Starting phenix.real_space_refine on Wed Jan 15 00:59:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rkb_19267/01_2025/8rkb_19267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rkb_19267/01_2025/8rkb_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_19267/01_2025/8rkb_19267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rkb_19267/01_2025/8rkb_19267.map" model { file = "/net/cci-nas-00/data/ceres_data/8rkb_19267/01_2025/8rkb_19267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rkb_19267/01_2025/8rkb_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-5571/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: 9.88, 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: 10.92 Conformation dependent library (CDL) restraints added in 5.1 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: 3.75 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: 18.18 Time building geometry restraints manager: 12.70 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: 0.45 Found NCS groups: 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' } 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' } 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: 6.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 1.890 Check model and map are aligned: 0.320 Set scattering table: 0.420 Process input model: 78.140 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.440 ------------------------------------------------------------------------------- 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 : 4.120 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: 0.5792 time to fit residues: 1280.5142 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 : 4.125 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.156848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125221 restraints weight = 64590.670| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.86 r_work: 0.3258 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 4.239 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: 0.7840 (mm-30) cc_final: 0.7137 (mm-30) REVERT: A 166 GLU cc_start: 0.7665 (mp0) cc_final: 0.7276 (mp0) REVERT: A 170 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6500 (tm-30) REVERT: A 229 ILE cc_start: 0.7749 (tt) cc_final: 0.7502 (tt) REVERT: A 380 MET cc_start: 0.5626 (tmm) cc_final: 0.5274 (tmm) REVERT: B 113 ASP cc_start: 0.7852 (p0) cc_final: 0.7552 (p0) REVERT: C 86 LEU cc_start: 0.8466 (mt) cc_final: 0.8228 (mp) REVERT: C 111 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7622 (mm-30) REVERT: C 125 ASP cc_start: 0.7878 (m-30) cc_final: 0.7664 (m-30) REVERT: C 166 GLU cc_start: 0.7435 (mp0) cc_final: 0.6876 (mp0) REVERT: C 229 ILE cc_start: 0.7687 (tt) cc_final: 0.7480 (tt) REVERT: C 380 MET cc_start: 0.6677 (tmm) cc_final: 0.6281 (tmm) REVERT: E 51 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7067 (mt-10) REVERT: E 154 HIS cc_start: 0.8091 (m-70) cc_final: 0.7879 (m-70) REVERT: E 181 GLU cc_start: 0.7392 (tt0) cc_final: 0.7103 (tt0) REVERT: E 202 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8294 (mtt180) REVERT: F 34 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7871 (p) REVERT: F 107 LYS cc_start: 0.8485 (mttt) cc_final: 0.8278 (mttm) REVERT: G 140 GLU cc_start: 0.6193 (mm-30) cc_final: 0.5929 (mm-30) REVERT: I 78 MET cc_start: 0.8338 (mmm) cc_final: 0.7853 (mmt) REVERT: I 140 GLU cc_start: 0.6663 (mm-30) cc_final: 0.6444 (mm-30) REVERT: I 181 GLU cc_start: 0.7311 (tt0) cc_final: 0.7028 (tp30) REVERT: J 49 ASP cc_start: 0.7989 (m-30) cc_final: 0.7721 (m-30) REVERT: K 47 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7895 (mtm-85) REVERT: K 65 MET cc_start: 0.8155 (mpp) cc_final: 0.7896 (mtt) REVERT: K 149 MET cc_start: 0.7195 (mmm) cc_final: 0.6901 (mmm) REVERT: K 176 ASN cc_start: 0.8331 (m110) cc_final: 0.8129 (m-40) REVERT: L 19 ARG cc_start: 0.7707 (ptp90) cc_final: 0.7339 (ptp90) REVERT: L 107 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8219 (mttm) REVERT: M 148 TRP cc_start: 0.7233 (m100) cc_final: 0.6825 (m-90) REVERT: M 176 ASN cc_start: 0.8139 (m110) cc_final: 0.7838 (m-40) REVERT: M 380 MET cc_start: 0.7067 (ttp) cc_final: 0.6836 (tmm) REVERT: N 84 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8145 (mtpt) REVERT: O 19 GLU cc_start: 0.7443 (pm20) cc_final: 0.6957 (pm20) REVERT: O 24 ARG cc_start: 0.7270 (ptp90) cc_final: 0.6994 (ptp90) REVERT: O 69 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7868 (mt-10) REVERT: O 117 GLU cc_start: 0.7417 (pm20) cc_final: 0.7179 (pm20) REVERT: O 380 MET cc_start: 0.7224 (ttp) cc_final: 0.7006 (tmm) REVERT: P 84 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8092 (mtmm) REVERT: P 101 SER cc_start: 0.8969 (t) cc_final: 0.8734 (m) REVERT: Q 15 GLN cc_start: 0.6782 (tm-30) cc_final: 0.6464 (tm-30) REVERT: Q 113 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6513 (mt) REVERT: Q 140 GLU cc_start: 0.7787 (tp30) cc_final: 0.7539 (tp30) REVERT: R 90 TYR cc_start: 0.8984 (t80) cc_final: 0.8692 (t80) REVERT: R 112 LEU cc_start: 0.8006 (mt) cc_final: 0.7610 (mp) REVERT: S 166 GLU cc_start: 0.7799 (mp0) cc_final: 0.7384 (mp0) REVERT: S 181 GLU cc_start: 0.7698 (tt0) cc_final: 0.7471 (tt0) REVERT: U 38 LYS cc_start: 0.7545 (mmtt) cc_final: 0.7290 (tppt) REVERT: U 78 MET cc_start: 0.8801 (mmm) cc_final: 0.8347 (mmt) REVERT: W 111 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7369 (mm-30) REVERT: W 166 GLU cc_start: 0.7723 (mp0) cc_final: 0.7411 (mp0) REVERT: W 218 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.7971 (t80) REVERT: W 289 MET cc_start: 0.8113 (mtp) cc_final: 0.7878 (mtt) REVERT: W 368 VAL cc_start: 0.8247 (t) cc_final: 0.7951 (m) outliers start: 118 outliers final: 66 residues processed: 1192 average time/residue: 0.5441 time to fit residues: 1033.6608 Evaluate side-chains 1026 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 956 time to evaluate : 4.225 ------------------------------------------------------------------------------- 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 427 optimal weight: 0.9980 chunk 342 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 463 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 590 optimal weight: 0.3980 chunk 566 optimal weight: 1.9990 chunk 445 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 374 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** U 10 ASN U 56 ASN U 60 GLN W 60 GLN X 126 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.156621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125322 restraints weight = 64643.490| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.80 r_work: 0.3266 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 51576 Z= 0.222 Angle : 0.605 11.547 70128 Z= 0.304 Chirality : 0.041 0.305 7800 Planarity : 0.005 0.049 9252 Dihedral : 5.022 175.352 7080 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.35 % Favored : 95.35 % Rotamer: Outliers : 1.97 % Allowed : 12.14 % Favored : 85.89 % 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: 1.54 (0.11), residues: 6456 helix: 2.37 (0.09), residues: 3156 sheet: 0.62 (0.21), residues: 612 loop : -0.54 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 138 HIS 0.009 0.001 HIS C 155 PHE 0.043 0.003 PHE W 75 TYR 0.026 0.001 TYR H 90 ARG 0.016 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 1119 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1016 time to evaluate : 5.486 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: 0.7933 (mm-30) cc_final: 0.7237 (mm-30) REVERT: B 15 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8607 (tm-30) REVERT: C 66 ASP cc_start: 0.8370 (t0) cc_final: 0.8167 (t70) REVERT: C 120 GLU cc_start: 0.6942 (tp30) cc_final: 0.6661 (tp30) REVERT: C 125 ASP cc_start: 0.8071 (m-30) cc_final: 0.7759 (m-30) REVERT: C 380 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6282 (tmm) REVERT: E 181 GLU cc_start: 0.7533 (tt0) cc_final: 0.7127 (tp30) REVERT: I 78 MET cc_start: 0.8488 (mmm) cc_final: 