Starting phenix.real_space_refine on Fri Dec 27 23:55:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rkb_19267/12_2024/8rkb_19267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rkb_19267/12_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/cci-nas-00/data/ceres_data/8rkb_19267/12_2024/8rkb_19267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rkb_19267/12_2024/8rkb_19267.map" model { file = "/net/cci-nas-00/data/ceres_data/8rkb_19267/12_2024/8rkb_19267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rkb_19267/12_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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.98, per 1000 atoms: 0.20 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=48, symmetry=0 Number of additional bonds: simple=48, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.35 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: 15.83 Time building geometry restraints manager: 12.06 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: 240 1.15 - 2.09: 539 2.09 - 3.03: 31972 3.03 - 3.96: 132894 3.96 - 4.90: 250188 Warning: very small nonbonded interaction distances. Nonbonded interactions: 415833 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 415828 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: 4.890 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: 1.450 Check model and map are aligned: 0.310 Set scattering table: 0.340 Process input model: 72.980 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.860 ------------------------------------------------------------------------------- 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= 0.164 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 to be fit. rotamer outliers: 0 poor density : 1418 time to evaluate : 4.145 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: 0.5748 time to fit residues: 1272.2869 Evaluate side-chains 942 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 942 time to evaluate : 4.201 ------------------------------------------------------------------------------- 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: 0.9980 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: 1.1586 ------------------------------------------------------------------------------- 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 321 GLN A 382 GLN B 53 HIS B 80 HIS ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN C 321 GLN C 328 HIS D 53 HIS D 87 ASN ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 321 GLN E 328 HIS E 354 ASN F 53 HIS F 80 HIS ** F 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 321 GLN G 328 HIS ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 HIS ** I 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 GLN I 321 GLN I 328 HIS I 354 ASN J 53 HIS ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 GLN K 321 GLN K 328 HIS L 53 HIS 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 321 GLN O 337 GLN P 53 HIS ** P 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 GLN Q 10 ASN Q 54 GLN ** Q 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 321 GLN R 53 HIS ** R 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 GLN S 10 ASN S 54 GLN S 321 GLN ** T 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 ASN ** T 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 GLN U 10 ASN U 60 GLN U 321 GLN V 53 HIS V 80 HIS ** V 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 GLN W 21 GLN W 60 GLN W 321 GLN X 53 HIS X 80 HIS Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 51576 Z= 0.371 Angle : 0.780 13.047 70128 Z= 0.401 Chirality : 0.048 0.383 7800 Planarity : 0.007 0.152 9252 Dihedral : 5.235 160.786 7080 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.86 % Favored : 94.76 % Rotamer: Outliers : 2.26 % Allowed : 9.48 % Favored : 88.26 % 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: 1.09 (0.11), residues: 6456 helix: 1.77 (0.09), residues: 3240 sheet: 0.27 (0.21), residues: 636 loop : -0.47 (0.13), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP L 138 HIS 0.010 0.002 HIS C 155 PHE 0.035 0.003 PHE W 75 TYR 0.033 0.002 TYR K 400 ARG 0.018 0.001 ARG U 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 1232 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1114 time to evaluate : 5.103 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: A 111 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7041 (mm-30) REVERT: A 166 GLU cc_start: 0.7095 (mp0) cc_final: 0.6777 (mp0) REVERT: A 170 GLU cc_start: 0.6639 (tm-30) cc_final: 0.6135 (tm-30) REVERT: A 229 ILE cc_start: 0.7542 (tt) cc_final: 0.7332 (tt) REVERT: A 380 MET cc_start: 0.5650 (tmm) cc_final: 0.5329 (tmm) REVERT: B 113 ASP cc_start: 0.7618 (p0) cc_final: 0.7322 (p0) REVERT: C 86 LEU cc_start: 0.8430 (mt) cc_final: 0.8171 (mp) REVERT: C 111 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7454 (mm-30) REVERT: C 125 ASP cc_start: 0.7596 (m-30) cc_final: 0.7307 (m-30) REVERT: C 166 GLU cc_start: 0.6930 (mp0) cc_final: 0.6539 (mp0) REVERT: C 380 MET cc_start: 0.6640 (tmm) cc_final: 0.6250 (tmm) REVERT: E 202 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8152 (mtt180) REVERT: F 34 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7730 (p) REVERT: F 98 LYS cc_start: 0.7957 (tttt) cc_final: 0.7756 (mtpp) REVERT: F 107 LYS cc_start: 0.8275 (mttt) cc_final: 0.8047 (mttm) REVERT: G 89 ASP cc_start: 0.6653 (p0) cc_final: 0.6426 (p0) REVERT: I 78 MET cc_start: 0.8293 (mmm) cc_final: 0.7717 (mmt) REVERT: J 49 ASP cc_start: 0.7786 (m-30) cc_final: 0.7475 (m-30) REVERT: J 120 PRO cc_start: 0.6527 (Cg_exo) cc_final: 0.6327 (Cg_endo) REVERT: K 47 ARG cc_start: 0.6880 (mtm-85) cc_final: 0.6633 (mtm-85) REVERT: K 65 MET cc_start: 0.7891 (mpp) cc_final: 0.7483 (mtt) REVERT: K 149 MET cc_start: 0.6726 (mmm) cc_final: 0.6463 (mmm) REVERT: K 176 ASN cc_start: 0.8171 (m110) cc_final: 0.7932 (m-40) REVERT: L 19 ARG cc_start: 0.7562 (ptp90) cc_final: 0.7156 (ptp90) REVERT: L 38 ASP cc_start: 0.8425 (m-30) cc_final: 0.8222 (m-30) REVERT: L 107 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7888 (mttm) REVERT: M 148 TRP cc_start: 0.7172 (m100) cc_final: 0.6842 (m-90) REVERT: M 176 ASN cc_start: 0.8001 (m110) cc_final: 0.7648 (m-40) REVERT: M 380 MET cc_start: 0.7170 (ttp) cc_final: 0.6945 (tmm) REVERT: O 19 GLU cc_start: 0.6949 (pm20) cc_final: 0.6679 (pm20) REVERT: O 69 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7635 (mt-10) REVERT: P 84 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7958 (mtmm) REVERT: P 101 SER cc_start: 0.8921 (t) cc_final: 0.8617 (m) REVERT: Q 113 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6654 (mt) REVERT: Q 140 GLU cc_start: 0.7183 (tp30) cc_final: 0.6947 (tp30) REVERT: R 90 TYR cc_start: 0.8531 (t80) cc_final: 0.8157 (t80) REVERT: R 107 LYS cc_start: 0.8401 (mtmm) cc_final: 0.8176 (mtmm) REVERT: S 166 GLU cc_start: 0.7216 (mp0) cc_final: 0.6997 (mp0) REVERT: S 181 GLU cc_start: 0.7296 (tt0) cc_final: 0.7036 (tt0) REVERT: U 78 MET cc_start: 0.8547 (mmm) cc_final: 0.8032 (mmt) REVERT: W 111 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7202 (mm-30) REVERT: W 218 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.7585 (t80) REVERT: W 289 MET cc_start: 0.7758 (mtp) cc_final: 0.7557 (mtt) REVERT: W 368 VAL cc_start: 0.8205 (t) cc_final: 0.7896 (m) outliers start: 118 outliers final: 66 residues processed: 1192 average time/residue: 0.5462 time to fit residues: 1041.0527 Evaluate side-chains 1025 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 955 time to evaluate : 4.