161 through 164 removed outlier: 6.208A pdb=" N GLU K 170 " --> pdb=" O ASN K 164 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'K' and resid 234 through 238 Processing sheet with id=25, first strand: chain 'M' and resid 90 through 93 Processing sheet with id=26, first strand: chain 'M' and resid 148 through 156 removed outlier: 6.622A pdb=" N GLU M 140 " --> pdb=" O LEU M 151 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE M 153 " --> pdb=" O GLU M 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU M 138 " --> pdb=" O PHE M 153 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS M 155 " --> pdb=" O CYS M 136 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS M 136 " --> pdb=" O HIS M 155 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'M' and resid 161 through 164 removed outlier: 6.208A pdb=" N GLU M 170 " --> pdb=" O ASN M 164 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'M' and resid 234 through 238 Processing sheet with id=29, first strand: chain 'O' and resid 90 through 93 Processing sheet with id=30, first strand: chain 'O' and resid 148 through 156 removed outlier: 6.622A pdb=" N GLU O 140 " --> pdb=" O LEU O 151 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE O 153 " --> pdb=" O GLU O 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU O 138 " --> pdb=" O PHE O 153 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS O 155 " --> pdb=" O CYS O 136 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS O 136 " --> pdb=" O HIS O 155 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'O' and resid 161 through 164 removed outlier: 6.209A pdb=" N GLU O 170 " --> pdb=" O ASN O 164 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'O' and resid 234 through 238 Processing sheet with id=33, first strand: chain 'Q' and resid 90 through 93 Processing sheet with id=34, first strand: chain 'Q' and resid 148 through 156 removed outlier: 6.622A pdb=" N GLU Q 140 " --> pdb=" O LEU Q 151 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE Q 153 " --> pdb=" O GLU Q 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU Q 138 " --> pdb=" O PHE Q 153 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS Q 155 " --> pdb=" O CYS Q 136 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS Q 136 " --> pdb=" O HIS Q 155 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'Q' and resid 161 through 164 removed outlier: 6.208A pdb=" N GLU Q 170 " --> pdb=" O ASN Q 164 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'Q' and resid 234 through 238 Processing sheet with id=37, first strand: chain 'S' and resid 90 through 93 Processing sheet with id=38, first strand: chain 'S' and resid 148 through 156 removed outlier: 6.622A pdb=" N GLU S 140 " --> pdb=" O LEU S 151 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE S 153 " --> pdb=" O GLU S 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU S 138 " --> pdb=" O PHE S 153 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS S 155 " --> pdb=" O CYS S 136 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS S 136 " --> pdb=" O HIS S 155 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'S' and resid 161 through 164 removed outlier: 6.208A pdb=" N GLU S 170 " --> pdb=" O ASN S 164 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'S' and resid 234 through 238 Processing sheet with id=41, first strand: chain 'U' and resid 90 through 93 Processing sheet with id=42, first strand: chain 'U' and resid 148 through 156 removed outlier: 6.622A pdb=" N GLU U 140 " --> pdb=" O LEU U 151 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE U 153 " --> pdb=" O GLU U 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU U 138 " --> pdb=" O PHE U 153 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS U 155 " --> pdb=" O CYS U 136 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS U 136 " --> pdb=" O HIS U 155 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'U' and resid 161 through 164 removed outlier: 6.209A pdb=" N GLU U 170 " --> pdb=" O ASN U 164 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'U' and resid 234 through 238 Processing sheet with id=45, first strand: chain 'W' and resid 90 through 93 Processing sheet with id=46, first strand: chain 'W' and resid 148 through 156 removed outlier: 6.623A pdb=" N GLU W 140 " --> pdb=" O LEU W 151 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE W 153 " --> pdb=" O GLU W 138 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU W 138 " --> pdb=" O PHE W 153 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N HIS W 155 " --> pdb=" O CYS W 136 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS W 136 " --> pdb=" O HIS W 155 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'W' and resid 161 through 164 removed outlier: 6.208A pdb=" N GLU W 170 " --> pdb=" O ASN W 164 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'W' and resid 234 through 238 2688 hydrogen bonds defined for protein. 7596 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: 17.14 Time building geometry restraints manager: 11.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 17316 1.34 - 1.46: 10218 1.46 - 1.58: 23790 1.58 - 1.69: 0 1.69 - 1.81: 252 Bond restraints: 51576 Sorted by residual: bond pdb=" CA ILE M 384 " pdb=" CB ILE M 384 " ideal model delta sigma weight residual 1.537 1.542 -0.005 5.00e-03 4.00e+04 1.02e+00 bond pdb=" CA ILE S 384 " pdb=" CB ILE S 384 " ideal model delta sigma weight residual 1.537 1.542 -0.005 5.00e-03 4.00e+04 1.02e+00 bond pdb=" CA ILE G 384 " pdb=" CB ILE G 384 " ideal model delta sigma weight residual 1.537 1.542 -0.005 5.00e-03 4.00e+04 1.02e+00 bond pdb=" CA ILE A 384 " pdb=" CB ILE A 384 " ideal model delta sigma weight residual 1.537 1.542 -0.005 5.00e-03 4.00e+04 1.02e+00 bond pdb=" C VAL B 25 " pdb=" O VAL B 25 " ideal model delta sigma weight residual 1.241 1.231 0.010 1.06e-02 8.90e+03 9.35e-01 ... (remaining 51571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 66376 0.90 - 1.79: 2684 1.79 - 2.69: 620 2.69 - 3.58: 316 3.58 - 4.48: 132 Bond angle restraints: 70128 Sorted by residual: angle pdb=" C ILE M 384 " pdb=" CA ILE M 384 " pdb=" CB ILE M 384 " ideal model delta sigma weight residual 113.70 110.78 2.92 9.50e-01 1.11e+00 9.44e+00 angle pdb=" C ILE S 384 " pdb=" CA ILE S 384 " pdb=" CB ILE S 384 " ideal model delta sigma weight residual 113.70 110.78 2.92 9.50e-01 1.11e+00 9.44e+00 angle pdb=" C ILE A 384 " pdb=" CA ILE A 384 " pdb=" CB ILE A 384 " ideal model delta sigma weight residual 113.70 110.78 2.92 9.50e-01 1.11e+00 9.44e+00 angle pdb=" C ILE G 384 " pdb=" CA ILE G 384 " pdb=" CB ILE G 384 " ideal model delta sigma weight residual 113.70 110.78 2.92 9.50e-01 1.11e+00 9.44e+00 angle pdb=" C ILE C 384 " pdb=" CA ILE C 384 " pdb=" CB ILE C 384 " ideal model delta sigma weight residual 113.70 110.78 2.92 9.50e-01 1.11e+00 9.44e+00 ... (remaining 70123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 28160 17.07 - 34.14: 2488 34.14 - 51.22: 456 51.22 - 68.29: 96 68.29 - 85.36: 48 Dihedral angle restraints: 31248 sinusoidal: 12480 harmonic: 18768 Sorted by residual: dihedral pdb=" CA HIS A 323 " pdb=" C HIS A 323 " pdb=" N ASN A 324 " pdb=" CA ASN A 324 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA HIS G 323 " pdb=" C HIS G 323 " pdb=" N ASN G 324 " pdb=" CA ASN G 324 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA HIS M 323 " pdb=" C HIS M 323 " pdb=" N ASN M 324 " pdb=" CA ASN M 324 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 31245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 5091 0.027 - 0.055: 1889 0.055 - 0.082: 526 0.082 - 0.109: 155 0.109 - 0.136: 139 Chirality restraints: 7800 Sorted by residual: chirality pdb=" CA ILE A 189 " pdb=" N ILE A 189 " pdb=" C ILE A 189 " pdb=" CB ILE A 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE G 189 " pdb=" N ILE G 189 " pdb=" C ILE G 189 " pdb=" CB ILE G 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 7797 not shown) Planarity restraints: 9252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU I 19 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO I 20 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 20 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 20 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU O 19 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO O 20 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO O 20 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO O 20 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU U 19 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO U 20 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO U 20 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO U 20 " -0.022 5.00e-02 4.00e+02 ... (remaining 9249 not shown) Histogram of nonbonded interaction distances: 0.21 - 1.15: 312 1.15 - 2.09: 647 2.09 - 3.03: 31996 3.03 - 3.96: 132894 3.96 - 4.90: 250188 Warning: very small nonbonded interaction distances. Nonbonded interactions: 416037 Sorted by model distance: nonbonded pdb=" CD LYS Q 248 " pdb=" OD1 ASN T 123 " model vdw 0.214 3.440 nonbonded pdb=" CD LYS E 248 " pdb=" OD1 ASN H 123 " model vdw 0.215 3.440 nonbonded pdb=" OD1 ASN B 123 " pdb=" CD LYS W 248 " model vdw 0.215 3.440 nonbonded pdb=" CD LYS K 248 " pdb=" OD1 ASN N 123 " model vdw 0.215 3.440 nonbonded pdb=" CD LYS A 248 " pdb=" OD1 ASN D 123 " model vdw 0.216 3.440 ... (remaining 416032 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: 5.220 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: 0.060 Extract box with map and model: 1.430 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 72.590 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 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 : 0.003 0.033 51576 Z= 0.165 Angle : 0.499 4.478 70128 Z= 0.268 Chirality : 0.035 0.136 7800 Planarity : 0.004 0.039 9252 Dihedral : 13.637 85.361 19128 Min Nonbonded Distance : 0.214 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.46 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.03 (0.11), residues: 6456 helix: 2.82 (0.09), residues: 3192 sheet: 0.04 (0.22), residues: 576 loop : -0.17 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 211 HIS 0.011 0.001 HIS Q 323 PHE 0.005 0.001 PHE Q 215 TYR 0.006 0.001 TYR K 230 ARG 0.003 0.000 ARG V 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1418 time to evaluate : 4.