0.8233 (mmt) REVERT: I 140 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6511 (mm-30) REVERT: I 181 GLU cc_start: 0.7515 (tt0) cc_final: 0.7147 (tp30) REVERT: K 140 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6606 (mt-10) REVERT: L 19 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7127 (ptt90) REVERT: M 102 GLU cc_start: 0.6314 (mt-10) cc_final: 0.6067 (mt-10) REVERT: M 148 TRP cc_start: 0.7240 (m100) cc_final: 0.6893 (m-90) REVERT: M 176 ASN cc_start: 0.8193 (m110) cc_final: 0.7858 (m-40) REVERT: M 380 MET cc_start: 0.7250 (ttp) cc_final: 0.7007 (tmm) REVERT: O 291 GLN cc_start: 0.8305 (tp40) cc_final: 0.7882 (tp40) REVERT: P 84 LYS cc_start: 0.8433 (mtpt) cc_final: 0.8000 (mtmm) REVERT: P 101 SER cc_start: 0.8915 (t) cc_final: 0.8693 (m) REVERT: Q 113 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6520 (mt) REVERT: Q 362 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.6045 (ttt-90) REVERT: R 90 TYR cc_start: 0.8932 (t80) cc_final: 0.8636 (t80) REVERT: R 112 LEU cc_start: 0.8087 (mt) cc_final: 0.7810 (mp) REVERT: S 181 GLU cc_start: 0.7762 (tt0) cc_final: 0.7338 (tt0) REVERT: S 366 ARG cc_start: 0.7278 (mtm-85) cc_final: 0.6999 (mtm-85) REVERT: U 65 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7939 (mtt) REVERT: U 66 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: U 78 MET cc_start: 0.8874 (mmm) cc_final: 0.8380 (mmt) REVERT: U 166 GLU cc_start: 0.7700 (mp0) cc_final: 0.7370 (mp0) REVERT: U 169 ASN cc_start: 0.8615 (t0) cc_final: 0.8382 (t0) REVERT: U 298 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8033 (mtpp) REVERT: U 366 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6942 (mtm-85) REVERT: V 28 PRO cc_start: 0.8256 (Cg_endo) cc_final: 0.7949 (Cg_exo) REVERT: W 60 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: W 111 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7421 (mm-30) REVERT: W 166 GLU cc_start: 0.7704 (mp0) cc_final: 0.7374 (mp0) REVERT: W 218 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.7724 (t80) REVERT: W 289 MET cc_start: 0.8264 (mtp) cc_final: 0.7991 (mtt) REVERT: X 15 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8759 (tm-30) outliers start: 103 outliers final: 57 residues processed: 1073 average time/residue: 0.5363 time to fit residues: 923.8428 Evaluate side-chains 1001 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 936 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain G residue 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 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 O residue 352 VAL Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 113 LEU 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 T residue 112 LEU Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 65 MET Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain U residue 67 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 555 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 168 optimal weight: 0.0270 chunk 489 optimal weight: 1.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- 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** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN I 217 HIS K 184 GLN K 276 GLN N 53 HIS ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN Q 328 HIS R 12 GLN S 10 ASN S 54 GLN T 12 GLN U 10 ASN W 60 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.152310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119805 restraints weight = 64351.224| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.87 r_work: 0.3181 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 51576 Z= 0.263 Angle : 0.628 14.362 70128 Z= 0.317 Chirality : 0.042 0.261 7800 Planarity : 0.005 0.047 9252 Dihedral : 4.678 29.393 7080 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.11 % Favored : 94.69 % Rotamer: Outliers : 2.83 % Allowed : 12.98 % Favored : 84.19 % 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: 1.49 (0.11), residues: 6456 helix: 2.36 (0.09), residues: 3156 sheet: 0.48 (0.21), residues: 636 loop : -0.59 (0.13), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 138 HIS 0.010 0.001 HIS C 155 PHE 0.040 0.003 PHE G 274 TYR 0.021 0.001 TYR N 90 ARG 0.014 0.001 ARG I 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 1179 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1031 time to evaluate : 4.318 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: A 78 MET cc_start: 0.9070 (mmm) cc_final: 0.8740 (mmt) REVERT: A 166 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7396 (mm-30) REVERT: A 366 ARG cc_start: 0.7084 (ptp90) cc_final: 0.6849 (mtm-85) REVERT: B 15 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8676 (tm-30) REVERT: C 77 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8201 (mm-30) REVERT: C 194 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7236 (mtm110) REVERT: C 279 GLN cc_start: 0.7056 (mt0) cc_final: 0.6736 (mt0) REVERT: C 366 ARG cc_start: 0.7396 (mtm110) cc_final: 0.7113 (mtm-85) REVERT: C 380 MET cc_start: 0.6824 (tmm) cc_final: 0.6291 (tmm) REVERT: E 18 ARG cc_start: 0.7151 (tpp-160) cc_final: 0.6348 (tpp-160) REVERT: E 70 ARG cc_start: 0.7713 (mtm180) cc_final: 0.7470 (mtm180) REVERT: E 218 TYR cc_start: 0.8908 (m-80) cc_final: 0.8701 (m-80) REVERT: E 253 ARG cc_start: 0.8280 (ptp-110) cc_final: 0.8077 (ptp90) REVERT: G 18 ARG cc_start: 0.6943 (tpp-160) cc_final: 0.6251 (tpp-160) REVERT: G 65 MET cc_start: 0.8286 (mpp) cc_final: 0.7918 (mtt) REVERT: G 170 GLU cc_start: 0.7323 (tt0) cc_final: 0.7023 (tt0) REVERT: I 56 ASN cc_start: 0.8433 (t0) cc_final: 0.8215 (t0) REVERT: I 66 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: I 78 MET cc_start: 0.8841 (mmm) cc_final: 0.8587 (mmt) REVERT: I 276 GLN cc_start: 0.7372 (mp10) cc_final: 0.6983 (mp10) REVERT: K 56 ASN cc_start: 0.8319 (t0) cc_final: 0.7992 (t0) REVERT: K 66 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: K 111 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6806 (mm-30) REVERT: K 140 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6955 (mt-10) REVERT: L 19 ARG cc_start: 0.8038 (ptp90) cc_final: 0.7585 (ptp90) REVERT: M 79 SER cc_start: 0.8407 (t) cc_final: 0.8061 (m) REVERT: M 102 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6205 (mt-10) REVERT: M 148 TRP cc_start: 0.7342 (m100) cc_final: 0.6970 (m-90) REVERT: M 380 MET cc_start: 0.7234 (ttp) cc_final: 0.6999 (tmm) REVERT: M 403 LEU cc_start: 0.6902 (mm) cc_final: 0.6701 (mt) REVERT: N 27 LYS cc_start: 0.6951 (tptp) cc_final: 0.6528 (mmmt) REVERT: O 291 GLN cc_start: 0.8326 (tp40) cc_final: 0.7942 (tp40) REVERT: P 90 TYR cc_start: 0.8923 (t80) cc_final: 0.8698 (t80) REVERT: P 101 SER cc_start: 0.9122 (t) cc_final: 0.8840 (m) REVERT: Q 105 ASP cc_start: 0.7443 (m-30) cc_final: 0.6943 (m-30) REVERT: Q 117 GLU cc_start: 0.6931 (pm20) cc_final: 0.6579 (pm20) REVERT: Q 238 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8568 (mtpp) REVERT: Q 362 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.5797 (ttt180) REVERT: R 90 TYR cc_start: 0.8990 (t80) cc_final: 0.8743 (t80) REVERT: T 110 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7879 (mp) REVERT: U 66 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: U 77 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7641 (mm-30) REVERT: U 78 MET cc_start: 0.8936 (mmm) cc_final: 0.8256 (mmt) REVERT: U 166 GLU cc_start: 0.7738 (mp0) cc_final: 0.7311 (mp0) REVERT: U 298 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8141 (mtpp) REVERT: U 330 LEU cc_start: 0.8086 (tp) cc_final: 0.7851 (tp) REVERT: W 66 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: W 111 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7421 (mm-30) REVERT: X 15 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8811 (tm-30) outliers start: 148 outliers final: 89 residues processed: 1114 average time/residue: 0.5410 time to fit residues: 962.9705 Evaluate side-chains 1054 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 958 time to evaluate : 4.269 ------------------------------------------------------------------------------- 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 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 7 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 79 SER 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 113 ASP Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain G residue 7 VAL 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 248 LYS Chi-restraints excluded: chain G residue 268 GLU Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain I residue 66 ASP Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 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 J residue 112 LEU Chi-restraints excluded: chain K residue 66 ASP 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 89 ASP Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 113 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 112 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 67 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 112 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 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 17 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 229 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 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 W residue 380 MET Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 471 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 523 optimal weight: 0.7980 chunk 532 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 365 optimal weight: 2.9990 chunk 441 optimal weight: 0.2980 chunk 467 optimal weight: 4.9990 chunk 331 optimal weight: 0.7980 chunk 572 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 ASN I 184 GLN K 184 GLN M 54 GLN M 176 ASN M 184 GLN ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN 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 144 GLN X 12 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.152839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120871 restraints weight = 64242.966| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.81 r_work: 0.3207 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 51576 Z= 0.221 Angle : 0.597 11.007 70128 Z= 0.301 Chirality : 0.041 0.213 7800 Planarity : 0.005 0.071 9252 Dihedral : 4.603 29.798 7080 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.74 % Favored : 95.06 % Rotamer: Outliers : 2.58 % Allowed : 14.83 % Favored : 82.59 % 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: 1.67 (0.11), residues: 6456 helix: 2.46 (0.09), residues: 3156 sheet: 1.43 (0.22), residues: 516 loop : -0.59 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 138 HIS 0.008 0.001 HIS C 155 PHE 0.035 0.003 PHE S 274 TYR 0.027 0.001 TYR J 90 ARG 0.022 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 1160 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 1025 time to evaluate : 4.300 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 78 MET cc_start: 0.9089 (mmm) cc_final: 0.8726 (mmt) REVERT: A 290 ARG cc_start: 0.8486 (ttm-80) cc_final: 0.8219 (mtm-85) REVERT: A 366 ARG cc_start: 0.7140 (ptp90) cc_final: 0.6886 (mtm-85) REVERT: B 15 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8604 (tm-30) REVERT: B 27 LYS cc_start: 0.6770 (tptt) cc_final: 0.6519 (tptp) REVERT: B 101 SER cc_start: 0.9101 (t) cc_final: 0.8743 (m) REVERT: C 77 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8145 (mm-30) REVERT: C 117 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: C 290 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.8050 (mtm-85) REVERT: C 325 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6575 (mt-10) REVERT: C 380 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6326 (tmm) REVERT: D 27 LYS cc_start: 0.6725 (tptt) cc_final: 0.6524 (tptp) REVERT: E 18 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.6496 (tpp-160) REVERT: E 117 GLU cc_start: 0.6536 (tt0) cc_final: 0.6142 (mt-10) REVERT: E 238 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8528 (mtpp) REVERT: F 27 LYS cc_start: 0.6902 (tptp) cc_final: 0.6692 (tptp) REVERT: G 18 ARG cc_start: 0.7000 (tpp-160) cc_final: 0.6307 (tpp-160) REVERT: G 65 MET cc_start: 0.8312 (mpp) cc_final: 0.8044 (mtt) REVERT: G 170 GLU cc_start: 0.7430 (tt0) cc_final: 0.7119 (tt0) REVERT: I 19 GLU cc_start: 0.7258 (pm20) cc_final: 0.7046 (pm20) REVERT: I 56 ASN cc_start: 0.8510 (t0) cc_final: 0.8287 (t0) REVERT: I 66 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: I 75 PHE cc_start: 0.8034 (t80) cc_final: 0.7753 (t80) REVERT: I 78 MET cc_start: 0.8914 (mmm) cc_final: 0.8648 (mmt) REVERT: I 102 GLU cc_start: 0.6261 (mt-10) cc_final: 0.5883 (mm-30) REVERT: I 380 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.6001 (tmm) REVERT: K 51 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7351 (mm-30) REVERT: K 56 ASN cc_start: 0.8393 (t0) cc_final: 0.7953 (t0) REVERT: K 62 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8184 (mt-10) REVERT: K 66 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8163 (m-30) REVERT: K 78 MET cc_start: 0.8819 (mmt) cc_final: 0.8515 (mmt) REVERT: K 79 SER cc_start: 0.8443 (t) cc_final: 0.8041 (m) REVERT: K 105 ASP cc_start: 0.6538 (m-30) cc_final: 0.6306 (m-30) REVERT: K 140 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6984 (mt-10) REVERT: K 149 MET cc_start: 0.7757 (mmm) cc_final: 0.7411 (mmm) REVERT: K 362 ARG cc_start: 0.6048 (ttt180) cc_final: 0.5622 (ttt180) REVERT: K 366 ARG cc_start: 0.7387 (mtm110) cc_final: 0.7184 (mtm-85) REVERT: L 19 ARG cc_start: 0.8034 (ptp90) cc_final: 0.7595 (ptp90) REVERT: M 51 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7488 (mm-30) REVERT: M 75 PHE cc_start: 0.8282 (t80) cc_final: 0.8028 (t80) REVERT: M 291 GLN cc_start: 0.8340 (tp40) cc_final: 0.8053 (tp40) REVERT: M 380 MET cc_start: 0.7216 (ttp) cc_final: 0.6960 (tmm) REVERT: M 403 LEU cc_start: 0.6926 (mm) cc_final: 0.6709 (mt) REVERT: N 27 LYS cc_start: 0.6902 (tptp) cc_final: 0.6501 (mmmt) REVERT: N 98 LYS cc_start: 0.8741 (tttp) cc_final: 0.8494 (ttmm) REVERT: N 110 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7865 (mp) REVERT: O 66 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: O 181 GLU cc_start: 0.8108 (tt0) cc_final: 0.7838 (tt0) REVERT: O 291 GLN cc_start: 0.8304 (tp40) cc_final: 0.8001 (tp40) REVERT: Q 56 ASN cc_start: 0.8538 (t0) cc_final: 0.8144 (t0) REVERT: Q 79 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8511 (m) REVERT: Q 105 ASP cc_start: 0.7409 (m-30) cc_final: 0.6900 (m-30) REVERT: Q 117 GLU cc_start: 0.6917 (pm20) cc_final: 0.6657 (pm20) REVERT: Q 140 GLU cc_start: 0.7767 (tp30) cc_final: 0.7424 (mt-10) REVERT: Q 181 GLU cc_start: 0.7998 (tt0) cc_final: 0.7775 (tt0) REVERT: Q 362 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.5666 (ttt180) REVERT: R 90 TYR cc_start: 0.8951 (t80) cc_final: 0.8735 (t80) REVERT: R 112 LEU cc_start: 0.8349 (mt) cc_final: 0.8024 (mp) REVERT: T 12 GLN cc_start: 0.8325 (tt0) cc_final: 0.8073 (tt0) REVERT: T 107 LYS cc_start: 0.9043 (mttp) cc_final: 0.8827 (mttt) REVERT: T 110 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7889 (mp) REVERT: U 56 ASN cc_start: 0.8766 (t0) cc_final: 0.8561 (t0) REVERT: U 66 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: U 78 MET cc_start: 0.9025 (mmm) cc_final: 0.8400 (mmt) REVERT: U 166 GLU cc_start: 0.7701 (mp0) cc_final: 0.7273 (mp0) REVERT: U 298 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: W 66 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8214 (m-30) REVERT: W 298 LYS cc_start: 0.8405 (mmtp) cc_final: 0.8078 (mmtm) REVERT: X 15 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8802 (tm-30) REVERT: X 27 LYS cc_start: 0.6574 (tptt) cc_final: 0.6314 (mmmt) outliers start: 135 outliers final: 93 residues processed: 1098 average time/residue: 0.5406 time to fit residues: 950.0003 Evaluate side-chains 1085 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 979 time to evaluate : 4.247 ------------------------------------------------------------------------------- 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 234 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 333 SER 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 114 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 333 SER 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 87 ASN Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 268 GLU 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 F residue 67 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 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 67 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 184 GLN Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain I residue 380 MET Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 184 GLN 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 14 THR 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 25 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 114 LEU 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 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 R residue 67 LEU Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 114 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 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 98 LYS Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain 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 66 ASP Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 221 SER Chi-restraints excluded: chain W residue 229 ILE Chi-restraints excluded: chain W residue 253 ARG Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 112 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 223 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 585 optimal weight: 0.0570 chunk 182 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 460 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 329 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 176 ASN I 155 HIS K 184 GLN M 184 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 328 HIS Q 10 ASN ** Q 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 GLN R 12 GLN S 10 ASN S 54 GLN U 10 ASN U 54 GLN V 126 GLN W 168 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117932 restraints weight = 63918.638| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.81 r_work: 0.3108 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.6967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 51576 Z= 0.330 Angle : 0.684 20.595 70128 Z= 0.344 Chirality : 0.043 0.229 7800 Planarity : 0.006 0.164 9252 Dihedral : 5.254 159.358 7080 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.99 % Favored : 94.76 % Rotamer: Outliers : 3.44 % Allowed : 14.97 % Favored : 81.59 % 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: 1.35 (0.11), residues: 6456 helix: 2.29 (0.09), residues: 3156 sheet: 0.46 (0.21), residues: 636 loop : -0.74 (0.13), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 138 HIS 0.009 0.001 HIS C 155 PHE 0.052 0.003 PHE O 274 TYR 0.029 0.002 TYR P 90 ARG 0.024 0.001 ARG A 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 1185 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 1005 time to evaluate : 4.351 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: A 92 VAL cc_start: 0.8491 (t) cc_final: 0.8072 (p) REVERT: A 290 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.8198 (mtm-85) REVERT: B 15 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8668 (tm-30) REVERT: B 27 LYS cc_start: 0.6689 (tptt) cc_final: 0.6451 (tptp) REVERT: B 101 SER cc_start: 0.9183 (t) cc_final: 0.8842 (m) REVERT: C 77 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8463 (mm-30) REVERT: C 176 ASN cc_start: 0.8604 (m110) cc_final: 0.8387 (m110) REVERT: C 290 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8149 (mtm-85) REVERT: C 325 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6487 (mt-10) REVERT: C 366 ARG cc_start: 0.7678 (mtm110) cc_final: 0.7273 (mtm110) REVERT: C 380 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6141 (tmm) REVERT: E 117 GLU cc_start: 0.6597 (tt0) cc_final: 0.6186 (mt-10) REVERT: E 202 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8261 (mtt180) REVERT: E 238 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8758 (mtpt) REVERT: F 101 SER cc_start: 0.9277 (t) cc_final: 0.8889 (m) REVERT: G 18 ARG cc_start: 0.7218 (tpp-160) cc_final: 0.6714 (tpp-160) REVERT: G 170 GLU cc_start: 0.7567 (tt0) cc_final: 0.7235 (tt0) REVERT: G 253 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7983 (ptp-110) REVERT: G 298 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8334 (ttpt) REVERT: H 27 LYS cc_start: 0.6716 (tptp) cc_final: 0.6381 (mmmt) REVERT: I 19 GLU cc_start: 0.7374 (pm20) cc_final: 0.7116 (pm20) REVERT: I 56 ASN cc_start: 0.8703 (t0) cc_final: 0.8459 (t0) REVERT: I 62 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8127 (mt-10) REVERT: I 66 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8101 (m-30) REVERT: I 78 MET cc_start: 0.8976 (mmm) cc_final: 0.8504 (mmt) REVERT: I 181 GLU cc_start: 0.8302 (tt0) cc_final: 0.7901 (tt0) REVERT: I 344 ARG cc_start: 0.8352 (ttm110) cc_final: 0.8032 (mtm-85) REVERT: K 51 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7666 (mm-30) REVERT: K 56 ASN cc_start: 0.8639 (t0) cc_final: 0.8210 (t0) REVERT: K 62 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8289 (mt-10) REVERT: K 66 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: K 111 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7199 (mm-30) REVERT: K 140 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7147 (mt-10) REVERT: K 362 ARG cc_start: 0.6056 (ttt180) cc_final: 0.5658 (ttt180) REVERT: K 366 ARG cc_start: 0.7594 (mtm110) cc_final: 0.7385 (mtm-85) REVERT: L 27 LYS cc_start: 0.6904 (tptp) cc_final: 0.6446 (mmmt) REVERT: L 98 LYS cc_start: 0.8860 (tttt) cc_final: 0.8558 (ttmm) REVERT: M 148 TRP cc_start: 0.7674 (m100) cc_final: 0.7293 (m-90) REVERT: M 291 GLN cc_start: 0.8355 (tp40) cc_final: 0.8089 (tp40) REVERT: M 380 MET cc_start: 0.7151 (ttp) cc_final: 0.6943 (tmm) REVERT: N 98 LYS cc_start: 0.8824 (tttp) cc_final: 0.8590 (ttmm) REVERT: N 110 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7933 (mp) REVERT: O 66 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: O 181 GLU cc_start: 0.8197 (tt0) cc_final: 0.7939 (tt0) REVERT: O 291 GLN cc_start: 0.8361 (tp40) cc_final: 0.8032 (tp40) REVERT: Q 56 ASN cc_start: 0.8650 (t0) cc_final: 0.8314 (t0) REVERT: Q 79 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8523 (m) REVERT: Q 117 GLU cc_start: 0.7087 (pm20) cc_final: 0.6836 (pm20) REVERT: Q 291 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8259 (tp40) REVERT: Q 362 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.5822 (ttt180) REVERT: Q 366 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7442 (mtm-85) REVERT: R 90 TYR cc_start: 0.8992 (t80) cc_final: 0.8781 (t80) REVERT: R 112 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8217 (mp) REVERT: S 15 GLN cc_start: 0.6876 (tm-30) cc_final: 0.6636 (tm-30) REVERT: S 353 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7680 (mt) REVERT: S 366 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7218 (ttm-80) REVERT: T 12 GLN cc_start: 0.8370 (tt0) cc_final: 0.8134 (tt0) REVERT: T 110 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7956 (mp) REVERT: U 56 ASN cc_start: 0.8843 (t0) cc_final: 0.8638 (t0) REVERT: U 66 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: U 77 GLU cc_start: 0.8663 (mm-30) cc_final: 0.7809 (mm-30) REVERT: U 99 SER cc_start: 0.7391 (p) cc_final: 0.6615 (t) REVERT: U 103 LYS cc_start: 0.7666 (mmtp) cc_final: 0.7318 (mmtt) REVERT: U 166 GLU cc_start: 0.7712 (mp0) cc_final: 0.7228 (mp0) REVERT: U 298 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8248 (mtpp) REVERT: W 56 ASN cc_start: 0.8721 (t0) cc_final: 0.8436 (t0) REVERT: W 66 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8319 (m-30) REVERT: W 290 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8066 (ttm-80) REVERT: X 15 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8747 (tm-30) REVERT: X 27 LYS cc_start: 0.6732 (tptt) cc_final: 0.6480 (mmmt) outliers start: 180 outliers final: 132 residues processed: 1122 average time/residue: 0.5559 time to fit residues: 995.4973 Evaluate side-chains 1106 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 957 time to evaluate : 4.302 ------------------------------------------------------------------------------- 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 333 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 65 THR 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 7 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 114 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 333 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 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 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 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 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 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 I residue 14 THR 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 298 LYS Chi-restraints excluded: chain J residue 21 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 112 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain L residue 58 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 114 LEU Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain M residue 352 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain N residue 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 110 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 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 65 THR 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 183 LEU Chi-restraints excluded: chain Q residue 291 GLN 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 R residue 112 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 253 ARG Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 353 LEU Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 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 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 229 ILE Chi-restraints excluded: chain W residue 235 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 34 optimal weight: 1.9990 chunk 352 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 387 optimal weight: 0.5980 chunk 617 optimal weight: 1.9990 chunk 543 optimal weight: 2.9990 chunk 327 optimal weight: 0.0770 chunk 276 optimal weight: 3.9990 chunk 573 optimal weight: 0.8980 chunk 400 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 HIS I 354 ASN ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN ** 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 U 10 ASN U 54 GLN W 10 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.153323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.121130 restraints weight = 63920.393| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.84 r_work: 0.3151 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.7142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 51576 Z= 0.209 Angle : 0.611 16.240 70128 Z= 0.307 Chirality : 0.040 0.241 7800 Planarity : 0.005 0.105 9252 Dihedral : 5.128 166.781 7080 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.72 % Favored : 95.07 % Rotamer: Outliers : 3.04 % Allowed : 16.25 % Favored : 80.71 % 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: 1.51 (0.11), residues: 6456 helix: 2.49 (0.09), residues: 3144 sheet: 0.49 (0.21), residues: 612 loop : -0.72 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 138 HIS 0.007 0.001 HIS C 155 PHE 0.055 0.003 PHE M 274 TYR 0.017 0.001 TYR N 90 ARG 0.015 0.001 ARG W 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 1150 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 991 time to evaluate : 4.367 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: A 92 VAL cc_start: 0.8465 (t) cc_final: 0.8052 (p) REVERT: A 290 ARG cc_start: 0.8495 (ttm-80) cc_final: 0.8173 (mtm-85) REVERT: B 15 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8647 (tm-30) REVERT: B 27 LYS cc_start: 0.6692 (tptt) cc_final: 0.6436 (tptp) REVERT: B 101 SER cc_start: 0.9147 (t) cc_final: 0.8798 (m) REVERT: C 77 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8109 (mm-30) REVERT: C 140 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7057 (pt0) REVERT: C 181 GLU cc_start: 0.8245 (tt0) cc_final: 0.7895 (tt0) REVERT: C 202 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8640 (mtt180) REVERT: C 290 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8154 (mtm-85) REVERT: C 325 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6474 (mt-10) REVERT: C 366 ARG cc_start: 0.7727 (mtm110) cc_final: 0.7329 (mtm110) REVERT: C 380 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6430 (tmm) REVERT: E 77 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8406 (mm-30) REVERT: E 117 GLU cc_start: 0.6570 (tt0) cc_final: 0.6150 (mt-10) REVERT: E 238 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8610 (mmmt) REVERT: E 250 THR cc_start: 0.9429 (m) cc_final: 0.9215 (m) REVERT: E 380 MET cc_start: 0.6668 (tmm) cc_final: 0.6313 (tmm) REVERT: F 27 LYS cc_start: 0.7125 (tptp) cc_final: 0.6773 (mmmt) REVERT: F 101 SER cc_start: 0.9228 (t) cc_final: 0.8857 (m) REVERT: G 18 ARG cc_start: 0.7234 (tpp-160) cc_final: 0.6625 (tpp-160) REVERT: G 170 GLU cc_start: 0.7625 (tt0) cc_final: 0.7307 (tt0) REVERT: G 298 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8254 (ttpt) REVERT: G 366 ARG cc_start: 0.7313 (ttp-110) cc_final: 0.7045 (ttp-110) REVERT: G 380 MET cc_start: 0.6678 (tmm) cc_final: 0.6460 (tmm) REVERT: H 27 LYS cc_start: 0.6773 (tptp) cc_final: 0.6453 (mmmt) REVERT: I 56 ASN cc_start: 0.8591 (t0) cc_final: 0.8350 (t0) REVERT: I 62 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8104 (mt-10) REVERT: I 66 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: I 78 MET cc_start: 0.8997 (mmm) cc_final: 0.8560 (mmt) REVERT: I 181 GLU cc_start: 0.8274 (tt0) cc_final: 0.7863 (tt0) REVERT: I 380 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6232 (tmm) REVERT: J 27 LYS cc_start: 0.6870 (tptp) cc_final: 0.6450 (mmmt) REVERT: K 56 ASN cc_start: 0.8510 (t0) cc_final: 0.8054 (t0) REVERT: K 62 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8284 (mt-10) REVERT: K 66 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: K 149 MET cc_start: 0.7792 (mmm) cc_final: 0.7548 (mmm) REVERT: K 362 ARG cc_start: 0.6098 (ttt180) cc_final: 0.5717 (ttt180) REVERT: L 19 ARG cc_start: 0.8054 (ptp90) cc_final: 0.7672 (ptp90) REVERT: L 27 LYS cc_start: 0.6926 (tptp) cc_final: 0.6494 (mmmt) REVERT: L 98 LYS cc_start: 0.8832 (tttt) cc_final: 0.8539 (ttmm) REVERT: M 19 GLU cc_start: 0.7290 (pm20) cc_final: 0.7081 (pm20) REVERT: M 148 TRP cc_start: 0.7694 (m100) cc_final: 0.7298 (m-90) REVERT: M 291 GLN cc_start: 0.8270 (tp40) cc_final: 0.8035 (tp40) REVERT: N 27 LYS cc_start: 0.6947 (tptp) cc_final: 0.6484 (mmmt) REVERT: N 98 LYS cc_start: 0.8755 (tttp) cc_final: 0.8541 (ttmm) REVERT: N 110 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7791 (mp) REVERT: O 140 GLU cc_start: 0.7455 (tp30) cc_final: 0.7218 (tt0) REVERT: O 181 GLU cc_start: 0.8196 (tt0) cc_final: 0.7940 (tt0) REVERT: O 291 GLN cc_start: 0.8328 (tp40) cc_final: 0.8057 (tp40) REVERT: O 380 MET cc_start: 0.7051 (ttp) cc_final: 0.6785 (tmm) REVERT: Q 56 ASN cc_start: 0.8611 (t0) cc_final: 0.8206 (t0) REVERT: Q 79 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8588 (m) REVERT: Q 117 GLU cc_start: 0.7073 (pm20) cc_final: 0.6803 (pm20) REVERT: Q 140 GLU cc_start: 0.7741 (tp30) cc_final: 0.7403 (tt0) REVERT: Q 291 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8169 (tp40) REVERT: Q 362 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.5726 (ttt180) REVERT: Q 366 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.7452 (mtm-85) REVERT: R 112 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8027 (mp) REVERT: S 15 GLN cc_start: 0.6925 (tm-30) cc_final: 0.6662 (tm-30) REVERT: S 80 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8702 (ttmm) REVERT: S 366 ARG cc_start: 0.7480 (mtm-85) cc_final: 0.7204 (ttm-80) REVERT: T 110 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7902 (mp) REVERT: U 65 MET cc_start: 0.8371 (mtp) cc_final: 0.8085 (mtt) REVERT: U 66 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: U 77 GLU cc_start: 0.8688 (mm-30) cc_final: 0.7758 (mm-30) REVERT: U 78 MET cc_start: 0.8962 (mmt) cc_final: 0.8649 (mmt) REVERT: U 99 SER cc_start: 0.7307 (p) cc_final: 0.6491 (t) REVERT: U 166 GLU cc_start: 0.7742 (mp0) cc_final: 0.7314 (mp0) REVERT: W 18 ARG cc_start: 0.7180 (mmm-85) cc_final: 0.6966 (mpp80) REVERT: W 56 ASN cc_start: 0.8670 (t0) cc_final: 0.8382 (t0) REVERT: W 66 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8267 (m-30) REVERT: W 298 LYS cc_start: 0.8477 (mmtp) cc_final: 0.8166 (mmtm) REVERT: W 366 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7266 (mtm-85) REVERT: X 27 LYS cc_start: 0.6816 (tptt) cc_final: 0.6530 (mmmt) outliers start: 159 outliers final: 123 residues processed: 1085 average time/residue: 0.5576 time to fit residues: 960.9034 Evaluate side-chains 1105 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 968 time to evaluate : 4.263 ------------------------------------------------------------------------------- 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 159 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 A residue 390 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 333 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 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 54 GLN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 235 ARG 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 F residue 112 LEU Chi-restraints excluded: chain G residue 7 VAL 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 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 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 114 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 380 MET Chi-restraints excluded: chain J residue 25 VAL Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 114 LEU 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 24 ARG Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 275 GLN Chi-restraints excluded: chain M residue 298 LYS 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 110 LEU 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 139 LEU 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 291 GLN 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 R residue 112 LEU Chi-restraints excluded: chain S residue 24 ARG 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 384 ILE Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 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 V residue 21 VAL Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 123 ASN 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 229 ILE Chi-restraints excluded: chain W residue 235 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 146 optimal weight: 1.9990 chunk 297 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 355 optimal weight: 0.9980 chunk 456 optimal weight: 0.6980 chunk 601 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 chunk 630 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 600 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN O 54 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN ** Q 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN S 10 ASN S 54 GLN T 12 GLN U 10 ASN W 10 ASN W 54 GLN X 12 GLN X 80 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.153192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.121192 restraints weight = 63614.376| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.81 r_work: 0.3185 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 51576 Z= 0.221 Angle : 0.616 17.312 70128 Z= 0.311 Chirality : 0.040 0.264 7800 Planarity : 0.007 0.332 9252 Dihedral : 6.318 174.686 7080 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.07 % Favored : 94.75 % Rotamer: Outliers : 3.23 % Allowed : 16.48 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.61 (0.11), residues: 6456 helix: 2.48 (0.09), residues: 3156 sheet: 1.37 (0.22), residues: 492 loop : -0.69 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP V 138 HIS 0.007 0.001 HIS C 155 PHE 0.052 0.003 PHE M 274 TYR 0.027 0.001 TYR P 90 ARG 0.014 0.001 ARG W 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 1166 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 997 time to evaluate : 4.415 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 18 ARG cc_start: 0.7123 (mpt-90) cc_final: 0.6787 (mpt-90) REVERT: A 92 VAL cc_start: 0.8492 (t) cc_final: 0.8090 (p) REVERT: A 290 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.8115 (mtm-85) REVERT: A 331 LEU cc_start: 0.8684 (tp) cc_final: 0.8477 (tp) REVERT: B 15 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8618 (tm-30) REVERT: B 27 LYS cc_start: 0.6620 (tptt) cc_final: 0.6294 (tptp) REVERT: B 101 SER cc_start: 0.9160 (t) cc_final: 0.8798 (m) REVERT: C 140 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7097 (pt0) REVERT: C 202 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8602 (mtt180) REVERT: C 290 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8125 (mtm-85) REVERT: C 325 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6411 (mt-10) REVERT: C 366 ARG cc_start: 0.7747 (mtm110) cc_final: 0.7378 (mtm110) REVERT: C 380 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6439 (tmm) REVERT: E 117 GLU cc_start: 0.6553 (tt0) cc_final: 0.6127 (mt-10) REVERT: E 238 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8756 (mtpt) REVERT: E 380 MET cc_start: 0.6713 (tmm) cc_final: 0.6371 (tmm) REVERT: F 27 LYS cc_start: 0.7138 (tptp) cc_final: 0.6807 (mmmt) REVERT: F 101 SER cc_start: 0.9224 (t) cc_final: 0.8868 (m) REVERT: G 18 ARG cc_start: 0.7210 (tpp-160) cc_final: 0.6570 (tpp-160) REVERT: G 170 GLU cc_start: 0.7635 (tt0) cc_final: 0.7314 (tt0) REVERT: G 253 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8089 (ptp90) REVERT: G 298 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8310 (ttpt) REVERT: G 366 ARG cc_start: 0.7327 (ttp-110) cc_final: 0.7072 (ttp-110) REVERT: H 27 LYS cc_start: 0.6825 (tptp) cc_final: 0.6520 (mmmt) REVERT: I 56 ASN cc_start: 0.8608 (t0) cc_final: 0.8384 (t0) REVERT: I 66 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: I 78 MET cc_start: 0.9006 (mmm) cc_final: 0.8594 (mmt) REVERT: I 181 GLU cc_start: 0.8287 (tt0) cc_final: 0.7860 (tt0) REVERT: I 380 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6273 (tmm) REVERT: J 27 LYS cc_start: 0.6912 (tptp) cc_final: 0.6516 (mmmt) REVERT: K 56 ASN cc_start: 0.8523 (t0) cc_final: 0.8121 (t0) REVERT: K 62 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8293 (mt-10) REVERT: K 66 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: K 149 MET cc_start: 0.7925 (mmm) cc_final: 0.7657 (mmm) REVERT: K 362 ARG cc_start: 0.6066 (ttt180) cc_final: 0.5689 (ttt180) REVERT: L 19 ARG cc_start: 0.8130 (ptp90) cc_final: 0.7653 (ptp90) REVERT: L 27 LYS cc_start: 0.6940 (tptp) cc_final: 0.6501 (mmmt) REVERT: L 98 LYS cc_start: 0.8865 (tttt) cc_final: 0.8573 (ttmm) REVERT: M 148 TRP cc_start: 0.7746 (m100) cc_final: 0.7344 (m-90) REVERT: M 181 GLU cc_start: 0.8020 (tt0) cc_final: 0.7810 (tt0) REVERT: M 291 GLN cc_start: 0.8201 (tp40) cc_final: 0.7916 (tp40) REVERT: N 98 LYS cc_start: 0.8798 (tttp) cc_final: 0.8579 (ttmm) REVERT: O 140 GLU cc_start: 0.7456 (tp30) cc_final: 0.7234 (tt0) REVERT: O 181 GLU cc_start: 0.8254 (tt0) cc_final: 0.7996 (tt0) REVERT: O 291 GLN cc_start: 0.8315 (tp40) cc_final: 0.8058 (tp40) REVERT: O 380 MET cc_start: 0.7070 (ttp) cc_final: 0.6590 (tmm) REVERT: Q 56 ASN cc_start: 0.8607 (t0) cc_final: 0.8223 (t0) REVERT: Q 79 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8650 (m) REVERT: Q 117 GLU cc_start: 