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 203 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 114 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 236 LEU 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 114 LEU Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 234 ILE 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 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 114 LEU 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 147 GLU Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain O residue 80 LYS Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 113 LEU 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 50 VAL Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 113 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 S residue 50 VAL Chi-restraints excluded: chain S residue 112 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 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: 2.9990 chunk 179 optimal weight: 0.5980 chunk 480 optimal weight: 0.7980 chunk 393 optimal weight: 0.5980 chunk 159 optimal weight: 6.9990 chunk 578 optimal weight: 0.0570 chunk 625 optimal weight: 3.9990 chunk 515 optimal weight: 0.0980 chunk 573 optimal weight: 0.8980 chunk 197 optimal weight: 0.2980 chunk 464 optimal weight: 1.9990 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 132 HIS ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN I 144 GLN I 184 GLN ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN K 217 HIS M 184 GLN ** N 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 HIS ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN Q 54 GLN ** Q 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN S 10 ASN S 54 GLN T 53 HIS U 10 ASN U 56 ASN U 60 GLN W 60 GLN X 126 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 51576 Z= 0.194 Angle : 0.594 11.798 70128 Z= 0.299 Chirality : 0.040 0.287 7800 Planarity : 0.005 0.052 9252 Dihedral : 4.966 173.751 7080 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.06 % Favored : 95.65 % Rotamer: Outliers : 1.78 % Allowed : 12.19 % Favored : 86.03 % 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: 1.70 (0.11), residues: 6456 helix: 2.45 (0.09), residues: 3144 sheet: 1.67 (0.21), residues: 492 loop : -0.53 (0.12), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 148 HIS 0.008 0.001 HIS C 155 PHE 0.037 0.003 PHE W 75 TYR 0.026 0.001 TYR H 90 ARG 0.015 0.001 ARG M 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 1101 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1008 time to evaluate : 4.217 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: A 111 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7044 (mm-30) REVERT: A 380 MET cc_start: 0.5604 (tmm) cc_final: 0.5260 (tmm) REVERT: B 15 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8321 (tm-30) REVERT: C 66 ASP cc_start: 0.8007 (t0) cc_final: 0.7753 (t70) REVERT: C 120 GLU cc_start: 0.6581 (tp30) cc_final: 0.6270 (tp30) REVERT: C 125 ASP cc_start: 0.7644 (m-30) cc_final: 0.7336 (m-30) REVERT: C 380 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6167 (tmm) REVERT: F 98 LYS cc_start: 0.7961 (tttt) cc_final: 0.7741 (ttmm) REVERT: H 98 LYS cc_start: 0.7986 (ttpp) cc_final: 0.7695 (ttmm) REVERT: I 78 MET cc_start: 0.8355 (mmm) cc_final: 0.7826 (mmt) REVERT: J 38 ASP cc_start: 0.7986 (m-30) cc_final: 0.7764 (m-30) REVERT: J 98 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7614 (ttmm) REVERT: K 140 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6083 (mt-10) REVERT: K 176 ASN cc_start: 0.8153 (m110) cc_final: 0.7925 (m-40) REVERT: L 19 ARG cc_start: 0.7559 (ptp90) cc_final: 0.6962 (ptt90) REVERT: M 102 GLU cc_start: 0.5907 (mt-10) cc_final: 0.5629 (mt-10) REVERT: M 148 TRP cc_start: 0.7114 (m100) cc_final: 0.6838 (m-90) REVERT: M 176 ASN cc_start: 0.8070 (m110) cc_final: 0.7687 (m-40) REVERT: M 346 LEU cc_start: 0.8682 (tp) cc_final: 0.8445 (tp) REVERT: M 380 MET cc_start: 0.7298 (ttp) cc_final: 0.7058 (tmm) REVERT: N 90 TYR cc_start: 0.8409 (t80) cc_final: 0.8191 (t80) REVERT: O 117 GLU cc_start: 0.6410 (pm20) cc_final: 0.5812 (pm20) REVERT: O 291 GLN cc_start: 0.7694 (tp40) cc_final: 0.7310 (tp40) REVERT: P 84 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7871 (mtmm) REVERT: P 101 SER cc_start: 0.8896 (t) cc_final: 0.8579 (m) REVERT: Q 19 GLU cc_start: 0.6485 (pm20) cc_final: 0.6258 (pm20) REVERT: Q 298 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7976 (mtpt) REVERT: Q 362 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.5766 (ttt-90) REVERT: R 90 TYR cc_start: 0.8498 (t80) cc_final: 0.8113 (t80) REVERT: S 181 GLU cc_start: 0.7346 (tt0) cc_final: 0.6974 (tt0) REVERT: U 51 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7266 (mt-10) REVERT: U 65 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7465 (mtt) REVERT: U 78 MET cc_start: 0.8582 (mmm) cc_final: 0.8032 (mmt) REVERT: U 169 ASN cc_start: 0.8582 (t0) cc_final: 0.8344 (t0) REVERT: U 298 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7645 (mtpp) REVERT: V 28 PRO cc_start: 0.8219 (Cg_endo) cc_final: 0.7919 (Cg_exo) REVERT: W 60 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: W 111 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7215 (mm-30) REVERT: W 218 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.7290 (t80) REVERT: W 289 MET cc_start: 0.7879 (mtp) cc_final: 0.7617 (mtt) outliers start: 93 outliers final: 49 residues processed: 1060 average time/residue: 0.5294 time to fit residues: 903.0761 Evaluate side-chains 979 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 923 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 14 SER 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 62 SER Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain G residue 114 LEU 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 47 ARG Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 184 GLN Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 268 GLU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain K residue 144 GLN Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 89 ASP 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 Q residue 112 LEU Chi-restraints excluded: chain Q residue 298 LYS Chi-restraints excluded: chain Q residue 362 ARG Chi-restraints excluded: chain Q residue 367 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 65 MET Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 229 ILE 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 65 MET Chi-restraints excluded: chain W residue 67 MET 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 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: 0.9980 chunk 300 optimal weight: 0.0060 chunk 64 optimal weight: 5.9990 chunk 276 optimal weight: 0.9990 chunk 388 optimal weight: 0.0060 chunk 580 optimal weight: 1.9990 chunk 614 optimal weight: 20.0000 chunk 303 optimal weight: 0.0870 chunk 550 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- 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** G 144 GLN G 184 GLN I 217 HIS K 144 GLN K 155 HIS K 276 GLN N 53 HIS ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** U 168 GLN W 60 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 51576 Z= 0.172 Angle : 0.565 13.530 70128 Z= 0.284 Chirality : 0.039 0.214 7800 Planarity : 0.005 0.045 9252 Dihedral : 4.419 26.324 7080 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.69 % Favored : 95.12 % Rotamer: Outliers : 2.06 % Allowed : 13.23 % Favored : 84.71 % 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: 1.82 (0.11), residues: 6456 helix: 2.58 (0.09), residues: 3144 sheet: 1.41 (0.21), residues: 516 loop : -0.46 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 138 HIS 0.007 0.001 HIS C 155 PHE 0.049 0.002 PHE G 274 TYR 0.017 0.001 TYR K 400 ARG 0.015 0.001 ARG A 196 *********************** 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 1083 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 975 time to evaluate : 4.270 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: A 111 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 15 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8399 (tm-30) REVERT: C 120 GLU cc_start: 0.6531 (tp30) cc_final: 0.6318 (tp30) REVERT: C 125 ASP cc_start: 0.7819 (m-30) cc_final: 0.7473 (m-30) REVERT: C 325 GLU cc_start: 0.6198 (mt-10) cc_final: 0.5949 (mt-10) REVERT: C 380 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.6191 (tmm) REVERT: F 22 SER cc_start: 0.8354 (t) cc_final: 0.8108 (t) REVERT: F 98 LYS cc_start: 0.8066 (tttt) cc_final: 0.7853 (ttmm) REVERT: G 124 LEU cc_start: 0.7790 (tp) cc_final: 0.7572 (tp) REVERT: H 98 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7799 (ttmm) REVERT: I 66 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: I 78 MET cc_start: 0.8468 (mmm) cc_final: 0.7839 (mmt) REVERT: J 98 LYS cc_start: 0.7979 (ttpp) cc_final: 0.7693 (ttmm) REVERT: K 65 MET cc_start: 0.7765 (mtt) cc_final: 0.7494 (mtt) REVERT: K 66 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: K 140 GLU cc_start: 0.6497 (mm-30) cc_final: 0.6102 (mt-10) REVERT: K 149 MET cc_start: 0.6803 (mmm) cc_final: 0.6486 (mmm) REVERT: K 176 ASN cc_start: 0.8206 (m110) cc_final: 0.7953 (m-40) REVERT: K 354 ASN cc_start: 0.7876 (m-40) cc_final: 0.7517 (m-40) REVERT: L 19 ARG cc_start: 0.7681 (ptp90) cc_final: 0.7035 (ptt90) REVERT: M 148 TRP cc_start: 0.7151 (m100) cc_final: 0.6885 (m-90) REVERT: M 176 ASN cc_start: 0.8145 (m110) cc_final: 0.7911 (m110) REVERT: M 380 MET cc_start: 0.7265 (ttp) cc_final: 0.7064 (tmm) REVERT: N 38 ASP cc_start: 0.8405 (m-30) cc_final: 0.8193 (m-30) REVERT: N 90 TYR cc_start: 0.8460 (t80) cc_final: 0.8242 (t80) REVERT: O 117 GLU cc_start: 0.6438 (pm20) cc_final: 0.6031 (pm20) REVERT: O 291 GLN cc_start: 0.7699 (tp40) cc_final: 0.7333 (tp40) REVERT: P 84 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7989 (mtmm) REVERT: P 90 TYR cc_start: 0.8546 (t80) cc_final: 0.8193 (t80) REVERT: P 101 SER cc_start: 0.8919 (t) cc_final: 0.8570 (m) REVERT: Q 117 GLU cc_start: 0.6080 (pm20) cc_final: 0.5767 (pm20) REVERT: Q 149 MET cc_start: 0.7368 (tpp) cc_final: 0.7136 (mmm) REVERT: Q 362 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5422 (ttt180) REVERT: R 90 TYR cc_start: 0.8512 (t80) cc_final: 0.8177 (t80) REVERT: S 181 GLU cc_start: 0.7381 (tt0) cc_final: 0.7027 (tt0) REVERT: U 54 GLN cc_start: 0.8168 (mt0) cc_final: 0.7807 (mt0) REVERT: U 78 MET cc_start: 0.8654 (mmm) cc_final: 0.8057 (mmt) REVERT: U 298 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7704 (mtpp) REVERT: V 28 PRO cc_start: 0.8239 (Cg_endo) cc_final: 0.7966 (Cg_exo) REVERT: W 60 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: W 111 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7162 (mm-30) REVERT: W 218 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.7321 (t80) REVERT: X 15 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8394 (tm-30) REVERT: X 16 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8096 (tm-30) outliers start: 108 outliers final: 67 residues processed: 1032 average time/residue: 0.5787 time to fit residues: 963.7446 Evaluate side-chains 994 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 920 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 159 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 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 117 GLU 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 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 116 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain G residue 114 LEU 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 I residue 47 ARG 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 268 GLU 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 L residue 67 LEU Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain M residue 89 ASP 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 P residue 112 LEU Chi-restraints excluded: chain Q residue 362 ARG Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 66 ASP Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 74 LEU Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 113 LEU 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 T residue 21 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 74 LEU Chi-restraints excluded: chain U residue 218 TYR Chi-restraints excluded: chain U residue 229 ILE 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 65 MET Chi-restraints excluded: chain W residue 67 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 511 optimal weight: 1.9990 chunk 348 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 457 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 524 optimal weight: 0.6980 chunk 424 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 313 optimal weight: 0.9990 chunk 551 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 HIS I 184 GLN K 184 GLN M 184 GLN ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 ASN O 54 GLN O 169 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 T 12 GLN U 10 ASN ** W 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 144 GLN W 168 GLN W 328 HIS X 12 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.6580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 51576 Z= 0.360 Angle : 0.729 14.404 70128 Z= 0.367 Chirality : 0.046 0.298 7800 Planarity : 0.006 0.125 9252 Dihedral : 4.952 26.489 7080 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.16 % Favored : 94.53 % Rotamer: Outliers : 3.02 % Allowed : 13.90 % Favored : 83.08 % 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: 1.26 (0.11), residues: 6456 helix: 2.18 (0.09), residues: 3168 sheet: 0.36 (0.23), residues: 564 loop : -0.69 (0.12), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 148 HIS 0.011 0.002 HIS C 155 PHE 0.061 0.004 PHE I 274 TYR 0.022 0.002 TYR D 90 ARG 0.033 0.001 ARG S 196 *********************** 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 1192 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1034 time to evaluate : 4.344 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: A 238 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8439 (mtmt) REVERT: B 15 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8379 (tm-30) REVERT: B 27 LYS cc_start: 0.6685 (tptt) cc_final: 0.6388 (tptp) REVERT: C 77 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7705 (mm-30) REVERT: C 325 GLU cc_start: 0.6554 (mt-10) cc_final: 0.6138 (mt-10) REVERT: C 380 MET cc_start: 0.6741 (tmm) cc_final: 0.6439 (tmm) REVERT: F 98 LYS cc_start: 0.8252 (tttt) cc_final: 0.7959 (ttmm) REVERT: G 18 ARG cc_start: 0.6170 (tpp-160) cc_final: 0.5836 (tpp-160) REVERT: G 298 LYS cc_start: 0.8309 (ttpt) cc_final: 0.8063 (ttpt) REVERT: H 90 TYR cc_start: 0.8626 (t80) cc_final: 0.8235 (t80) REVERT: H 98 LYS cc_start: 0.8254 (ttpp) cc_final: 0.8022 (ttmm) REVERT: I 19 GLU cc_start: 0.7105 (pm20) cc_final: 0.6897 (pm20) REVERT: I 66 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: I 75 PHE cc_start: 0.8062 (t80) cc_final: 0.7814 (t80) REVERT: I 291 GLN cc_start: 0.7875 (tp40) cc_final: 0.7360 (tp40) REVERT: J 98 LYS cc_start: 0.8276 (ttpp) cc_final: 0.7946 (ttmm) REVERT: K 56 ASN cc_start: 0.8434 (t0) cc_final: 0.7983 (t0) REVERT: K 62 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7754 (mt-10) REVERT: K 66 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: K 111 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6818 (mm-30) REVERT: K 176 ASN cc_start: 0.8333 (m110) cc_final: 0.7990 (m-40) REVERT: K 366 ARG cc_start: 0.6918 (mtm110) cc_final: 0.6718 (mtm-85) REVERT: L 19 ARG cc_start: 0.7978 (ptp90) cc_final: 0.7344 (ptp90) REVERT: M 51 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6938 (mm-30) REVERT: M 148 TRP cc_start: 0.7467 (m100) cc_final: 0.7226 (m-90) REVERT: M 238 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8434 (mtmt) REVERT: M 273 ASP cc_start: 0.7318 (m-30) cc_final: 0.7095 (m-30) REVERT: N 27 LYS cc_start: 0.6665 (tptp) cc_final: 0.6305 (mmmt) REVERT: N 98 LYS cc_start: 0.8360 (tttp) cc_final: 0.8075 (ttmm) REVERT: N 110 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7871 (mp) REVERT: O 56 ASN cc_start: 0.8578 (t0) cc_final: 0.8373 (t0) REVERT: O 380 MET cc_start: 0.7160 (ttp) cc_final: 0.6855 (tmm) REVERT: P 90 TYR cc_start: 0.8546 (t80) cc_final: 0.8258 (t80) REVERT: Q 56 ASN cc_start: 0.8476 (t0) cc_final: 0.8095 (t0) REVERT: Q 79 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8186 (m) REVERT: Q 105 ASP cc_start: 0.7009 (m-30) cc_final: 0.6534 (m-30) REVERT: Q 140 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6305 (tt0) REVERT: Q 298 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8071 (mtpt) REVERT: Q 362 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.5262 (ttt180) REVERT: R 90 TYR cc_start: 0.8582 (t80) cc_final: 0.8294 (t80) REVERT: S 181 GLU cc_start: 0.7479 (tt0) cc_final: 0.7265 (tt0) REVERT: T 110 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7738 (mp) REVERT: U 54 GLN cc_start: 0.8234 (mt0) cc_final: 0.7902 (mt0) REVERT: U 62 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7621 (mt-10) REVERT: U 66 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: U 77 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7647 (mm-30) REVERT: U 78 MET cc_start: 0.8756 (mmm) cc_final: 0.7850 (mmt) REVERT: U 103 LYS cc_start: 0.7601 (mmtp) cc_final: 0.7275 (mmtt) REVERT: U 298 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7893 (mtpp) REVERT: U 382 GLN cc_start: 0.5733 (mp10) cc_final: 0.5464 (mp10) REVERT: W 65 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7507 (mtt) REVERT: W 66 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: W 293 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7507 (mt-10) REVERT: W 298 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7555 (mmtm) REVERT: X 15 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8395 (tm-30) outliers start: 158 outliers final: 102 residues processed: 1126 average time/residue: 0.5463 time to fit residues: 981.1284 Evaluate side-chains 1075 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 962 time to evaluate : 5.