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6539 (mm-30) REVERT: A 149 MET cc_start: 0.6695 (tpp) cc_final: 0.6438 (tpt) REVERT: A 166 GLU cc_start: 0.7070 (mp0) cc_final: 0.6814 (mp0) REVERT: C 62 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6728 (mt-10) REVERT: C 111 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6651 (mm-30) REVERT: C 164 ASN cc_start: 0.6501 (t0) cc_final: 0.6228 (t0) REVERT: C 166 GLU cc_start: 0.6538 (mp0) cc_final: 0.5951 (mp0) REVERT: C 380 MET cc_start: 0.6369 (tmm) cc_final: 0.5861 (tmm) REVERT: E 62 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6198 (mt-10) REVERT: E 111 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6991 (mm-30) REVERT: E 380 MET cc_start: 0.6220 (tmm) cc_final: 0.5813 (tmm) REVERT: F 45 ASP cc_start: 0.7143 (m-30) cc_final: 0.6908 (m-30) REVERT: G 132 HIS cc_start: 0.5863 (m-70) cc_final: 0.5504 (m-70) REVERT: G 354 ASN cc_start: 0.6158 (m-40) cc_final: 0.5887 (m110) REVERT: I 78 MET cc_start: 0.7487 (mmm) cc_final: 0.7097 (mmt) REVERT: I 140 GLU cc_start: 0.5552 (mm-30) cc_final: 0.5349 (mm-30) REVERT: I 297 SER cc_start: 0.8291 (m) cc_final: 0.7858 (t) REVERT: I 398 TRP cc_start: 0.6397 (t60) cc_final: 0.5875 (t60) REVERT: K 8 TYR cc_start: 0.5545 (m-80) cc_final: 0.5319 (m-80) REVERT: K 18 ARG cc_start: 0.5508 (tpp-160) cc_final: 0.5224 (tpp-160) REVERT: K 176 ASN cc_start: 0.7919 (m110) cc_final: 0.7639 (m-40) REVERT: K 346 LEU cc_start: 0.8237 (tp) cc_final: 0.8008 (tp) REVERT: K 407 GLN cc_start: 0.6082 (pp30) cc_final: 0.4875 (tt0) REVERT: L 49 ASP cc_start: 0.7263 (m-30) cc_final: 0.7010 (m-30) REVERT: M 22 THR cc_start: 0.7473 (p) cc_final: 0.7145 (m) REVERT: M 50 VAL cc_start: 0.7886 (t) cc_final: 0.7667 (t) REVERT: M 71 ASP cc_start: 0.7508 (t70) cc_final: 0.7299 (t0) REVERT: M 176 ASN cc_start: 0.7458 (m110) cc_final: 0.7129 (m-40) REVERT: O 102 GLU cc_start: 0.6120 (mt-10) cc_final: 0.5892 (mt-10) REVERT: O 135 SER cc_start: 0.8619 (t) cc_final: 0.8249 (p) REVERT: O 298 LYS cc_start: 0.7501 (mtmt) cc_final: 0.7202 (ptpt) REVERT: P 38 ASP cc_start: 0.7990 (m-30) cc_final: 0.7759 (m-30) REVERT: P 101 SER cc_start: 0.8660 (t) cc_final: 0.8348 (m) REVERT: P 105 ASN cc_start: 0.8530 (m110) cc_final: 0.8294 (m-40) REVERT: Q 77 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7520 (mm-30) REVERT: S 291 GLN cc_start: 0.6607 (tp40) cc_final: 0.6384 (tm-30) REVERT: U 78 MET cc_start: 0.7664 (mmm) cc_final: 0.7366 (mmt) REVERT: U 220 THR cc_start: 0.7666 (m) cc_final: 0.7385 (m) REVERT: V 28 PRO cc_start: 0.7969 (Cg_endo) cc_final: 0.7636 (Cg_exo) REVERT: W 111 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6669 (mm-30) REVERT: W 366 ARG cc_start: 0.5641 (mtm-85) cc_final: 0.5342 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 1418 average time/residue: 0.5677 time to fit residues: 1253.6894 Evaluate side-chains 942 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 942 time to evaluate : 4.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 537 optimal weight: 0.7980 chunk 482 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 325 optimal weight: 0.7980 chunk 257 optimal weight: 0.9990 chunk 498 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 577 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 132 HIS ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 382 GLN B 53 HIS B 80 HIS ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 328 HIS D 53 HIS D 87 ASN E 132 HIS ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN E 321 GLN E 328 HIS F 53 HIS F 80 HIS ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 HIS G 275 GLN G 321 GLN G 328 HIS ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 GLN I 155 HIS I 158 GLN I 321 GLN I 328 HIS I 354 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 GLN K 321 GLN K 328 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 GLN M 169 ASN M 321 GLN M 328 HIS ** N 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 GLN O 10 ASN O 35 HIS O 184 GLN O 275 GLN O 321 GLN ** P 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 GLN Q 10 ASN Q 54 GLN ** Q 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 321 GLN R 53 HIS R 126 GLN S 10 ASN S 54 GLN ** S 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 321 GLN ** T 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 ASN T 126 GLN U 10 ASN U 60 GLN ** U 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 321 GLN V 53 HIS V 80 HIS V 126 GLN W 21 GLN W 60 GLN ** W 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 321 GLN X 53 HIS X 80 HIS Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 51576 Z= 0.371 Angle : 0.822 14.782 70128 Z= 0.419 Chirality : 0.050 0.436 7800 Planarity : 0.007 0.089 9252 Dihedral : 4.927 27.203 7080 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.89 % Favored : 94.73 % Rotamer: Outliers : 2.54 % Allowed : 9.61 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.06 (0.10), residues: 6456 helix: 1.75 (0.09), residues: 3240 sheet: 0.32 (0.21), residues: 612 loop : -0.50 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 138 HIS 0.015 0.002 HIS C 155 PHE 0.028 0.004 PHE M 75 TYR 0.028 0.002 TYR K 400 ARG 0.044 0.001 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1118 time to evaluate : 4.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLU cc_start: 0.6650 (tm-30) cc_final: 0.6146 (tm-30) REVERT: A 229 ILE cc_start: 0.7509 (tt) cc_final: 0.7291 (tt) REVERT: B 113 ASP cc_start: 0.7623 (p0) cc_final: 0.7293 (p0) REVERT: C 125 ASP cc_start: 0.7485 (m-30) cc_final: 0.7204 (m-30) REVERT: C 380 MET cc_start: 0.6617 (tmm) cc_final: 0.6252 (tmm) REVERT: E 70 ARG cc_start: 0.6963 (mtm180) cc_final: 0.6670 (mtm180) REVERT: E 202 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8131 (mtt180) REVERT: E 238 LYS cc_start: 0.8433 (mtpt) cc_final: 0.8195 (mtpp) REVERT: E 253 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6912 (ptp-110) REVERT: F 34 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7648 (p) REVERT: F 98 LYS cc_start: 0.7936 (tttt) cc_final: 0.7661 (mtpp) REVERT: G 67 MET cc_start: 0.7648 (ttp) cc_final: 0.7342 (mtp) REVERT: G 89 ASP cc_start: 0.6614 (p0) cc_final: 0.6393 (p0) REVERT: I 78 MET cc_start: 0.8466 (mmm) cc_final: 0.8022 (mmt) REVERT: I 114 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6662 (tp) REVERT: I 398 TRP cc_start: 0.6415 (t60) cc_final: 0.5884 (t60) REVERT: J 49 ASP cc_start: 0.7718 (m-30) cc_final: 0.7402 (m-30) REVERT: K 21 GLN cc_start: 0.8118 (tt0) cc_final: 0.7877 (tt0) REVERT: K 65 MET cc_start: 0.7911 (mpp) cc_final: 0.7450 (mtt) REVERT: K 176 ASN cc_start: 0.8163 (m110) cc_final: 0.7919 (m-40) REVERT: L 19 ARG cc_start: 0.7512 (ptp90) cc_final: 0.6827 (ptt90) REVERT: L 38 ASP cc_start: 0.8411 (m-30) cc_final: 0.8209 (m-30) REVERT: L 107 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7848 (mttm) REVERT: M 77 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7183 (mm-30) REVERT: M 148 TRP cc_start: 0.7170 (m100) cc_final: 0.6925 (m100) REVERT: M 176 ASN cc_start: 0.7990 (m110) cc_final: 0.7635 (m-40) REVERT: M 234 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8350 (mp) REVERT: M 346 LEU cc_start: 0.8723 (tp) cc_final: 0.8508 (tp) REVERT: M 380 MET cc_start: 0.7151 (ttp) cc_final: 0.6924 (tmm) REVERT: O 19 GLU cc_start: 0.6895 (pm20) cc_final: 0.6677 (pm20) REVERT: O 380 MET cc_start: 0.7327 (ttp) cc_final: 0.7115 (tmm) REVERT: P 84 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7939 (mtmm) REVERT: P 101 SER cc_start: 0.8910 (t) cc_final: 0.8611 (m) REVERT: P 107 LYS cc_start: 0.8240 (mttp) cc_final: 0.8013 (mtpp) REVERT: Q 140 GLU cc_start: 0.7205 (tp30) cc_final: 0.6980 (tp30) REVERT: R 90 TYR cc_start: 0.8550 (t80) cc_final: 0.8165 (t80) REVERT: R 107 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8150 (mtmm) REVERT: R 112 LEU cc_start: 0.7928 (mt) cc_final: 0.7533 (mp) REVERT: S 