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 ILE 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 25 VAL 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 7 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 234 ILE 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 234 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 200 VAL 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 66 ASP Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain I residue 352 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 184 GLN Chi-restraints excluded: chain K residue 298 LYS 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 24 ARG Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 352 VAL 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 79 SER 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 345 ASP Chi-restraints excluded: chain Q residue 362 ARG Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 229 ILE Chi-restraints excluded: chain S residue 253 ARG 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 98 LYS Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 65 MET 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 114 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 206 optimal weight: 1.9990 chunk 553 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 360 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 615 optimal weight: 4.9990 chunk 510 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 323 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** C 176 ASN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN G 176 ASN G 184 GLN I 354 ASN M 176 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN ** Q 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN S 10 ASN S 54 GLN T 12 GLN U 10 ASN W 10 ASN W 54 GLN W 60 GLN X 12 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.6864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 51576 Z= 0.239 Angle : 0.633 19.402 70128 Z= 0.316 Chirality : 0.041 0.208 7800 Planarity : 0.005 0.048 9252 Dihedral : 4.768 40.524 7080 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.88 % Favored : 94.92 % Rotamer: Outliers : 2.87 % Allowed : 15.48 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.38 (0.11), residues: 6456 helix: 2.36 (0.09), residues: 3156 sheet: 0.37 (0.23), residues: 564 loop : -0.73 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP X 138 HIS 0.008 0.001 HIS C 155 PHE 0.048 0.003 PHE M 274 TYR 0.025 0.001 TYR J 90 ARG 0.027 0.001 ARG E 196 *********************** 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 1153 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1003 time to evaluate : 4.404 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: A 218 TYR cc_start: 0.8723 (m-80) cc_final: 0.8489 (m-80) REVERT: A 290 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.7358 (mtm-85) REVERT: B 15 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8336 (tm-30) REVERT: B 27 LYS cc_start: 0.6567 (tptt) cc_final: 0.6271 (tptp) REVERT: B 101 SER cc_start: 0.8985 (t) cc_final: 0.8589 (m) REVERT: C 77 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7661 (mm-30) REVERT: C 181 GLU cc_start: 0.7633 (tt0) cc_final: 0.7226 (tt0) REVERT: C 290 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7389 (mtm-85) REVERT: C 325 GLU cc_start: 0.6458 (mt-10) cc_final: 0.6100 (mt-10) REVERT: C 380 MET cc_start: 0.6729 (tmm) cc_final: 0.6205 (tmm) REVERT: E 327 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7385 (mmm-85) REVERT: F 98 LYS cc_start: 0.8231 (tttt) cc_final: 0.7972 (ttmm) REVERT: G 18 ARG cc_start: 0.6242 (tpp-160) cc_final: 0.5888 (tpp-160) REVERT: H 16 GLN cc_start: 0.8637 (tt0) cc_final: 0.8409 (tt0) REVERT: H 90 TYR cc_start: 0.8520 (t80) cc_final: 0.8241 (t80) REVERT: H 98 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7916 (ttmm) REVERT: I 66 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: I 75 PHE cc_start: 0.8007 (t80) cc_final: 0.7767 (t80) REVERT: I 78 MET cc_start: 0.8656 (mmt) cc_final: 0.8363 (mmt) REVERT: I 380 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6203 (tmm) REVERT: J 98 LYS cc_start: 0.8294 (ttpp) cc_final: 0.8038 (ttmm) REVERT: K 56 ASN cc_start: 0.8345 (t0) cc_final: 0.7916 (t0) REVERT: K 62 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7822 (mt-10) REVERT: K 66 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: K 111 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6832 (mm-30) REVERT: K 149 MET cc_start: 0.7202 (mmm) cc_final: 0.6859 (mmm) REVERT: K 176 ASN cc_start: 0.8308 (m110) cc_final: 0.8006 (m-40) REVERT: K 362 ARG cc_start: 0.5727 (ttt180) cc_final: 0.5256 (ttt180) REVERT: L 19 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7410 (ptp90) REVERT: L 27 LYS cc_start: 0.6618 (tptp) cc_final: 0.6232 (mmmt) REVERT: M 19 GLU cc_start: 0.7066 (pm20) cc_final: 0.6819 (pm20) REVERT: M 51 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6902 (mm-30) REVERT: M 291 GLN cc_start: 0.7693 (tp40) cc_final: 0.7487 (tp40) REVERT: N 27 LYS cc_start: 0.6704 (tptp) cc_final: 0.6371 (mmmt) REVERT: N 98 LYS cc_start: 0.8334 (tttp) cc_final: 0.8084 (ttmm) REVERT: O 56 ASN cc_start: 0.8539 (t0) cc_final: 0.8281 (t0) REVERT: O 66 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: O 78 MET cc_start: 0.8748 (mmt) cc_final: 0.8198 (mmt) REVERT: O 380 MET cc_start: 0.7107 (ttp) cc_final: 0.6772 (tmm) REVERT: P 90 TYR cc_start: 0.8488 (t80) cc_final: 0.8215 (t80) REVERT: Q 56 ASN cc_start: 0.8415 (t0) cc_final: 0.8042 (t0) REVERT: Q 79 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8200 (m) REVERT: Q 362 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5489 (ttt180) REVERT: Q 366 ARG cc_start: 0.7083 (mtm-85) cc_final: 0.6836 (mtm-85) REVERT: R 90 TYR cc_start: 0.8496 (t80) cc_final: 0.8252 (t80) REVERT: S 353 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7627 (mt) REVERT: T 110 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7725 (mp) REVERT: U 54 GLN cc_start: 0.8220 (mt0) cc_final: 0.7873 (mt0) REVERT: U 62 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7676 (mt-10) REVERT: U 66 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: U 99 SER cc_start: 0.7666 (p) cc_final: 0.7011 (t) REVERT: U 170 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6950 (tm-30) REVERT: U 298 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7871 (mtpp) REVERT: U 366 ARG cc_start: 0.6811 (mtm-85) cc_final: 0.6608 (mtm-85) REVERT: U 382 GLN cc_start: 0.5796 (mp10) cc_final: 0.5586 (mp10) REVERT: W 56 ASN cc_start: 0.8529 (t0) cc_final: 0.8251 (t0) REVERT: W 66 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: W 290 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.7197 (ttm-80) REVERT: W 298 LYS cc_start: 0.7994 (mmtp) cc_final: 0.7455 (mttt) outliers start: 150 outliers final: 103 residues processed: 1085 average time/residue: 0.5493 time to fit residues: 950.4734 Evaluate side-chains 1079 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 965 time to evaluate : 4.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 114 LEU 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 58 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 125 VAL 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 79 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 221 SER 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 112 LEU Chi-restraints excluded: chain D residue 113 ASP 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 114 LEU Chi-restraints excluded: chain E residue 288 MET 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 G residue 114 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 288 MET 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 H residue 112 LEU Chi-restraints excluded: chain I residue 66 ASP Chi-restraints excluded: chain I residue 114 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 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 14 THR Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 65 THR 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 113 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 79 SER Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain Q residue 362 ARG Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 229 ILE Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 353 LEU 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 66 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 173 LEU Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain U residue 298 LYS 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 114 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 25 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 593 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 350 optimal weight: 0.8980 chunk 449 optimal weight: 2.9990 chunk 348 optimal weight: 9.9990 chunk 518 optimal weight: 1.9990 chunk 343 optimal weight: 4.9990 chunk 613 optimal weight: 0.0170 chunk 383 optimal weight: 2.9990 chunk 373 optimal weight: 3.9990 chunk 283 optimal weight: 0.5980 overall best weight: 0.8220 ------------------------------------------------------------------------------- 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** C 176 ASN D 12 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN I 154 HIS K 184 GLN M 54 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN R 12 GLN S 10 ASN S 54 GLN T 12 GLN U 10 ASN W 10 ASN W 54 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 51576 Z= 0.235 Angle : 0.635 32.096 70128 Z= 0.317 Chirality : 0.041 0.211 7800 Planarity : 0.007 0.424 9252 Dihedral : 4.830 82.760 7080 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.14 % Favored : 94.67 % Rotamer: Outliers : 3.08 % Allowed : 15.86 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.49 (0.11), residues: 6456 helix: 2.42 (0.09), residues: 3144 sheet: 1.30 (0.24), residues: 444 loop : -0.75 (0.12), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 138 HIS 0.008 0.001 HIS C 155 PHE 0.071 0.003 PHE A 274 TYR 0.016 0.001 TYR D 90 ARG 0.033 0.001 ARG U 196 *********************** 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 1160 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 999 time to evaluate : 4.342 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: A 111 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7204 (mm-30) REVERT: A 275 GLN cc_start: 0.6512 (mm-40) cc_final: 0.6296 (mm-40) REVERT: A 290 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7411 (mtm-85) REVERT: B 15 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 27 LYS cc_start: 0.6552 (tptt) cc_final: 0.6255 (tptp) REVERT: B 101 SER cc_start: 0.8974 (t) cc_final: 0.8580 (m) REVERT: C 181 GLU cc_start: 0.7673 (tt0) cc_final: 0.7229 (tt0) REVERT: C 290 ARG cc_start: 0.7631 (ttm-80) cc_final: 0.7416 (mtm-85) REVERT: C 325 GLU cc_start: 0.6520 (mt-10) cc_final: 0.6145 (mt-10) REVERT: C 380 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6351 (tmm) REVERT: E 202 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7892 (mtp180) REVERT: E 380 MET cc_start: 0.6659 (tmm) cc_final: 0.6368 (tmm) REVERT: F 27 LYS cc_start: 0.6770 (tptp) cc_final: 0.6556 (mmmt) REVERT: F 98 LYS cc_start: 0.8272 (tttt) cc_final: 0.7986 (ttmm) REVERT: G 18 ARG cc_start: 0.6351 (tpp-160) cc_final: 0.5832 (tpp-160) REVERT: G 253 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7717 (ptp90) REVERT: G 366 ARG cc_start: 0.6745 (ttp-110) cc_final: 0.6517 (ttp-110) REVERT: G 380 MET cc_start: 0.6616 (tmm) cc_final: 0.6410 (tmm) REVERT: H 16 GLN cc_start: 0.8663 (tt0) cc_final: 0.8404 (tt0) REVERT: H 27 LYS cc_start: 0.6598 (tptp) cc_final: 0.6333 (mmmt) REVERT: H 98 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7970 (ttmm) REVERT: I 66 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: I 75 PHE cc_start: 0.8026 (t80) cc_final: 0.7797 (t80) REVERT: I 78 MET cc_start: 0.8651 (mmt) cc_final: 0.8210 (mmt) REVERT: I 181 GLU cc_start: 0.7473 (tt0) cc_final: 0.7051 (tt0) REVERT: I 276 GLN cc_start: 0.6912 (mp10) cc_final: 0.6677 (mp10) REVERT: I 380 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6263 (tmm) REVERT: J 98 LYS cc_start: 0.8325 (ttpp) cc_final: 0.8061 (ttmm) REVERT: K 56 ASN cc_start: 0.8375 (t0) cc_final: 0.7943 (t0) REVERT: K 62 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7691 (mt-10) REVERT: K 66 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: K 111 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6903 (mm-30) REVERT: K 149 MET cc_start: 0.7309 (mmm) cc_final: 0.7007 (mmm) REVERT: K 176 ASN cc_start: 0.8317 (m110) cc_final: 0.7964 (m-40) REVERT: K 181 GLU cc_start: 0.7530 (tt0) cc_final: 0.7192 (tt0) REVERT: K 290 ARG cc_start: 0.7496 (ttp-110) cc_final: 0.7289 (ttp-110) REVERT: K 362 ARG cc_start: 0.5772 (ttt180) cc_final: 0.5253 (ttt180) REVERT: L 19 ARG cc_start: 0.7961 (ptp90) cc_final: 0.7535 (ptp90) REVERT: L 27 LYS cc_start: 0.6639 (tptp) cc_final: 0.6274 (mmmt) REVERT: M 291 GLN cc_start: 0.7712 (tp40) cc_final: 0.7483 (tp40) REVERT: N 27 LYS cc_start: 0.6670 (tptp) cc_final: 0.6317 (mmmt) REVERT: N 98 LYS cc_start: 0.8347 (tttp) cc_final: 0.8102 (ttmm) REVERT: O 56 ASN cc_start: 0.8549 (t0) cc_final: 0.8292 (t0) REVERT: O 66 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: O 78 MET cc_start: 0.8723 (mmt) cc_final: 0.8155 (mmt) REVERT: O 380 MET cc_start: 0.7080 (ttp) cc_final: 0.6741 (tmm) REVERT: P 90 TYR cc_start: 0.8493 (t80) cc_final: 0.8221 (t80) REVERT: Q 56 ASN cc_start: 0.8413 (t0) cc_final: 0.7994 (t0) REVERT: Q 79 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8169 (m) REVERT: Q 362 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.5387 (ttt180) REVERT: Q 366 ARG cc_start: 0.7089 (mtm-85) cc_final: 0.6812 (mtm-85) REVERT: R 90 TYR cc_start: 0.8534 (t80) cc_final: 0.8286 (t80) REVERT: S 353 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7630 (mt) REVERT: T 110 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7760 (mp) REVERT: U 54 GLN cc_start: 0.8202 (mt0) cc_final: 0.7963 (mt0) REVERT: U 62 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7686 (mt-10) REVERT: U 66 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: U 77 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7816 (mm-30) REVERT: U 99 SER cc_start: 0.7617 (p) cc_final: 0.6917 (t) REVERT: U 331 LEU cc_start: 0.8620 (tp) cc_final: 0.8381 (tp) REVERT: U 366 ARG cc_start: 0.6799 (mtm-85) cc_final: 0.6558 (mtm-85) REVERT: U 382 GLN cc_start: 0.5782 (mp10) cc_final: 0.5556 (mp10) REVERT: W 56 ASN cc_start: 0.8535 (t0) cc_final: 0.8231 (t0) REVERT: W 66 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: W 290 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.7223 (ttm-80) REVERT: W 298 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7629 (mmtm) outliers start: 161 outliers final: 130 residues processed: 1101 average time/residue: 0.5610 time to fit residues: 984.3813 Evaluate side-chains 1113 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 970 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 ILE 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 58 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 125 VAL 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 79 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 LEU 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 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 58 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 65 THR 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 127 ILE Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 235 ARG Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain F residue 34 THR 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 114 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 253 ARG Chi-restraints excluded: chain G residue 288 MET 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 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 234 ILE 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 J residue 127 ILE Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 298 LYS 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 114 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 65 THR 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 113 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 352 VAL Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 79 SER Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 226 MET Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain Q residue 