67 MET cc_start: 0.7300 (ttm) cc_final: 0.6999 (mtp) REVERT: S 166 GLU cc_start: 0.7201 (mp0) cc_final: 0.6984 (mp0) REVERT: S 181 GLU cc_start: 0.7329 (tt0) cc_final: 0.6991 (tt0) REVERT: W 111 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7102 (mm-30) REVERT: W 218 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7581 (t80) REVERT: W 289 MET cc_start: 0.7735 (mtp) cc_final: 0.7521 (mtt) outliers start: 133 outliers final: 59 residues processed: 1199 average time/residue: 0.5463 time to fit residues: 1045.8760 Evaluate side-chains 1006 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 940 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 144 GLN Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 268 GLU Chi-restraints excluded: chain I residue 352 VAL Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 367 LEU Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 107 LYS Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 218 TYR Chi-restraints excluded: chain U residue 382 GLN Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 218 TYR Chi-restraints excluded: chain W residue 221 SER Chi-restraints excluded: chain W residue 269 THR Chi-restraints excluded: chain W residue 399 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 320 optimal weight: 1.9990 chunk 179 optimal weight: 0.0970 chunk 480 optimal weight: 2.9990 chunk 393 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 578 optimal weight: 0.7980 chunk 625 optimal weight: 1.9990 chunk 515 optimal weight: 0.0980 chunk 573 optimal weight: 1.9990 chunk 197 optimal weight: 0.0980 chunk 464 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN C 58 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 132 HIS ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN G 217 HIS ** H 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 GLN I 184 GLN I 217 HIS I 275 GLN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 ASN K 144 GLN K 217 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 HIS M 184 GLN M 217 HIS M 275 GLN N 53 HIS O 35 HIS O 155 HIS O 337 GLN P 53 HIS Q 10 ASN ** Q 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN S 10 ASN S 54 GLN ** T 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 10 ASN U 56 ASN U 60 GLN W 60 GLN X 126 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 51576 Z= 0.185 Angle : 0.573 9.462 70128 Z= 0.285 Chirality : 0.040 0.284 7800 Planarity : 0.005 0.045 9252 Dihedral : 4.344 23.893 7080 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.79 % Favored : 95.93 % Rotamer: Outliers : 1.91 % Allowed : 12.44 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.73 (0.11), residues: 6456 helix: 2.53 (0.09), residues: 3144 sheet: 1.13 (0.21), residues: 516 loop : -0.49 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 148 HIS 0.007 0.001 HIS C 155 PHE 0.024 0.001 PHE S 274 TYR 0.024 0.001 TYR K 400 ARG 0.011 0.001 ARG G 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 997 time to evaluate : 4.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLU cc_start: 0.6661 (tm-30) cc_final: 0.6316 (tt0) REVERT: A 380 MET cc_start: 0.5376 (tmm) cc_final: 0.5126 (tmm) REVERT: B 5 THR cc_start: 0.8552 (p) cc_final: 0.8327 (p) REVERT: B 15 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8371 (tm-30) REVERT: C 120 GLU cc_start: 0.6653 (tp30) cc_final: 0.6404 (tp30) REVERT: C 125 ASP cc_start: 0.7724 (m-30) cc_final: 0.7388 (m-30) REVERT: C 380 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.6179 (tmm) REVERT: D 45 ASP cc_start: 0.7939 (m-30) cc_final: 0.7728 (m-30) REVERT: F 98 LYS cc_start: 0.8008 (tttt) cc_final: 0.7784 (ttmm) REVERT: F 107 LYS cc_start: 0.8240 (mttt) cc_final: 0.7868 (mttm) REVERT: H 98 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7706 (ttmm) REVERT: I 78 MET cc_start: 0.8631 (mmm) cc_final: 0.8136 (mmt) REVERT: J 38 ASP cc_start: 0.8004 (m-30) cc_final: 0.7776 (m-30) REVERT: J 98 LYS cc_start: 0.7898 (ttpp) cc_final: 0.7630 (ttmm) REVERT: K 140 GLU cc_start: 0.6490 (mm-30) cc_final: 0.6157 (mt-10) REVERT: K 176 ASN cc_start: 0.8179 (m110) cc_final: 0.7940 (m-40) REVERT: K 380 MET cc_start: 0.6733 (ttp) cc_final: 0.6458 (tmm) REVERT: L 19 ARG cc_start: 0.7611 (ptp90) cc_final: 0.6954 (ptt90) REVERT: M 148 TRP cc_start: 0.7152 (m100) cc_final: 0.6867 (m-90) REVERT: M 176 ASN cc_start: 0.8111 (m110) cc_final: 0.7725 (m-40) REVERT: M 234 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8353 (mt) REVERT: M 275 GLN cc_start: 0.7565 (tp40) cc_final: 0.7163 (tp-100) REVERT: M 380 MET cc_start: 0.7316 (ttp) cc_final: 0.7109 (tmm) REVERT: N 90 TYR cc_start: 0.8440 (t80) cc_final: 0.8213 (t80) REVERT: O 117 GLU cc_start: 0.6449 (pm20) cc_final: 0.5845 (pm20) REVERT: O 291 GLN cc_start: 0.7687 (tp40) cc_final: 0.7285 (tp40) REVERT: P 84 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7844 (mtmm) REVERT: P 101 SER cc_start: 0.8930 (t) cc_final: 0.8586 (m) REVERT: Q 19 GLU cc_start: 0.6506 (pm20) cc_final: 0.6293 (pm20) REVERT: Q 298 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7983 (mtpt) REVERT: Q 362 ARG cc_start: 0.6303 (ttt180) cc_final: 0.5997 (ttt180) REVERT: R 90 TYR cc_start: 0.8513 (t80) cc_final: 0.8131 (t80) REVERT: R 112 LEU cc_start: 0.7881 (mt) cc_final: 0.7547 (mp) REVERT: S 181 GLU cc_start: 0.7370 (tt0) cc_final: 0.7085 (tt0) REVERT: S 380 MET cc_start: 0.6105 (tmm) cc_final: 0.5713 (tmm) REVERT: S 382 GLN cc_start: 0.7099 (mt0) cc_final: 0.6636 (mp10) REVERT: U 77 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7153 (mm-30) REVERT: U 169 ASN cc_start: 0.8609 (t0) cc_final: 0.8354 (t0) REVERT: U 298 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7655 (mtpp) REVERT: V 28 PRO cc_start: 0.8222 (Cg_endo) cc_final: 0.7930 (Cg_exo) REVERT: W 60 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: W 111 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7119 (mm-30) REVERT: W 113 LEU cc_start: 0.7455 (mt) cc_final: 0.7233 (mt) REVERT: W 218 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.7282 (t80) REVERT: W 289 MET cc_start: 0.7918 (mtp) cc_final: 0.7640 (mtt) outliers start: 100 outliers final: 52 residues processed: 1057 average time/residue: 0.5752 time to fit residues: 980.1530 Evaluate side-chains 995 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 938 time to evaluate : 4.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 184 GLN Chi-restraints excluded: chain I residue 226 MET Chi-restraints excluded: chain I residue 268 GLU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain S residue 24 ARG Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 275 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain W residue 60 GLN Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 218 TYR Chi-restraints excluded: chain W residue 221 SER Chi-restraints excluded: chain W residue 253 ARG Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 571 optimal weight: 1.9990 chunk 435 optimal weight: 1.9990 chunk 300 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 chunk 388 optimal weight: 0.0980 chunk 580 optimal weight: 0.7980 chunk 614 optimal weight: 9.9990 chunk 303 optimal weight: 0.0050 chunk 550 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN H 53 HIS J 53 HIS K 275 GLN M 184 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 GLN Q 10 ASN R 12 GLN S 10 ASN S 54 GLN T 12 GLN U 10 ASN ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 51576 Z= 0.183 Angle : 0.556 8.756 70128 Z= 0.278 Chirality : 0.039 0.226 7800 Planarity : 0.005 0.045 9252 Dihedral : 4.261 24.870 7080 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.31 % Favored : 95.51 % Rotamer: Outliers : 2.01 % Allowed : 13.49 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.77 (0.11), residues: 6456 helix: 2.65 (0.09), residues: 3144 sheet: 0.32 (0.21), residues: 636 loop : -0.44 (0.13), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 148 HIS 0.008 0.001 HIS C 155 PHE 0.019 0.001 PHE S 274 TYR 0.026 0.001 TYR H 90 ARG 0.007 0.001 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 986 time to evaluate : 4.