362 ARG 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 114 LEU 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 353 LEU 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 66 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 173 LEU Chi-restraints excluded: chain U residue 253 ARG 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 114 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 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: 1.9990 chunk 244 optimal weight: 0.9980 chunk 366 optimal weight: 0.0870 chunk 184 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 389 optimal weight: 1.9990 chunk 417 optimal weight: 1.9990 chunk 303 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 481 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN C 132 HIS ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 184 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 HIS Q 10 ASN R 12 GLN S 10 ASN S 54 GLN T 12 GLN U 10 ASN W 10 ASN X 12 GLN X 80 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.7230 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= 0.206 Angle : 0.620 21.320 70128 Z= 0.312 Chirality : 0.040 0.267 7800 Planarity : 0.007 0.420 9252 Dihedral : 5.368 150.686 7080 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.86 % Favored : 94.95 % Rotamer: Outliers : 3.17 % Allowed : 16.17 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.47 (0.11), residues: 6456 helix: 2.53 (0.09), residues: 3132 sheet: 0.44 (0.23), residues: 540 loop : -0.77 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 138 HIS 0.007 0.001 HIS C 155 PHE 0.054 0.003 PHE U 274 TYR 0.016 0.001 TYR B 90 ARG 0.037 0.001 ARG U 196 *********************** 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 1162 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 996 time to evaluate : 4.375 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: A 218 TYR cc_start: 0.8707 (m-80) cc_final: 0.8473 (m-80) REVERT: A 290 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7370 (mtm-85) REVERT: B 15 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8299 (tm-30) REVERT: B 27 LYS cc_start: 0.6516 (tptt) cc_final: 0.6215 (tptp) REVERT: B 101 SER cc_start: 0.8968 (t) cc_final: 0.8550 (m) REVERT: C 77 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7730 (mm-30) REVERT: C 181 GLU cc_start: 0.7698 (tt0) cc_final: 0.7252 (tt0) REVERT: C 290 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.7340 (ttm-80) REVERT: C 325 GLU cc_start: 0.6482 (mt-10) cc_final: 0.6111 (mt-10) REVERT: D 98 LYS cc_start: 0.8436 (ttpp) cc_final: 0.8171 (ttmm) REVERT: E 80 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8313 (mtpp) REVERT: E 202 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7733 (mtp180) REVERT: E 380 MET cc_start: 0.6686 (tmm) cc_final: 0.6412 (tmm) REVERT: F 27 LYS cc_start: 0.6742 (tptp) cc_final: 0.6531 (mmmt) REVERT: F 98 LYS cc_start: 0.8273 (tttt) cc_final: 0.7991 (ttmm) REVERT: F 101 SER cc_start: 0.9080 (t) cc_final: 0.8557 (m) REVERT: G 18 ARG cc_start: 0.6375 (tpp-160) cc_final: 0.5841 (tpp-160) REVERT: G 194 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6943 (ttp80) REVERT: G 253 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7765 (ptp90) REVERT: G 298 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8020 (ttpt) REVERT: G 366 ARG cc_start: 0.6736 (ttp-110) cc_final: 0.6463 (mtm110) REVERT: H 16 GLN cc_start: 0.8656 (tt0) cc_final: 0.8399 (tt0) REVERT: H 27 LYS cc_start: 0.6613 (tptp) cc_final: 0.6359 (mmmt) REVERT: H 98 LYS cc_start: 0.8253 (ttpp) cc_final: 0.7983 (ttmm) REVERT: I 66 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: I 78 MET cc_start: 0.8620 (mmt) cc_final: 0.8245 (mmt) REVERT: I 181 GLU cc_start: 0.7527 (tt0) cc_final: 0.7097 (tt0) REVERT: I 276 GLN cc_start: 0.6918 (mp10) cc_final: 0.6685 (mp10) REVERT: I 380 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6294 (tmm) REVERT: J 27 LYS cc_start: 0.6596 (tptp) cc_final: 0.6267 (mmmt) REVERT: J 90 TYR cc_start: 0.8422 (t80) cc_final: 0.8082 (t80) REVERT: J 98 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8069 (ttmm) REVERT: K 56 ASN cc_start: 0.8346 (t0) cc_final: 0.7927 (t0) REVERT: K 62 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7681 (mt-10) REVERT: K 66 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: K 111 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6902 (mm-30) REVERT: K 176 ASN cc_start: 0.8317 (m110) cc_final: 0.7954 (m-40) REVERT: K 181 GLU cc_start: 0.7541 (tt0) cc_final: 0.7211 (tt0) REVERT: K 362 ARG cc_start: 0.5747 (ttt180) cc_final: 0.5281 (ttt180) REVERT: K 380 MET cc_start: 0.6948 (ttp) cc_final: 0.6511 (tmm) REVERT: L 19 ARG cc_start: 0.7935 (ptp90) cc_final: 0.7461 (ptp90) REVERT: L 27 LYS cc_start: 0.6654 (tptp) cc_final: 0.6297 (mmmt) REVERT: M 148 TRP cc_start: 0.7569 (m100) cc_final: 0.7300 (m-90) REVERT: N 15 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7990 (tm-30) REVERT: N 27 LYS cc_start: 0.6664 (tptp) cc_final: 0.6314 (mmmt) REVERT: N 98 LYS cc_start: 0.8322 (tttp) cc_final: 0.8088 (ttmm) REVERT: O 56 ASN cc_start: 0.8506 (t0) cc_final: 0.8252 (t0) REVERT: O 78 MET cc_start: 0.8704 (mmt) cc_final: 0.8174 (mmt) REVERT: O 380 MET cc_start: 0.7093 (ttp) cc_final: 0.6769 (tmm) REVERT: P 90 TYR cc_start: 0.8479 (t80) cc_final: 0.8216 (t80) REVERT: Q 56 ASN cc_start: 0.8386 (t0) cc_final: 0.7964 (t0) REVERT: Q 79 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8254 (m) REVERT: Q 362 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5379 (ttt180) REVERT: R 90 TYR cc_start: 0.8520 (t80) cc_final: 0.8289 (t80) REVERT: S 353 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7637 (mt) REVERT: T 110 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7772 (mp) REVERT: U 54 GLN cc_start: 0.8178 (mt0) cc_final: 0.7927 (mt0) REVERT: U 62 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7654 (mt-10) REVERT: U 66 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7269 (m-30) REVERT: U 77 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7112 (mm-30) REVERT: U 99 SER cc_start: 0.7577 (p) cc_final: 0.6664 (t) REVERT: U 170 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6911 (tt0) REVERT: U 331 LEU cc_start: 0.8616 (tp) cc_final: 0.8393 (tp) REVERT: U 382 GLN cc_start: 0.5779 (mp10) cc_final: 0.5536 (mp10) REVERT: W 56 ASN cc_start: 0.8497 (t0) cc_final: 0.8180 (t0) REVERT: W 66 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: W 290 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7216 (ttm-80) REVERT: W 298 LYS cc_start: 0.7987 (mmtp) cc_final: 0.7644 (mmtm) outliers start: 166 outliers final: 124 residues processed: 1097 average time/residue: 0.5467 time to fit residues: 953.1115 Evaluate side-chains 1101 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 964 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 125 VAL 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 114 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 25 VAL 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 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 18 ARG Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 235 ARG Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 34 THR 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 F residue 127 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 194 ARG 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 G residue 298 LYS Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 25 VAL 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 114 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 234 ILE 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 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 114 LEU Chi-restraints excluded: chain K residue 116 LEU 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 111 GLU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 140 GLU Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 79 SER Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 226 MET Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain Q residue 362 ARG Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 253 ARG Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 353 LEU 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 66 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 173 LEU Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain U residue 253 ARG Chi-restraints excluded: chain V residue 21 VAL 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 114 LEU 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 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: 0.7980 chunk 587 optimal weight: 0.0770 chunk 535 optimal weight: 0.6980 chunk 571 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 448 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 516 optimal weight: 0.8980 chunk 540 optimal weight: 0.8980 chunk 569 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN B 80 HIS ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 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 S 54 GLN T 12 GLN U 10 ASN V 126 GLN W 10 ASN X 12 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.7361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 51576 Z= 0.220 Angle : 0.629 17.426 70128 Z= 0.318 Chirality : 0.040 0.427 7800 Planarity : 0.008 0.395 9252 Dihedral : 6.138 163.795 7080 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.02 % Favored : 94.80 % Rotamer: Outliers : 3.04 % Allowed : 16.70 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.56 (0.11), residues: 6456 helix: 2.51 (0.09), residues: 3156 sheet: 1.34 (0.25), residues: 420 loop : -0.74 (0.12), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP N 138 HIS 0.007 0.001 HIS C 155 PHE 0.131 0.004 PHE G 274 TYR 0.016 0.001 TYR T 90 ARG 0.043 0.001 ARG U 196 *********************** 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 1152 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 993 time to evaluate : 4.297 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: A 92 VAL cc_start: 0.8299 (t) cc_final: 0.7958 (p) REVERT: A 238 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8403 (mttt) REVERT: A 290 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7345 (mtm-85) REVERT: B 15 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8325 (tm-30) REVERT: B 27 LYS cc_start: 0.6496 (tptt) cc_final: 0.6149 (tptp) REVERT: B 101 SER cc_start: 0.8966 (t) cc_final: 0.8543 (m) REVERT: C 77 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7726 (mm-30) REVERT: C 181 GLU cc_start: 0.7712 (tt0) cc_final: 0.7216 (tt0) REVERT: C 290 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.7308 (ttm-80) REVERT: C 325 GLU cc_start: 0.6511 (mt-10) cc_final: 0.6152 (mt-10) REVERT: D 98 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8166 (ttmm) REVERT: E 80 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8344 (mtpp) REVERT: E 202 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7859 (mtp180) REVERT: E 380 MET cc_start: 0.6745 (tmm) cc_final: 0.6480 (tmm) REVERT: F 27 LYS cc_start: 0.6758 (tptp) cc_final: 0.6510 (mmmt) REVERT: F 98 LYS cc_start: 0.8278 (tttt) cc_final: 0.7997 (ttmm) REVERT: F 101 SER cc_start: 0.9075 (t) cc_final: 0.8554 (m) REVERT: G 194 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6907 (ttp80) REVERT: G 298 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7983 (ttpt) REVERT: H 16 GLN cc_start: 0.8676 (tt0) cc_final: 0.8399 (tt0) REVERT: H 27 LYS cc_start: 0.6657 (tptp) cc_final: 0.6405 (mmmt) REVERT: H 98 LYS cc_start: 0.8245 (ttpp) cc_final: 0.7976 (ttmm) REVERT: I 66 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: I 78 MET cc_start: 0.8581 (mmt) cc_final: 0.8335 (mmt) REVERT: I 79 SER cc_start: 0.8002 (t) cc_final: 0.7775 (m) REVERT: I 80 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8188 (mtpp) REVERT: I 181 GLU cc_start: 0.7547 (tt0) cc_final: 0.7102 (tt0) REVERT: I 380 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6288 (tmm) REVERT: J 27 LYS cc_start: 0.6698 (tptp) cc_final: 0.6388 (mmmt) REVERT: J 90 TYR cc_start: 0.8465 (t80) cc_final: 0.8199 (t80) REVERT: J 98 LYS cc_start: 0.8349 (ttpp) cc_final: 0.8085 (ttmm) REVERT: K 56 ASN cc_start: 0.8360 (t0) cc_final: 0.7945 (t0) REVERT: K 62 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7640 (mt-10) REVERT: K 66 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: K 111 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6856 (mm-30) REVERT: K 149 MET cc_start: 0.7384 (mmm) cc_final: 0.7065 (mmm) REVERT: K 181 GLU cc_start: 0.7562 (tt0) cc_final: 0.7226 (tt0) REVERT: K 362 ARG cc_start: 0.5776 (ttt180) cc_final: 0.5290 (ttt180) REVERT: K 380 MET cc_start: 0.6959 (ttp) cc_final: 0.6488 (tmm) REVERT: L 19 ARG cc_start: 0.8044 (ptp90) cc_final: 0.7504 (ptp90) REVERT: L 27 LYS cc_start: 0.6668 (tptp) cc_final: 0.6305 (mmmt) REVERT: M 148 TRP cc_start: 0.7581 (m100) cc_final: 0.7368 (m-90) REVERT: M 181 GLU cc_start: 0.7533 (tt0) cc_final: 0.7299 (tt0) REVERT: N 15 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8073 (tm-30) REVERT: N 98 LYS cc_start: 0.8327 (tttp) cc_final: 0.8090 (ttmm) REVERT: O 56 ASN cc_start: 0.8516 (t0) cc_final: 0.8260 (t0) REVERT: O 380 MET cc_start: 0.7124 (ttp) cc_final: 0.6778 (tmm) REVERT: P 90 TYR cc_start: 0.8488 (t80) cc_final: 0.8239 (t80) REVERT: Q 56 ASN cc_start: 0.8380 (t0) cc_final: 0.7945 (t0) REVERT: Q 362 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.5367 (ttt180) REVERT: R 90 TYR cc_start: 0.8521 (t80) cc_final: 0.8291 (t80) REVERT: S 371 LEU cc_start: 0.7950 (mm) cc_final: 0.7733 (mm) REVERT: T 110 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7811 (mp) REVERT: U 54 GLN cc_start: 0.8193 (mt0) cc_final: 0.7929 (mt0) REVERT: U 66 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: U 77 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7626 (mm-30) REVERT: U 99 SER cc_start: 0.7480 (p) cc_final: 0.6856 (t) REVERT: U 331 LEU cc_start: 0.8609 (tp) cc_final: 0.8400 (tp) REVERT: W 56 ASN cc_start: 0.8483 (t0) cc_final: 0.8160 (t0) REVERT: W 66 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: W 290 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.7211 (ttm-80) REVERT: W 298 LYS cc_start: 0.7983 (mmtp) cc_final: 0.7538 (mttt) outliers start: 159 outliers final: 134 residues processed: 1094 average time/residue: 0.5497 time to fit residues: 956.3768 Evaluate side-chains 1114 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 970 time to evaluate : 4.248 ------------------------------------------------------------------------------- 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 79 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 25 VAL 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 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 18 ARG Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 235 ARG Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 34 THR 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 F residue 127 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 194 ARG Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 25 VAL 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 114 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 232 LEU 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 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 J residue 127 ILE Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 LEU 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 111 GLU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 275 GLN Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 65 THR 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 183 LEU Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain Q residue 362 ARG Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 333 SER 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 66 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 173 LEU Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain U residue 253 ARG 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 17 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 114 LEU Chi-restraints excluded: chain W residue 221 SER Chi-restraints excluded: chain W residue 253 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 375 optimal weight: 2.9990 chunk 604 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 419 optimal weight: 1.9990 chunk 633 optimal weight: 2.9990 chunk 583 optimal weight: 4.9990 chunk 504 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 389 optimal weight: 0.1980 chunk 309 optimal weight: 0.5980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 ASN ** 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 U 10 ASN V 126 GLN W 10 ASN X 12 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.7544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 51576 Z= 0.297 Angle : 0.715 35.958 