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.5625 (tt0) cc_final: 0.5423 (mt-10) REVERT: B 15 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8452 (tm-30) REVERT: C 77 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7310 (mm-30) REVERT: C 86 LEU cc_start: 0.8488 (mt) cc_final: 0.8250 (mp) REVERT: C 120 GLU cc_start: 0.6726 (tp30) cc_final: 0.6499 (tp30) REVERT: C 194 ARG cc_start: 0.7297 (ttp80) cc_final: 0.7097 (ttp80) REVERT: C 325 GLU cc_start: 0.6254 (mt-10) cc_final: 0.5999 (mt-10) REVERT: C 380 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6226 (tmm) REVERT: F 22 SER cc_start: 0.8490 (t) cc_final: 0.8281 (t) REVERT: F 98 LYS cc_start: 0.8091 (tttt) cc_final: 0.7862 (ttmm) REVERT: G 124 LEU cc_start: 0.7888 (tp) cc_final: 0.7686 (tp) REVERT: G 170 GLU cc_start: 0.6793 (tt0) cc_final: 0.6479 (tt0) REVERT: H 98 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7860 (ttmm) REVERT: I 56 ASN cc_start: 0.8029 (t0) cc_final: 0.7796 (t0) REVERT: I 66 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7491 (m-30) REVERT: I 78 MET cc_start: 0.8679 (mmm) cc_final: 0.7961 (mmt) REVERT: J 98 LYS cc_start: 0.8072 (ttpp) cc_final: 0.7776 (ttmm) REVERT: K 65 MET cc_start: 0.7798 (mtt) cc_final: 0.7512 (mtt) REVERT: K 66 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: K 140 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6187 (mt-10) REVERT: K 176 ASN cc_start: 0.8240 (m110) cc_final: 0.7975 (m-40) REVERT: K 354 ASN cc_start: 0.7904 (m-40) cc_final: 0.7541 (m-40) REVERT: L 19 ARG cc_start: 0.7842 (ptp90) cc_final: 0.7115 (ptt90) REVERT: M 148 TRP cc_start: 0.7184 (m100) cc_final: 0.6968 (m-90) REVERT: M 234 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8445 (mp) REVERT: N 90 TYR cc_start: 0.8537 (t80) cc_final: 0.8284 (t80) REVERT: O 117 GLU cc_start: 0.6552 (pm20) cc_final: 0.6159 (pm20) REVERT: O 291 GLN cc_start: 0.7688 (tp40) cc_final: 0.7319 (tp40) REVERT: P 84 LYS cc_start: 0.8380 (mtpt) cc_final: 0.7962 (mtmm) REVERT: P 90 TYR cc_start: 0.8527 (t80) cc_final: 0.8194 (t80) REVERT: P 101 SER cc_start: 0.8954 (t) cc_final: 0.8592 (m) REVERT: P 112 LEU cc_start: 0.7417 (mm) cc_final: 0.6366 (mp) REVERT: Q 105 ASP cc_start: 0.6812 (m-30) cc_final: 0.6361 (m-30) REVERT: Q 298 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.8001 (mtpt) REVERT: Q 362 ARG cc_start: 0.6342 (ttt180) cc_final: 0.5910 (ttt180) REVERT: Q 368 VAL cc_start: 0.8490 (t) cc_final: 0.8234 (m) REVERT: R 90 TYR cc_start: 0.8524 (t80) cc_final: 0.8194 (t80) REVERT: T 110 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7716 (mp) REVERT: U 54 GLN cc_start: 0.8188 (mt0) cc_final: 0.7868 (mt0) REVERT: U 166 GLU cc_start: 0.7162 (mp0) cc_final: 0.6948 (mp0) REVERT: U 298 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7737 (mtpp) REVERT: V 28 PRO cc_start: 0.8265 (Cg_endo) cc_final: 0.7989 (Cg_exo) REVERT: W 111 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7155 (mm-30) REVERT: W 218 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.7237 (t80) REVERT: W 289 MET cc_start: 0.8164 (mtp) cc_final: 0.7938 (mtt) REVERT: X 15 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8417 (tm-30) outliers start: 105 outliers final: 61 residues processed: 1042 average time/residue: 0.5557 time to fit residues: 929.1161 Evaluate side-chains 1001 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 932 time to evaluate : 4.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain I residue 66 ASP Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 298 LYS Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain S residue 274 PHE Chi-restraints excluded: chain S residue 275 GLN Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 275 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 218 TYR Chi-restraints excluded: chain W residue 221 SER Chi-restraints excluded: chain W residue 253 ARG Chi-restraints excluded: chain W residue 269 THR Chi-restraints excluded: chain W residue 380 MET Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 511 optimal weight: 1.9990 chunk 348 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 457 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 524 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 313 optimal weight: 2.9990 chunk 551 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN I 184 GLN K 184 GLN K 279 GLN M 176 ASN M 407 GLN O 10 ASN O 328 HIS P 12 GLN Q 10 ASN Q 154 HIS Q 184 GLN Q 328 HIS R 12 GLN S 10 ASN S 54 GLN ** S 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN U 10 ASN ** V 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 60 GLN ** W 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 168 GLN ** W 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.7235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 51576 Z= 0.486 Angle : 0.780 10.267 70128 Z= 0.388 Chirality : 0.049 0.362 7800 Planarity : 0.006 0.056 9252 Dihedral : 5.119 28.121 7080 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.00 % Favored : 94.64 % Rotamer: Outliers : 2.98 % Allowed : 14.45 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.11 (0.10), residues: 6456 helix: 2.04 (0.09), residues: 3156 sheet: 0.81 (0.23), residues: 456 loop : -0.81 (0.12), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 148 HIS 0.010 0.002 HIS K 110 PHE 0.040 0.002 PHE Q 274 TYR 0.027 0.002 TYR U 230 ARG 0.010 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1003 time to evaluate : 4.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.8203 (mt0) cc_final: 0.7990 (mt0) REVERT: A 111 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 117 GLU cc_start: 0.5910 (tt0) cc_final: 0.5690 (mt-10) REVERT: B 15 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8305 (tm-30) REVERT: B 16 GLN cc_start: 0.8601 (tt0) cc_final: 0.8343 (tt0) REVERT: B 27 LYS cc_start: 0.6515 (tptt) cc_final: 0.6250 (tptp) REVERT: C 77 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7684 (mm-30) REVERT: C 78 MET cc_start: 0.8731 (mmt) cc_final: 0.8290 (mmt) REVERT: C 176 ASN cc_start: 0.8527 (m110) cc_final: 0.8323 (m110) REVERT: C 181 GLU cc_start: 0.7623 (tt0) cc_final: 0.7213 (tt0) REVERT: C 325 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6044 (mt-10) REVERT: F 27 LYS cc_start: 0.6884 (tptp) cc_final: 0.6665 (tptp) REVERT: F 98 LYS cc_start: 0.8271 (tttt) cc_final: 0.7972 (ttmm) REVERT: F 101 SER cc_start: 0.9095 (t) cc_final: 0.8692 (m) REVERT: G 18 ARG cc_start: 0.6394 (tpp-160) cc_final: 0.6036 (tpp-160) REVERT: G 170 GLU cc_start: 0.7225 (tt0) cc_final: 0.6924 (tt0) REVERT: G 181 GLU cc_start: 0.7677 (tt0) cc_final: 0.7447 (tt0) REVERT: G 253 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7806 (ptp90) REVERT: H 27 LYS cc_start: 0.6686 (tptp) cc_final: 0.6343 (mmmt) REVERT: H 98 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7970 (ttmm) REVERT: I 66 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: I 276 GLN cc_start: 0.7075 (mp10) cc_final: 0.6858 (mp10) REVERT: I 366 ARG cc_start: 0.7288 (mtp85) cc_final: 0.7029 (mtm110) REVERT: J 27 LYS cc_start: 0.6629 (tptp) cc_final: 0.6157 (mmmt) REVERT: J 98 LYS cc_start: 0.8364 (ttpp) cc_final: 0.8073 (ttmm) REVERT: K 56 ASN cc_start: 0.8681 (t0) cc_final: 0.8328 (t0) REVERT: K 62 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7703 (mt-10) REVERT: K 66 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: K 78 MET cc_start: 0.8561 (mmt) cc_final: 0.8197 (mmt) REVERT: K 140 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6656 (mt-10) REVERT: K 149 MET cc_start: 0.7493 (mmm) cc_final: 0.7193 (mmm) REVERT: K 181 GLU cc_start: 0.7504 (tt0) cc_final: 0.7276 (tt0) REVERT: K 390 VAL cc_start: 0.6748 (t) cc_final: 0.6508 (t) REVERT: L 98 LYS cc_start: 0.8425 (tttt) cc_final: 0.8094 (ttmm) REVERT: M 234 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8467 (mp) REVERT: M 390 VAL cc_start: 0.7219 (t) cc_final: 0.6983 (t) REVERT: N 98 LYS cc_start: 0.8366 (tttp) cc_final: 0.8138 (ttmm) REVERT: O 56 ASN cc_start: 0.8735 (t0) cc_final: 0.8476 (t0) REVERT: O 77 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7886 (mm-30) REVERT: O 380 MET cc_start: 0.7050 (ttp) cc_final: 0.6841 (tmm) REVERT: P 90 TYR cc_start: 0.8544 (t80) cc_final: 0.8297 (t80) REVERT: Q 56 ASN cc_start: 0.8596 (t0) cc_final: 0.8237 (t0) REVERT: Q 77 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7937 (mm-30) REVERT: Q 147 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6336 (mm-30) REVERT: Q 170 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: Q 275 GLN cc_start: 0.7114 (tt0) cc_final: 0.6740 (tt0) REVERT: Q 362 ARG cc_start: 0.6380 (ttt180) cc_final: 0.5956 (ttt180) REVERT: R 90 TYR cc_start: 0.8615 (t80) cc_final: 0.8361 (t80) REVERT: S 66 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7772 (m-30) REVERT: S 325 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6170 (mt-10) REVERT: S 329 ASP cc_start: 0.8138 (m-30) cc_final: 0.7924 (m-30) REVERT: S 366 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6348 (ttm-80) REVERT: U 54 GLN cc_start: 0.8324 (mt0) cc_final: 0.7993 (mt0) REVERT: U 65 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7689 (mtt) REVERT: U 166 GLU cc_start: 0.7215 (mp0) cc_final: 0.6901 (mp0) REVERT: W 56 ASN cc_start: 0.8651 (t0) cc_final: 0.8352 (t0) REVERT: W 149 MET cc_start: 0.7404 (tpp) cc_final: 0.7147 (tpp) REVERT: W 290 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7238 (ttm-80) REVERT: W 298 LYS cc_start: 0.8047 (mmtp) cc_final: 0.7631 (mmtm) REVERT: X 27 LYS cc_start: 0.6608 (tptt) cc_final: 0.6398 (mmmt) outliers start: 156 outliers final: 97 residues processed: 1109 average time/residue: 0.5637 time to fit residues: 984.0912 Evaluate side-chains 1059 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 954 time to evaluate : 4.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 253 ARG Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 66 ASP Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain I residue 352 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain O residue 384 ILE Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 274 PHE Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain S residue 66 ASP Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 229 ILE Chi-restraints excluded: chain S residue 275 GLN Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 366 ARG Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 65 MET Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 221 SER Chi-restraints excluded: chain W residue 253 ARG Chi-restraints excluded: chain W residue 380 MET Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 112 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 206 optimal weight: 0.8980 chunk 553 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 360 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 615 optimal weight: 0.4980 chunk 510 optimal weight: 0.9990 chunk 284 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 323 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN K 176 ASN K 184 GLN M 337 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN ** Q 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 354 ASN R 12 GLN S 10 ASN S 54 GLN T 12 GLN T 53 HIS U 10 ASN V 80 HIS V 126 GLN W 10 ASN W 54 GLN W 328 HIS ** X 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 51576 Z= 0.211 Angle : 0.593 8.392 70128 Z= 0.297 Chirality : 0.041 0.249 7800 Planarity : 0.005 0.051 9252 Dihedral : 4.646 28.740 7080 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 2.45 % Allowed : 16.09 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.50 (0.11), residues: 6456 helix: 2.43 (0.09), residues: 3144 sheet: 1.05 (0.21), residues: 516 loop : -0.74 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 141 HIS 0.013 0.001 HIS K 110 PHE 0.012 0.001 PHE Q 274 TYR 0.019 0.001 TYR N 90 ARG 0.009 0.001 ARG S 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1010 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.8295 (t) cc_final: 0.8008 (p) REVERT: A 111 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7282 (mm-30) REVERT: A 117 GLU cc_start: 0.5900 (tt0) cc_final: 0.5679 (mt-10) REVERT: A 290 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7359 (mtm-85) REVERT: B 15 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 27 LYS cc_start: 0.6519 (tptt) cc_final: 0.6148 (tptp) REVERT: B 101 SER cc_start: 0.8965 (t) cc_final: 0.8550 (m) REVERT: C 77 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7697 (mm-30) REVERT: C 181 GLU cc_start: 0.7610 (tt0) cc_final: 0.7330 (tt0) REVERT: C 290 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7294 (ttm-80) REVERT: C 325 GLU cc_start: 0.6473 (mt-10) cc_final: 0.6100 (mt-10) REVERT: D 101 SER cc_start: 0.8907 (t) cc_final: 0.8547 (m) REVERT: E 380 MET cc_start: 0.6755 (tmm) cc_final: 0.6461 (tmm) REVERT: F 27 LYS cc_start: 0.6889 (tptp) cc_final: 0.6558 (mmmt) REVERT: F 98 LYS cc_start: 0.8247 (tttt) cc_final: 0.7990 (ttmm) REVERT: F 101 SER cc_start: 0.9008 (t) cc_final: 0.8630 (m) REVERT: G 18 ARG cc_start: 0.6410 (tpp-160) cc_final: 0.5984 (tpp-160) REVERT: G 170 GLU cc_start: 0.7169 (tt0) cc_final: 0.6914 (tt0) REVERT: G 380 MET cc_start: 0.6732 (tmm) cc_final: 0.6521 (tmm) REVERT: H 27 LYS cc_start: 0.6698 (tptp) cc_final: 0.6382 (mmmt) REVERT: H 98 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7961 (ttmm) REVERT: H 101 SER cc_start: 0.8992 (t) cc_final: 0.8576 (m) REVERT: I 66 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: I 181 GLU cc_start: 0.7556 (tt0) cc_final: 0.7098 (tt0) REVERT: I 380 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6303 (tmm) REVERT: J 27 LYS cc_start: 0.6742 (tptp) cc_final: 0.6346 (mmmt) REVERT: J 98 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8092 (ttmm) REVERT: K 56 ASN cc_start: 0.8496 (t0) cc_final: 0.8112 (t0) REVERT: K 62 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7660 (mt-10) REVERT: K 66 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: K 181 GLU cc_start: 0.7523 (tt0) cc_final: 0.7285 (tt0) REVERT: K 362 ARG cc_start: 0.5743 (ttt180) cc_final: 0.5481 (ttt180) REVERT: L 19 ARG cc_start: 0.7956 (ptp90) cc_final: 0.7470 (ptp90) REVERT: L 27 LYS cc_start: 0.6590 (tptp) cc_final: 0.6277 (mmmt) REVERT: L 98 LYS cc_start: 0.8394 (tttt) cc_final: 0.8078 (ttmm) REVERT: L 101 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8584 (m) REVERT: M 38 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8611 (mttm) REVERT: M 148 TRP cc_start: 0.7648 (m100) cc_final: 0.7444 (m-90) REVERT: M 234 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8411 (mt) REVERT: N 98 LYS cc_start: 0.8330 (tttp) cc_final: 0.8102 (ttmm) REVERT: N 110 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7703 (mp) REVERT: O 56 ASN cc_start: 0.8560 (t0) cc_final: 0.8319 (t0) REVERT: O 77 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7893 (mm-30) REVERT: O 181 GLU cc_start: 0.7488 (tt0) cc_final: 0.7197 (tt0) REVERT: P 90 TYR cc_start: 0.8461 (t80) cc_final: 0.8218 (t80) REVERT: Q 56 ASN cc_start: 0.8429 (t0) cc_final: 0.8021 (t0) REVERT: Q 77 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7919 (mm-30) REVERT: Q 362 ARG cc_start: 0.6287 (ttt180) cc_final: 0.5908 (ttt180) REVERT: R 90 TYR cc_start: 0.8502 (t80) cc_final: 0.8287 (t80) REVERT: S 99 SER cc_start: 0.7727 (p) cc_final: 0.7031 (t) REVERT: S 325 GLU cc_start: 0.6441 (mt-10) cc_final: 0.5993 (mt-10) REVERT: S 366 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6321 (ttm-80) REVERT: U 65 MET cc_start: 0.8065 (mtp) cc_final: 0.7648 (mtt) REVERT: U 77 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7074 (mm-30) REVERT: U 99 SER cc_start: 0.7604 (p) cc_final: 0.7053 (m) REVERT: U 382 GLN cc_start: 0.5661 (mp10) cc_final: 0.5396 (mp10) REVERT: W 56 ASN cc_start: 0.8541 (t0) cc_final: 0.8211 (t0) REVERT: W 66 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: W 298 LYS cc_start: 0.7979 (mmtp) cc_final: 0.7618 (mmtm) REVERT: X 27 LYS cc_start: 0.6661 (tptt) cc_final: 0.6420 (mmmt) outliers start: 128 outliers final: 90 residues processed: 1085 average time/residue: 0.5630 time to fit residues: 966.2500 Evaluate side-chains 1067 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 969 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 248 LYS Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 66 ASP Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain I residue 380 MET Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain O residue 384 ILE Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain S residue 229 ILE Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 366 ARG Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 173 LEU Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 221 SER Chi-restraints excluded: chain W residue 253 ARG Chi-restraints excluded: chain W residue 380 MET Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 593 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 350 optimal weight: 0.7980 chunk 449 optimal weight: 0.6980 chunk 348 optimal weight: 8.9990 chunk 518 optimal weight: 0.0030 chunk 343 optimal weight: 0.9990 chunk 613 optimal weight: 0.9990 chunk 383 optimal weight: 4.9990 chunk 373 optimal weight: 0.9980 chunk 283 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS I 354 ASN K 15 GLN K 276 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN Q 97 ASN R 12 GLN S 10 ASN S 54 GLN S 276 GLN T 12 GLN ** T 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 10 ASN U 54 GLN W 54 GLN X 12 GLN X 80 HIS ** X 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.7512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 51576 Z= 0.202 Angle : 0.577 8.926 70128 Z= 0.288 Chirality : 0.040 0.210 7800 Planarity : 0.005 0.051 9252 Dihedral : 4.495 27.915 7080 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.74 % Favored : 95.07 % Rotamer: Outliers : 2.37 % Allowed : 16.82 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.63 (0.11), residues: 6456 helix: 2.52 (0.09), residues: 3156 sheet: 1.14 (0.22), residues: 516 loop : -0.68 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 148 HIS 0.006 0.001 HIS C 155 PHE 0.010 0.001 PHE Q 274 TYR 0.013 0.001 TYR H 90 ARG 0.013 0.001 ARG O 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 992 time to evaluate : 4.