70128 Z= 0.357 Chirality : 0.043 0.332 7800 Planarity : 0.009 0.376 9252 Dihedral : 6.832 170.826 7080 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.99 % Favored : 94.81 % Rotamer: Outliers : 3.00 % Allowed : 16.72 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.32 (0.11), residues: 6456 helix: 2.41 (0.09), residues: 3156 sheet: 0.13 (0.23), residues: 564 loop : -0.84 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP V 138 HIS 0.008 0.001 HIS C 155 PHE 0.068 0.004 PHE U 274 TYR 0.015 0.001 TYR D 90 ARG 0.041 0.001 ARG U 196 ********************** 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 1125 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 968 time to evaluate : 4.526 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: A 66 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: A 238 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8440 (mttt) REVERT: A 275 GLN cc_start: 0.6787 (mm-40) cc_final: 0.6495 (mm-40) REVERT: A 290 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7344 (mtm-85) REVERT: B 15 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8347 (tm-30) REVERT: B 27 LYS cc_start: 0.6568 (tptt) cc_final: 0.6273 (tptp) REVERT: B 101 SER cc_start: 0.8976 (t) cc_final: 0.8579 (m) REVERT: C 77 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7776 (mm-30) REVERT: C 290 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.7342 (ttm-80) REVERT: C 325 GLU cc_start: 0.6411 (mt-10) cc_final: 0.6052 (mt-10) REVERT: D 98 LYS cc_start: 0.8399 (ttpp) cc_final: 0.8175 (ttmm) REVERT: D 101 SER cc_start: 0.8931 (t) cc_final: 0.8557 (m) REVERT: E 80 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8367 (mtpp) REVERT: E 117 GLU cc_start: 0.6080 (tt0) cc_final: 0.5815 (mt-10) REVERT: E 202 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7816 (mtp180) REVERT: E 380 MET cc_start: 0.6880 (tmm) cc_final: 0.6609 (tmm) REVERT: F 27 LYS cc_start: 0.6832 (tptp) cc_final: 0.6593 (mmmt) REVERT: F 98 LYS cc_start: 0.8283 (tttt) cc_final: 0.7980 (ttmm) REVERT: F 101 SER cc_start: 0.9099 (t) cc_final: 0.8595 (m) REVERT: G 194 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6982 (ttp80) REVERT: G 298 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8094 (ttpt) REVERT: H 27 LYS cc_start: 0.6676 (tptp) cc_final: 0.6394 (mmmt) REVERT: H 98 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7978 (ttmm) REVERT: I 66 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: I 78 MET cc_start: 0.8616 (mmt) cc_final: 0.8164 (mmt) REVERT: I 79 SER cc_start: 0.8115 (t) cc_final: 0.7874 (m) REVERT: I 80 LYS cc_start: 0.8472 (ttmt) cc_final: 0.8177 (mtpp) REVERT: I 181 GLU cc_start: 0.7593 (tt0) cc_final: 0.7101 (tt0) REVERT: I 380 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.6332 (tmm) REVERT: J 27 LYS cc_start: 0.6801 (tptp) cc_final: 0.6438 (mmmt) REVERT: J 90 TYR cc_start: 0.8569 (t80) cc_final: 0.8235 (t80) REVERT: J 98 LYS cc_start: 0.8387 (ttpp) cc_final: 0.8104 (ttmm) REVERT: K 56 ASN cc_start: 0.8409 (t0) cc_final: 0.8019 (t0) REVERT: K 62 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7711 (mt-10) REVERT: K 66 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7768 (m-30) REVERT: K 111 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6900 (mm-30) REVERT: K 149 MET cc_start: 0.7401 (mmm) cc_final: 0.7096 (mmm) REVERT: K 181 GLU cc_start: 0.7588 (tt0) cc_final: 0.7311 (tt0) REVERT: K 362 ARG cc_start: 0.5768 (ttt180) cc_final: 0.5277 (ttt180) REVERT: K 380 MET cc_start: 0.7049 (ttp) cc_final: 0.6593 (tmm) REVERT: K 390 VAL cc_start: 0.6798 (t) cc_final: 0.6582 (t) REVERT: L 19 ARG cc_start: 0.8018 (ptp90) cc_final: 0.7489 (ptp90) REVERT: L 27 LYS cc_start: 0.6703 (tptp) cc_final: 0.6296 (mmmt) REVERT: L 98 LYS cc_start: 0.8414 (tttt) cc_final: 0.8085 (ttmm) REVERT: M 148 TRP cc_start: 0.7655 (m100) cc_final: 0.7428 (m-90) REVERT: N 15 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8150 (tm-30) REVERT: N 98 LYS cc_start: 0.8337 (tttp) cc_final: 0.8108 (ttmm) REVERT: O 56 ASN cc_start: 0.8576 (t0) cc_final: 0.8327 (t0) REVERT: O 380 MET cc_start: 0.7099 (ttp) cc_final: 0.6751 (tmm) REVERT: P 90 TYR cc_start: 0.8507 (t80) cc_final: 0.8265 (t80) REVERT: Q 56 ASN cc_start: 0.8457 (t0) cc_final: 0.8050 (t0) REVERT: Q 362 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.5346 (ttt180) REVERT: R 90 TYR cc_start: 0.8548 (t80) cc_final: 0.8328 (t80) REVERT: T 110 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7815 (mp) REVERT: U 54 GLN cc_start: 0.8227 (mt0) cc_final: 0.7968 (mt0) REVERT: U 66 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: U 77 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7120 (mm-30) REVERT: U 99 SER cc_start: 0.7416 (p) cc_final: 0.6889 (m) REVERT: U 331 LEU cc_start: 0.8638 (tp) cc_final: 0.8436 (tp) REVERT: U 366 ARG cc_start: 0.6828 (mtm110) cc_final: 0.6605 (mtm-85) REVERT: U 382 GLN cc_start: 0.5731 (mp10) cc_final: 0.5460 (mp10) REVERT: W 56 ASN cc_start: 0.8506 (t0) cc_final: 0.8180 (t0) REVERT: W 290 ARG cc_start: 0.7444 (ttm-80) cc_final: 0.7232 (ttm-80) REVERT: X 15 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8308 (tm-30) outliers start: 157 outliers final: 136 residues processed: 1067 average time/residue: 0.5457 time to fit residues: 924.6792 Evaluate side-chains 1095 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 949 time to evaluate : 4.247 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 25 VAL 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 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 18 ARG Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 235 ARG Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain F residue 25 VAL 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 F residue 127 ILE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 194 ARG Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 25 VAL 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 114 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 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 J residue 127 ILE Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 LEU 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 24 ARG Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 269 THR Chi-restraints excluded: chain M residue 275 GLN Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 361 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 114 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 333 SER Chi-restraints excluded: chain Q residue 362 ARG Chi-restraints excluded: chain Q residue 384 ILE Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain S residue 253 ARG 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 66 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 173 LEU Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain U residue 253 ARG Chi-restraints excluded: chain U residue 275 GLN 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 114 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 400 optimal weight: 0.8980 chunk 537 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 465 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 505 optimal weight: 0.9990 chunk 211 optimal weight: 0.0470 chunk 518 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN ** Q 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 337 GLN R 12 GLN S 10 ASN T 12 GLN U 10 ASN X 12 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.150773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.119151 restraints weight = 63909.361| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.90 r_work: 0.3143 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.7648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 51576 Z= 0.226 Angle : 0.667 29.220 70128 Z= 0.334 Chirality : 0.041 0.291 7800 Planarity : 0.009 0.345 9252 Dihedral : 6.974 174.527 7080 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.05 % Favored : 94.76 % Rotamer: Outliers : 2.92 % Allowed : 17.26 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 1.42 (0.11), residues: 6456 helix: 2.53 (0.09), residues: 3144 sheet: 0.02 (0.23), residues: 564 loop : -0.80 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 138 HIS 0.007 0.001 HIS C 155 PHE 0.079 0.003 PHE S 75 TYR 0.018 0.001 TYR Q 199 ARG 0.036 0.001 ARG U 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14940.85 seconds wall clock time: 259 minutes 12.35 seconds (15552.35 seconds total)