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 117 GLU cc_start: 0.5930 (tt0) cc_final: 0.5676 (mt-10) REVERT: A 290 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7376 (mtm-85) REVERT: B 15 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8264 (tm-30) REVERT: B 27 LYS cc_start: 0.6486 (tptt) cc_final: 0.6175 (tptp) REVERT: B 101 SER cc_start: 0.8969 (t) cc_final: 0.8554 (m) REVERT: C 77 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7728 (mm-30) REVERT: C 181 GLU cc_start: 0.7594 (tt0) cc_final: 0.7300 (tt0) REVERT: C 290 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7268 (ttm-80) REVERT: C 325 GLU cc_start: 0.6430 (mt-10) cc_final: 0.6097 (mt-10) REVERT: D 101 SER cc_start: 0.8928 (t) cc_final: 0.8564 (m) REVERT: E 51 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6927 (mm-30) REVERT: E 380 MET cc_start: 0.6757 (tmm) cc_final: 0.6477 (tmm) REVERT: F 27 LYS cc_start: 0.6874 (tptp) cc_final: 0.6553 (mmmt) REVERT: F 98 LYS cc_start: 0.8256 (tttt) cc_final: 0.8000 (ttmm) REVERT: F 101 SER cc_start: 0.9027 (t) cc_final: 0.8650 (m) REVERT: G 18 ARG cc_start: 0.6366 (tpp-160) cc_final: 0.5895 (tpp-160) REVERT: G 170 GLU cc_start: 0.7197 (tt0) cc_final: 0.6958 (tt0) REVERT: G 275 GLN cc_start: 0.7800 (tp40) cc_final: 0.7470 (tp-100) REVERT: G 380 MET cc_start: 0.6567 (tmm) cc_final: 0.6226 (tmm) REVERT: H 27 LYS cc_start: 0.6754 (tptp) cc_final: 0.6466 (mmmt) REVERT: H 98 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7943 (ttmm) REVERT: H 101 SER cc_start: 0.8979 (t) cc_final: 0.8562 (m) REVERT: I 66 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: I 78 MET cc_start: 0.8703 (mmt) cc_final: 0.8266 (mmt) REVERT: I 181 GLU cc_start: 0.7555 (tt0) cc_final: 0.7083 (tt0) REVERT: I 380 MET cc_start: 0.6639 (tmm) cc_final: 0.6337 (tmm) REVERT: J 27 LYS cc_start: 0.6791 (tptp) cc_final: 0.6414 (mmmt) REVERT: J 98 LYS cc_start: 0.8363 (ttpp) cc_final: 0.8096 (ttmm) REVERT: K 56 ASN cc_start: 0.8475 (t0) cc_final: 0.8055 (t0) REVERT: K 62 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7657 (mt-10) REVERT: K 66 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: K 149 MET cc_start: 0.7455 (mmm) cc_final: 0.7177 (mmm) REVERT: L 19 ARG cc_start: 0.7973 (ptp90) cc_final: 0.7493 (ptp90) REVERT: L 27 LYS cc_start: 0.6584 (tptp) cc_final: 0.6276 (mmmt) REVERT: L 98 LYS cc_start: 0.8394 (tttt) cc_final: 0.8073 (ttmm) REVERT: L 101 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8572 (m) REVERT: M 38 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8611 (mttm) REVERT: M 140 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6610 (mm-30) REVERT: M 234 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8435 (mp) REVERT: N 98 LYS cc_start: 0.8317 (tttp) cc_final: 0.8104 (ttmm) REVERT: N 110 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7773 (mp) REVERT: O 56 ASN cc_start: 0.8538 (t0) cc_final: 0.8305 (t0) REVERT: O 66 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: O 77 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7702 (mm-30) REVERT: O 78 MET cc_start: 0.8700 (mmt) cc_final: 0.8128 (mmt) REVERT: O 181 GLU cc_start: 0.7513 (tt0) cc_final: 0.7258 (tt0) REVERT: P 90 TYR cc_start: 0.8474 (t80) cc_final: 0.8228 (t80) REVERT: Q 56 ASN cc_start: 0.8421 (t0) cc_final: 0.7996 (t0) REVERT: Q 77 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7874 (mm-30) REVERT: Q 362 ARG cc_start: 0.6266 (ttt180) cc_final: 0.5866 (ttt180) REVERT: R 90 TYR cc_start: 0.8507 (t80) cc_final: 0.8288 (t80) REVERT: R 110 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7979 (mp) REVERT: S 99 SER cc_start: 0.7637 (p) cc_final: 0.6932 (t) REVERT: S 325 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6020 (mt-10) REVERT: S 371 LEU cc_start: 0.7961 (mm) cc_final: 0.7752 (mm) REVERT: T 110 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7796 (mp) REVERT: U 99 SER cc_start: 0.7475 (p) cc_final: 0.7210 (m) REVERT: U 170 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6944 (tt0) REVERT: U 382 GLN cc_start: 0.5718 (mp10) cc_final: 0.5412 (mp10) REVERT: W 56 ASN cc_start: 0.8523 (t0) cc_final: 0.8185 (t0) REVERT: W 66 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: W 298 LYS cc_start: 0.7986 (mmtp) cc_final: 0.7577 (mttt) REVERT: X 27 LYS cc_start: 0.6617 (tptt) cc_final: 0.6340 (mmmt) outliers start: 124 outliers final: 93 residues processed: 1069 average time/residue: 0.5629 time to fit residues: 951.7570 Evaluate side-chains 1074 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 972 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 248 LYS Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 66 ASP Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 15 GLN Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain O residue 384 ILE Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 229 ILE Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 221 SER Chi-restraints excluded: chain W residue 253 ARG Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 112 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 379 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 366 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 120 optimal weight: 0.1980 chunk 118 optimal weight: 3.9990 chunk 389 optimal weight: 0.9980 chunk 417 optimal weight: 1.9990 chunk 303 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 481 optimal weight: 1.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 54 GLN A 328 HIS ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN K 97 ASN ** K 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 HIS Q 10 ASN ** Q 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN S 10 ASN S 54 GLN T 12 GLN U 10 ASN X 12 GLN ** X 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.7650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 51576 Z= 0.254 Angle : 0.603 9.132 70128 Z= 0.301 Chirality : 0.041 0.206 7800 Planarity : 0.005 0.051 9252 Dihedral : 4.559 26.834 7080 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 2.50 % Allowed : 17.26 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.57 (0.11), residues: 6456 helix: 2.49 (0.09), residues: 3156 sheet: 1.19 (0.22), residues: 516 loop : -0.75 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 148 HIS 0.007 0.001 HIS C 155 PHE 0.012 0.001 PHE S 274 TYR 0.018 0.001 TYR N 90 ARG 0.016 0.001 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 976 time to evaluate : 4.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7394 (mm-30) REVERT: A 117 GLU cc_start: 0.5970 (tt0) cc_final: 0.5738 (mt-10) REVERT: A 290 ARG cc_start: 0.7618 (ttm-80) cc_final: 0.7318 (mtm-85) REVERT: B 15 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8270 (tm-30) REVERT: B 27 LYS cc_start: 0.6542 (tptt) cc_final: 0.6232 (tptp) REVERT: B 101 SER cc_start: 0.8961 (t) cc_final: 0.8569 (m) REVERT: C 77 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7792 (mm-30) REVERT: C 290 ARG cc_start: 0.7672 (ttm-80) cc_final: 0.7333 (ttm-80) REVERT: C 325 GLU cc_start: 0.6254 (mt-10) cc_final: 0.5868 (mt-10) REVERT: D 101 SER cc_start: 0.8936 (t) cc_final: 0.8571 (m) REVERT: E 51 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6992 (mm-30) REVERT: E 69 GLU cc_start: 0.7748 (tt0) cc_final: 0.7526 (tt0) REVERT: E 114 LEU cc_start: 0.7850 (tt) cc_final: 0.7433 (tp) REVERT: E 366 ARG cc_start: 0.7016 (ttp-110) cc_final: 0.6581 (mtm110) REVERT: E 380 MET cc_start: 0.6943 (tmm) cc_final: 0.6606 (tmm) REVERT: F 27 LYS cc_start: 0.6675 (tptp) cc_final: 0.6440 (mmmt) REVERT: F 98 LYS cc_start: 0.8252 (tttt) cc_final: 0.7982 (ttmm) REVERT: F 101 SER cc_start: 0.9038 (t) cc_final: 0.8660 (m) REVERT: G 18 ARG cc_start: 0.6360 (tpp-160) cc_final: 0.5839 (tpp-160) REVERT: G 275 GLN cc_start: 0.7784 (tp40) cc_final: 0.7438 (mm-40) REVERT: G 298 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8111 (ttpt) REVERT: G 380 MET cc_start: 0.6562 (tmm) cc_final: 0.6351 (tmm) REVERT: H 27 LYS cc_start: 0.6776 (tptp) cc_final: 0.6461 (mmmt) REVERT: H 98 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7936 (ttmm) REVERT: H 101 SER cc_start: 0.9002 (t) cc_final: 0.8586 (m) REVERT: I 66 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: I 78 MET cc_start: 0.8692 (mmt) cc_final: 0.8162 (mmt) REVERT: I 181 GLU cc_start: 0.7565 (tt0) cc_final: 0.7055 (tt0) REVERT: I 380 MET cc_start: 0.6581 (OUTLIER) cc_final: 0.6322 (tmm) REVERT: J 27 LYS cc_start: 0.6813 (tptp) cc_final: 0.6421 (mmmt) REVERT: J 90 TYR cc_start: 0.8514 (t80) cc_final: 0.8258 (t80) REVERT: J 98 LYS cc_start: 0.8377 (ttpp) cc_final: 0.8107 (ttmm) REVERT: K 56 ASN cc_start: 0.8539 (t0) cc_final: 0.8142 (t0) REVERT: K 62 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7660 (mt-10) REVERT: K 66 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: K 362 ARG cc_start: 0.5858 (ttt180) cc_final: 0.5566 (ttt180) REVERT: K 380 MET cc_start: 0.7057 (ttp) cc_final: 0.6732 (tmm) REVERT: K 390 VAL cc_start: 0.6783 (t) cc_final: 0.6562 (t) REVERT: L 19 ARG cc_start: 0.7974 (ptp90) cc_final: 0.7474 (ptp90) REVERT: L 27 LYS cc_start: 0.6609 (tptp) cc_final: 0.6290 (mmmt) REVERT: L 98 LYS cc_start: 0.8408 (tttt) cc_final: 0.8088 (ttmm) REVERT: L 101 SER cc_start: 0.9082 (t) cc_final: 0.8589 (m) REVERT: M 38 LYS cc_start: 0.8846 (ttmm) cc_final: 0.8622 (mttm) REVERT: M 56 ASN cc_start: 0.8563 (t0) cc_final: 0.8305 (t0) REVERT: M 93 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6906 (mm-30) REVERT: M 234 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8466 (mp) REVERT: N 98 LYS cc_start: 0.8303 (tttp) cc_final: 0.8095 (ttmm) REVERT: N 110 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7768 (mp) REVERT: O 56 ASN cc_start: 0.8589 (t0) cc_final: 0.8358 (t0) REVERT: O 66 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: O 77 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7737 (mm-30) REVERT: O 181 GLU cc_start: 0.7550 (tt0) cc_final: 0.7309 (tt0) REVERT: P 90 TYR cc_start: 0.8500 (t80) cc_final: 0.8253 (t80) REVERT: Q 56 ASN cc_start: 0.8466 (t0) cc_final: 0.8062 (t0) REVERT: Q 77 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7929 (mm-30) REVERT: Q 362 ARG cc_start: 0.6179 (ttt180) cc_final: 0.5807 (ttt180) REVERT: R 90 TYR cc_start: 0.8523 (t80) cc_final: 0.8296 (t80) REVERT: R 110 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8003 (mp) REVERT: S 99 SER cc_start: 0.7628 (p) cc_final: 0.6921 (t) REVERT: S 238 LYS cc_start: 0.8552 (mtpp) cc_final: 0.8293 (mttt) REVERT: S 325 GLU cc_start: 0.6496 (mt-10) cc_final: 0.5982 (mt-10) REVERT: S 371 LEU cc_start: 0.7957 (mm) cc_final: 0.7732 (mm) REVERT: S 382 GLN cc_start: 0.7252 (tp40) cc_final: 0.6815 (tp40) REVERT: T 110 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7804 (mp) REVERT: U 99 SER cc_start: 0.7461 (p) cc_final: 0.7008 (m) REVERT: U 170 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6893 (tt0) REVERT: U 382 GLN cc_start: 0.5771 (mp10) cc_final: 0.5444 (mp10) REVERT: W 56 ASN cc_start: 0.8517 (t0) cc_final: 0.8179 (t0) REVERT: W 66 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: W 103 LYS cc_start: 0.7098 (mtmm) cc_final: 0.6873 (mtmm) REVERT: W 290 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7293 (ttm-80) REVERT: W 298 LYS cc_start: 0.8042 (mmtp) cc_final: 0.7673 (mttt) REVERT: X 27 LYS cc_start: 0.6653 (tptt) cc_final: 0.6351 (mmmt) outliers start: 131 outliers final: 110 residues processed: 1060 average time/residue: 0.5469 time to fit residues: 917.4485 Evaluate side-chains 1069 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 949 time to evaluate : 4.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 248 LYS Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 66 ASP Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 380 MET Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 140 GLU Chi-restraints excluded: chain O residue 275 GLN Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain O residue 384 ILE Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 229 ILE Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 96 ARG Chi-restraints excluded: chain U residue 173 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 221 SER Chi-restraints excluded: chain W residue 253 ARG Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 112 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 557 optimal weight: 3.9990 chunk 587 optimal weight: 2.9990 chunk 535 optimal weight: 0.8980 chunk 571 optimal weight: 1.9990 chunk 343 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 448 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 516 optimal weight: 0.6980 chunk 540 optimal weight: 0.9980 chunk 569 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN K 15 GLN K 276 GLN ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN ** Q 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN S 10 ASN S 54 GLN T 12 GLN ** T 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 10 ASN U 276 GLN X 12 GLN ** X 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.7734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 51576 Z= 0.189 Angle : 0.570 9.043 70128 Z= 0.284 Chirality : 0.040 0.189 7800 Planarity : 0.005 0.052 9252 Dihedral : 4.426 27.210 7080 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.52 % Favored : 95.29 % Rotamer: Outliers : 2.39 % Allowed : 17.58 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.71 (0.11), residues: 6456 helix: 2.63 (0.09), residues: 3144 sheet: 1.24 (0.22), residues: 516 loop : -0.69 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Q 90 HIS 0.006 0.001 HIS C 155 PHE 0.012 0.001 PHE Q 274 TYR 0.007 0.001 TYR I 134 ARG 0.010 0.000 ARG K 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 979 time to evaluate : 4.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6834 (mm-30) REVERT: A 111 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7388 (mm-30) REVERT: A 238 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8299 (mtmt) REVERT: A 290 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7295 (mtm-85) REVERT: B 15 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8280 (tm-30) REVERT: B 27 LYS cc_start: 0.6529 (tptt) cc_final: 0.6234 (tptp) REVERT: B 101 SER cc_start: 0.8942 (t) cc_final: 0.8553 (m) REVERT: C 77 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7774 (mm-30) REVERT: C 202 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8480 (mtt180) REVERT: C 290 ARG cc_start: 0.7596 (ttm-80) cc_final: 0.7286 (ttm-80) REVERT: C 325 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5890 (mt-10) REVERT: C 331 LEU cc_start: 0.8529 (tp) cc_final: 0.8311 (tp) REVERT: D 101 SER cc_start: 0.8914 (t) cc_final: 0.8551 (m) REVERT: E 51 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6824 (mm-30) REVERT: E 114 LEU cc_start: 0.7842 (tt) cc_final: 0.7410 (tp) REVERT: E 275 GLN cc_start: 0.7726 (tp40) cc_final: 0.7501 (mm-40) REVERT: E 366 ARG cc_start: 0.7007 (ttp-110) cc_final: 0.6647 (mtm110) REVERT: E 380 MET cc_start: 0.6887 (tmm) cc_final: 0.6643 (tmm) REVERT: F 27 LYS cc_start: 0.6888 (tptp) cc_final: 0.6615 (mmmt) REVERT: F 98 LYS cc_start: 0.8257 (tttt) cc_final: 0.8021 (ttmm) REVERT: F 101 SER cc_start: 0.9022 (t) cc_final: 0.8644 (m) REVERT: G 18 ARG cc_start: 0.6365 (tpp-160) cc_final: 0.5824 (tpp-160) REVERT: G 275 GLN cc_start: 0.7733 (tp40) cc_final: 0.7385 (mm110) REVERT: H 27 LYS cc_start: 0.6685 (tptp) cc_final: 0.6417 (mmmt) REVERT: H 98 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7969 (ttmm) REVERT: H 101 SER cc_start: 0.8967 (t) cc_final: 0.8538 (m) REVERT: H 126 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.5373 (mp10) REVERT: I 54 GLN cc_start: 0.8037 (mt0) cc_final: 0.7663 (mt0) REVERT: I 66 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: I 78 MET cc_start: 0.8656 (mmt) cc_final: 0.8321 (mmt) REVERT: I 181 GLU cc_start: 0.7570 (tt0) cc_final: 0.7072 (tt0) REVERT: I 380 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6306 (tmm) REVERT: I 390 VAL cc_start: 0.6428 (t) cc_final: 0.6195 (t) REVERT: J 27 LYS cc_start: 0.6838 (tptp) cc_final: 0.6516 (mmmt) REVERT: J 90 TYR cc_start: 0.8533 (t80) cc_final: 0.8220 (t80) REVERT: J 98 LYS cc_start: 0.8372 (ttpp) cc_final: 0.8118 (ttmm) REVERT: K 56 ASN cc_start: 0.8484 (t0) cc_final: 0.8078 (t0) REVERT: K 62 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7660 (mt-10) REVERT: K 66 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: K 380 MET cc_start: 0.7037 (ttp) cc_final: 0.6695 (tmm) REVERT: K 390 VAL cc_start: 0.6831 (t) cc_final: 0.6601 (t) REVERT: L 19 ARG cc_start: 0.7973 (ptp90) cc_final: 0.7529 (ptp90) REVERT: L 27 LYS cc_start: 0.6631 (tptp) cc_final: 0.6290 (mmmt) REVERT: L 98 LYS cc_start: 0.8409 (tttt) cc_final: 0.8086 (ttmm) REVERT: L 101 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8574 (m) REVERT: L 112 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7057 (mm) REVERT: M 38 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8623 (mttm) REVERT: M 56 ASN cc_start: 0.8466 (t0) cc_final: 0.8210 (t0) REVERT: M 181 GLU cc_start: 0.7565 (tt0) cc_final: 0.7354 (tt0) REVERT: M 234 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8467 (mt) REVERT: N 15 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8082 (tm-30) REVERT: N 98 LYS cc_start: 0.8292 (tttp) cc_final: 0.8091 (ttmm) REVERT: O 56 ASN cc_start: 0.8530 (t0) cc_final: 0.8292 (t0) REVERT: O 66 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: O 77 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7692 (mm-30) REVERT: O 78 MET cc_start: 0.8717 (mmt) cc_final: 0.8227 (mmt) REVERT: O 181 GLU cc_start: 0.7543 (tt0) cc_final: 0.7313 (tt0) REVERT: P 90 TYR cc_start: 0.8461 (t80) cc_final: 0.8203 (t80) REVERT: Q 56 ASN cc_start: 0.8393 (t0) cc_final: 0.7945 (t0) REVERT: Q 77 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7818 (mm-30) REVERT: R 90 TYR cc_start: 0.8470 (t80) cc_final: 0.8254 (t80) REVERT: R 110 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7949 (mp) REVERT: S 99 SER cc_start: 0.7627 (p) cc_final: 0.6883 (t) REVERT: S 238 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8274 (mttt) REVERT: S 382 GLN cc_start: 0.7233 (tp40) cc_final: 0.6836 (tp40) REVERT: T 110 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7770 (mp) REVERT: U 77 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7579 (mm-30) REVERT: U 99 SER cc_start: 0.7281 (p) cc_final: 0.7061 (m) REVERT: U 382 GLN cc_start: 0.5757 (mp10) cc_final: 0.5451 (mp10) REVERT: W 19 GLU cc_start: 0.6597 (pm20) cc_final: 0.6333 (pp20) REVERT: W 56 ASN cc_start: 0.8435 (t0) cc_final: 0.8100 (t0) REVERT: W 66 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: W 290 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7296 (ttm-80) REVERT: W 298 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7577 (mttt) REVERT: X 27 LYS cc_start: 0.6652 (tptt) cc_final: 0.6363 (mmmt) outliers start: 125 outliers final: 104 residues processed: 1061 average time/residue: 0.5581 time to fit residues: 935.3521 Evaluate side-chains 1081 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 965 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 248 LYS Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 66 ASP Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain I residue 380 MET Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 275 GLN Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain O residue 384 ILE Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 229 ILE Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 96 ARG Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 173 LEU Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 221 SER Chi-restraints excluded: chain W residue 253 ARG Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 375 optimal weight: 0.9980 chunk 604 optimal weight: 0.7980 chunk 368 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 419 optimal weight: 2.9990 chunk 633 optimal weight: 0.5980 chunk 583 optimal weight: 4.9990 chunk 504 optimal weight: 0.0570 chunk 52 optimal weight: 3.9990 chunk 389 optimal weight: 0.9990 chunk 309 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** K 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN ** Q 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN S 10 ASN T 12 GLN ** T 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 10 ASN X 12 GLN ** X 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.7820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 51576 Z= 0.200 Angle : 0.578 18.102 70128 Z= 0.287 Chirality : 0.040 0.188 7800 Planarity : 0.005 0.051 9252 Dihedral : 4.380 26.096 7080 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.37 % Favored : 95.45 % Rotamer: Outliers : 2.41 % Allowed : 17.55 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.69 (0.11), residues: 6456 helix: 2.66 (0.09), residues: 3144 sheet: 1.33 (0.23), residues: 456 loop : -0.73 (0.12), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 90 HIS 0.006 0.001 HIS C 155 PHE 0.016 0.001 PHE Q 274 TYR 0.020 0.001 TYR N 90 ARG 0.011 0.000 ARG Q 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 974 time to evaluate : 4.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 238 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8308 (mtmt) REVERT: A 290 ARG cc_start: 0.7559 (ttm-80) cc_final: 0.7300 (mtm-85) REVERT: B 15 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8312 (tm-30) REVERT: B 27 LYS cc_start: 0.6556 (tptt) cc_final: 0.6256 (tptp) REVERT: B 101 SER cc_start: 0.8945 (t) cc_final: 0.8552 (m) REVERT: C 77 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7790 (mm-30) REVERT: C 202 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8485 (mtt180) REVERT: C 290 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7301 (ttm-80) REVERT: C 325 GLU cc_start: 0.6234 (mt-10) cc_final: 0.5872 (mt-10) REVERT: C 331 LEU cc_start: 0.8532 (tp) cc_final: 0.8325 (tp) REVERT: D 101 SER cc_start: 0.8938 (t) cc_final: 0.8554 (m) REVERT: E 51 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6855 (mm-30) REVERT: E 114 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7475 (tp) REVERT: E 366 ARG cc_start: 0.7026 (ttp-110) cc_final: 0.6677 (mtm110) REVERT: E 380 MET cc_start: 0.6945 (tmm) cc_final: 0.6701 (tmm) REVERT: F 27 LYS cc_start: 0.6784 (tptp) cc_final: 0.6582 (mmmt) REVERT: F 98 LYS cc_start: 0.8260 (tttt) cc_final: 0.8032 (ttmm) REVERT: F 101 SER cc_start: 0.9053 (t) cc_final: 0.8691 (m) REVERT: G 18 ARG cc_start: 0.6391 (tpp-160) cc_final: 0.5830 (tpp-160) REVERT: G 275 GLN cc_start: 0.7658 (tp40) cc_final: 0.7393 (mm110) REVERT: H 15 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8183 (tm-30) REVERT: H 27 LYS cc_start: 0.6715 (tptp) cc_final: 0.6444 (mmmt) REVERT: H 98 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7974 (ttmm) REVERT: H 101 SER cc_start: 0.8976 (t) cc_final: 0.8541 (m) REVERT: H 126 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.5417 (mp10) REVERT: I 54 GLN cc_start: 0.8045 (mt0) cc_final: 0.7674 (mt0) REVERT: I 66 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: I 78 MET cc_start: 0.8654 (mmt) cc_final: 0.8290 (mmt) REVERT: I 181 GLU cc_start: 0.7579 (tt0) cc_final: 0.7069 (tt0) REVERT: I 380 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6291 (tmm) REVERT: I 390 VAL cc_start: 0.6543 (t) cc_final: 0.6294 (t) REVERT: J 27 LYS cc_start: 0.6844 (tptp) cc_final: 0.6522 (mmmt) REVERT: J 90 TYR cc_start: 0.8526 (t80) cc_final: 0.8276 (t80) REVERT: J 98 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8120 (ttmm) REVERT: K 56 ASN cc_start: 0.8494 (t0) cc_final: 0.8102 (t0) REVERT: K 62 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7657 (mt-10) REVERT: K 66 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: K 276 GLN cc_start: 0.7744 (tp40) cc_final: 0.7541 (tt0) REVERT: K 380 MET cc_start: 0.7009 (ttp) cc_final: 0.6524 (tmm) REVERT: K 390 VAL cc_start: 0.6844 (t) cc_final: 0.6625 (t) REVERT: L 19 ARG cc_start: 0.7972 (ptp90) cc_final: 0.7529 (ptp90) REVERT: L 27 LYS cc_start: 0.6638 (tptp) cc_final: 0.6307 (mmmt) REVERT: L 98 LYS cc_start: 0.8416 (tttt) cc_final: 0.8096 (ttmm) REVERT: L 101 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8561 (m) REVERT: L 112 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7076 (mm) REVERT: M 38 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8632 (mttm) REVERT: M 56 ASN cc_start: 0.8472 (t0) cc_final: 0.8212 (t0) REVERT: M 181 GLU cc_start: 0.7612 (tt0) cc_final: 0.7401 (tt0) REVERT: M 234 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8477 (mp) REVERT: N 15 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8081 (tm-30) REVERT: N 98 LYS cc_start: 0.8299 (tttp) cc_final: 0.8094 (ttmm) REVERT: O 56 ASN cc_start: 0.8523 (t0) cc_final: 0.8285 (t0) REVERT: O 66 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: O 77 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7682 (mm-30) REVERT: O 78 MET cc_start: 0.8715 (mmt) cc_final: 0.8271 (mmt) REVERT: O 181 GLU cc_start: 0.7508 (tt0) cc_final: 0.7289 (tt0) REVERT: P 90 TYR cc_start: 0.8487 (t80) cc_final: 0.8260 (t80) REVERT: Q 56 ASN cc_start: 0.8400 (t0) cc_final: 0.7949 (t0) REVERT: R 90 TYR cc_start: 0.8486 (t80) cc_final: 0.8270 (t80) REVERT: R 110 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7981 (mp) REVERT: S 99 SER cc_start: 0.7590 (p) cc_final: 0.6814 (t) REVERT: S 238 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8286 (mttt) REVERT: S 371 LEU cc_start: 0.7958 (mm) cc_final: 0.7718 (mm) REVERT: S 382 GLN cc_start: 0.7209 (tp40) cc_final: 0.6794 (tp40) REVERT: T 110 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7795 (mp) REVERT: U 77 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7583 (mm-30) REVERT: U 99 SER cc_start: 0.7204 (p) cc_final: 0.6963 (m) REVERT: W 56 ASN cc_start: 0.8437 (t0) cc_final: 0.8098 (t0) REVERT: W 276 GLN cc_start: 0.7303 (mp10) cc_final: 0.6892 (mp10) REVERT: W 290 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.7280 (ttm-80) REVERT: W 298 LYS cc_start: 0.7993 (mmtp) cc_final: 0.7639 (mttt) REVERT: X 27 LYS cc_start: 0.6651 (tptt) cc_final: 0.6342 (mmmt) outliers start: 126 outliers final: 100 residues processed: 1056 average time/residue: 0.5678 time to fit residues: 948.1034 Evaluate side-chains 1083 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 971 time to evaluate : 4.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 248 LYS Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 66 ASP Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain I residue 380 MET Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 275 GLN Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain O residue 384 ILE Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 229 ILE Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 173 LEU Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 221 SER Chi-restraints excluded: chain W residue 253 ARG Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 400 optimal weight: 0.9980 chunk 537 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 465 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 505 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 518 optimal weight: 0.0970 chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** K 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN R 12 GLN S 10 ASN T 12 GLN ** T 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 10 ASN U 97 ASN U 276 GLN X 12 GLN ** X 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.148155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.116803 restraints weight = 63783.498| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.84 r_work: 0.3112 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.7878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 51576 Z= 0.204 Angle : 0.576 16.024 70128 Z= 0.286 Chirality : 0.040 0.183 7800 Planarity : 0.005 0.052 9252 Dihedral : 4.373 26.223 7080 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.52 % Favored : 95.29 % Rotamer: Outliers : 2.39 % Allowed : 17.78 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.71 (0.11), residues: 6456 helix: 2.67 (0.09), residues: 3144 sheet: 1.37 (0.23), residues: 456 loop : -0.73 (0.12), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 148 HIS 0.006 0.001 HIS C 155 PHE 0.012 0.001 PHE Q 274 TYR 0.011 0.001 TYR C 134 ARG 0.010 0.001 ARG Q 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15023.09 seconds wall clock time: 263 minutes 41.87 seconds (15821.87 seconds total)