0.6995 (pm20) cc_final: 0.6735 (pm20) REVERT: Q 140 GLU cc_start: 0.7694 (tp30) cc_final: 0.7376 (tt0) REVERT: Q 291 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8144 (tp40) REVERT: Q 362 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.5672 (ttt180) REVERT: Q 366 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7467 (mtm-85) REVERT: R 112 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8073 (mp) REVERT: S 15 GLN cc_start: 0.6945 (tm-30) cc_final: 0.6683 (tm-30) REVERT: T 110 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7908 (mp) REVERT: U 66 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: U 77 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8075 (mm-30) REVERT: U 78 MET cc_start: 0.8948 (mmt) cc_final: 0.8713 (mmt) REVERT: U 99 SER cc_start: 0.7245 (p) cc_final: 0.6832 (m) REVERT: U 170 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: W 56 ASN cc_start: 0.8645 (t0) cc_final: 0.8351 (t0) REVERT: W 298 LYS cc_start: 0.8490 (mmtp) cc_final: 0.8061 (mttt) REVERT: W 366 ARG cc_start: 0.7532 (mtm110) cc_final: 0.7240 (mtm-85) REVERT: X 27 LYS cc_start: 0.6804 (tptt) cc_final: 0.6459 (mmmt) REVERT: X 112 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6973 (mm) outliers start: 169 outliers final: 124 residues processed: 1099 average time/residue: 0.5527 time to fit residues: 965.2100 Evaluate side-chains 1120 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 981 time to evaluate : 4.237 ------------------------------------------------------------------------------- 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 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 A residue 390 VAL 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 202 ARG Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 333 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 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 54 GLN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 74 LEU 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 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 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 I residue 14 THR 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 232 LEU 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 58 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 114 LEU 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 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 275 GLN Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 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 114 LEU 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 291 GLN 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 R residue 112 LEU Chi-restraints excluded: chain S residue 67 MET 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 384 ILE Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 173 LEU Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain U residue 330 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 123 ASN 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 229 ILE Chi-restraints excluded: chain W residue 235 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 98 optimal weight: 0.7980 chunk 566 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 626 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 381 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 489 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 412 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN C 132 HIS ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN ** Q 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN S 10 ASN S 54 GLN T 12 GLN U 10 ASN ** U 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 10 ASN X 12 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.153127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.121227 restraints weight = 63821.297| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.90 r_work: 0.3141 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.7402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 51576 Z= 0.223 Angle : 0.627 21.897 70128 Z= 0.317 Chirality : 0.041 0.383 7800 Planarity : 0.008 0.298 9252 Dihedral : 6.831 175.975 7080 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.08 % Favored : 94.73 % Rotamer: Outliers : 3.10 % Allowed : 16.80 % Favored : 80.10 % 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: 1.61 (0.11), residues: 6456 helix: 2.51 (0.09), residues: 3156 sheet: 1.27 (0.22), residues: 492 loop : -0.70 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 138 HIS 0.007 0.001 HIS C 155 PHE 0.122 0.003 PHE I 274 TYR 0.018 0.001 TYR N 90 ARG 0.033 0.001 ARG A 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 1145 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 983 time to evaluate : 4.283 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: A 92 VAL cc_start: 0.8513 (t) cc_final: 0.8100 (p) REVERT: A 238 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8659 (mttt) REVERT: A 275 GLN cc_start: 0.6826 (mm-40) cc_final: 0.6390 (mm-40) REVERT: A 290 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8154 (mtm-85) REVERT: B 15 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8581 (tm-30) REVERT: B 27 LYS cc_start: 0.6650 (tptt) cc_final: 0.6338 (tptp) REVERT: B 101 SER cc_start: 0.9137 (t) cc_final: 0.8779 (m) REVERT: C 202 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8576 (mtt180) REVERT: C 290 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8143 (mtm-85) REVERT: C 325 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6370 (mt-10) REVERT: C 366 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7408 (mtm110) REVERT: C 380 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6444 (tmm) REVERT: D 101 SER cc_start: 0.9084 (t) cc_final: 0.8774 (m) REVERT: E 117 GLU cc_start: 0.6542 (tt0) cc_final: 0.6075 (mt-10) REVERT: E 238 LYS cc_start: 0.8958 (mtpp) cc_final: 0.8622 (mmmt) REVERT: E 366 ARG cc_start: 0.7642 (ttp-110) cc_final: 0.7056 (mtm110) REVERT: E 380 MET cc_start: 0.6706 (tmm) cc_final: 0.6369 (tmm) REVERT: F 27 LYS cc_start: 0.7081 (tptp) cc_final: 0.6762 (mmmt) REVERT: F 101 SER cc_start: 0.9228 (t) cc_final: 0.8885 (m) REVERT: G 18 ARG cc_start: 0.7281 (tpp-160) cc_final: 0.6659 (tpp-160) REVERT: G 170 GLU cc_start: 0.7617 (tt0) cc_final: 0.7269 (tt0) REVERT: G 253 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7927 (ptp-110) REVERT: G 298 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8363 (ttpt) REVERT: G 366 ARG cc_start: 0.7403 (ttp-110) cc_final: 0.7137 (ttp-110) REVERT: H 27 LYS cc_start: 0.6849 (tptp) cc_final: 0.6499 (mmmt) REVERT: I 56 ASN cc_start: 0.8625 (t0) cc_final: 0.8404 (t0) REVERT: I 66 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: I 78 MET cc_start: 0.9019 (mmm) cc_final: 0.8632 (mmt) REVERT: I 181 GLU cc_start: 0.8328 (tt0) cc_final: 0.8022 (tt0) REVERT: I 380 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.6240 (tmm) REVERT: J 27 LYS cc_start: 0.7024 (tptp) cc_final: 0.6619 (mmmt) REVERT: K 56 ASN cc_start: 0.8529 (t0) cc_final: 0.8117 (t0) REVERT: K 62 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8285 (mt-10) REVERT: K 66 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: K 149 MET cc_start: 0.7949 (mmm) cc_final: 0.7693 (mmm) REVERT: K 362 ARG cc_start: 0.6102 (ttt180) cc_final: 0.5726 (ttt180) REVERT: L 19 ARG cc_start: 0.8145 (ptp90) cc_final: 0.7643 (ptp90) REVERT: L 27 LYS cc_start: 0.6988 (tptp) cc_final: 0.6513 (mmmt) REVERT: M 148 TRP cc_start: 0.7739 (m100) cc_final: 0.7351 (m-90) REVERT: M 181 GLU cc_start: 0.8079 (tt0) cc_final: 0.7851 (tt0) REVERT: M 291 GLN cc_start: 0.8203 (tp40) cc_final: 0.7966 (tp40) REVERT: M 403 LEU cc_start: 0.7078 (mt) cc_final: 0.6849 (mt) REVERT: N 98 LYS cc_start: 0.8766 (tttp) cc_final: 0.8554 (ttmm) REVERT: O 291 GLN cc_start: 0.8294 (tp40) cc_final: 0.8042 (tp40) REVERT: O 380 MET cc_start: 0.7059 (ttp) cc_final: 0.6600 (tmm) REVERT: P 84 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8284 (mtmm) REVERT: Q 56 ASN cc_start: 0.8596 (t0) cc_final: 0.8198 (t0) REVERT: Q 79 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8624 (m) REVERT: Q 117 GLU cc_start: 0.7044 (pm20) cc_final: 0.6779 (pm20) REVERT: Q 140 GLU cc_start: 0.7710 (tp30) cc_final: 0.7393 (tt0) REVERT: Q 291 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8158 (tp40) REVERT: Q 362 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.5690 (ttt180) REVERT: Q 366 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7496 (mtm-85) REVERT: R 112 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8021 (mp) REVERT: S 15 GLN cc_start: 0.6955 (tm-30) cc_final: 0.6694 (tm-30) REVERT: T 12 GLN cc_start: 0.8321 (tt0) cc_final: 0.8087 (tt0) REVERT: T 110 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7886 (mp) REVERT: U 66 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: U 77 GLU cc_start: 0.8665 (mm-30) cc_final: 0.7779 (mm-30) REVERT: U 78 MET cc_start: 0.8948 (mmt) cc_final: 0.8659 (mmt) REVERT: U 99 SER cc_start: 0.7189 (p) cc_final: 0.6830 (m) REVERT: W 56 ASN cc_start: 0.8614 (t0) cc_final: 0.8319 (t0) REVERT: W 66 ASP cc_start: 0.8361 (m-30) cc_final: 0.8077 (m-30) REVERT: W 111 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7405 (mm-30) REVERT: W 298 LYS cc_start: 0.8468 (mmtp) cc_final: 0.8048 (mttt) REVERT: W 366 ARG cc_start: 0.7566 (mtm110) cc_final: 0.7258 (mtm-85) REVERT: X 27 LYS cc_start: 0.6764 (tptt) cc_final: 0.6396 (mmmt) outliers start: 162 outliers final: 133 residues processed: 1078 average time/residue: 0.5544 time to fit residues: 951.0096 Evaluate side-chains 1108 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 962 time to evaluate : 4.262 ------------------------------------------------------------------------------- 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 A residue 380 MET Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 16 GLN 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 202 ARG Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 380 MET 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 54 GLN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 114 LEU 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 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 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 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 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 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 58 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 114 LEU 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 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 298 LYS 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 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 65 THR 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 183 LEU Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 291 GLN 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 R residue 112 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 276 GLN Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 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 330 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 123 ASN 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 229 ILE Chi-restraints excluded: chain W residue 235 ARG 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 62 SER Chi-restraints excluded: chain X residue 108 LEU 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 430 optimal weight: 1.9990 chunk 534 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 398 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 606 optimal weight: 0.7980 chunk 450 optimal weight: 0.0470 chunk 545 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 468 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 HIS Q 10 ASN ** Q 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN S 10 ASN S 54 GLN U 10 ASN ** U 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.153651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121908 restraints weight = 63841.591| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.90 r_work: 0.3183 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.7508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 51576 Z= 0.220 Angle : 0.639 21.454 70128 Z= 0.320 Chirality : 0.041 0.529 7800 Planarity : 0.008 0.319 9252 Dihedral : 7.130 176.649 7080 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.02 % Favored : 94.80 % Rotamer: Outliers : 2.87 % Allowed : 17.26 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.64 (0.11), residues: 6456 helix: 2.58 (0.09), residues: 3144 sheet: 1.22 (0.22), residues: 492 loop : -0.72 (0.12), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J 138 HIS 0.008 0.001 HIS C 155 PHE 0.085 0.003 PHE I 274 TYR 0.024 0.001 TYR P 90 ARG 0.011 0.001 ARG Q 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 972 time to evaluate : 4.380 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 238 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8668 (mttt) REVERT: A 275 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6583 (mm-40) REVERT: A 290 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.8158 (mtm-85) REVERT: B 15 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8596 (tm-30) REVERT: B 27 LYS cc_start: 0.6688 (tptt) cc_final: 0.6391 (tptp) REVERT: B 101 SER cc_start: 0.9134 (t) cc_final: 0.8773 (m) REVERT: C 202 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8540 (mtt180) REVERT: C 290 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8181 (ttm-80) REVERT: C 325 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6371 (mt-10) REVERT: C 366 ARG cc_start: 0.7793 (mtm110) cc_final: 0.7419 (mtm110) REVERT: C 380 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6611 (tmm) REVERT: D 101 SER cc_start: 0.9081 (t) cc_final: 0.8766 (m) REVERT: E 117 GLU cc_start: 0.6485 (tt0) cc_final: 0.6000 (mt-10) REVERT: E 202 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7893 (mtp180) REVERT: E 238 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8647 (mmmt) REVERT: E 290 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.7958 (ttm-80) REVERT: E 366 ARG cc_start: 0.7656 (ttp-110) cc_final: 0.7089 (mtm110) REVERT: E 380 MET cc_start: 0.6706 (tmm) cc_final: 0.6372 (tmm) REVERT: F 27 LYS cc_start: 0.6941 (tptp) cc_final: 0.6672 (mmmt) REVERT: F 101 SER cc_start: 0.9253 (t) cc_final: 0.8920 (m) REVERT: G 18 ARG cc_start: 0.7264 (tpp-160) cc_final: 0.6668 (tpp-160) REVERT: G 194 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7204 (ttp80) REVERT: G 253 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7981 (ptp-110) REVERT: G 366 ARG cc_start: 0.7393 (ttp-110) cc_final: 0.7151 (ttp-110) REVERT: H 27 LYS cc_start: 0.6853 (tptp) cc_final: 0.6544 (mmmt) REVERT: I 56 ASN cc_start: 0.8619 (t0) cc_final: 0.8388 (t0) REVERT: I 78 MET cc_start: 0.9021 (mmm) cc_final: 0.8588 (mmt) REVERT: I 181 GLU cc_start: 0.8329 (tt0) cc_final: 0.8022 (tt0) REVERT: I 380 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.6230 (tmm) REVERT: J 27 LYS cc_start: 0.7033 (tptp) cc_final: 0.6634 (mmmt) REVERT: K 41 THR cc_start: 0.8363 (p) cc_final: 0.8145 (p) REVERT: K 56 ASN cc_start: 0.8512 (t0) cc_final: 0.8101 (t0) REVERT: K 62 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8278 (mt-10) REVERT: K 66 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: K 149 MET cc_start: 0.7936 (mmm) cc_final: 0.7693 (mmm) REVERT: K 362 ARG cc_start: 0.6030 (ttt180) cc_final: 0.5677 (ttt180) REVERT: K 380 MET cc_start: 0.7080 (ttp) cc_final: 0.6598 (tmm) REVERT: L 19 ARG cc_start: 0.8154 (ptp90) cc_final: 0.7656 (ptp90) REVERT: L 27 LYS cc_start: 0.6991 (tptp) cc_final: 0.6524 (mmmt) REVERT: M 56 ASN cc_start: 0.8626 (t0) cc_final: 0.8376 (t0) REVERT: M 148 TRP cc_start: 0.7740 (m100) cc_final: 0.7371 (m-90) REVERT: M 181 GLU cc_start: 0.8074 (tt0) cc_final: 0.7841 (tt0) REVERT: M 291 GLN cc_start: 0.8152 (tp40) cc_final: 0.7928 (tp40) REVERT: N 98 LYS cc_start: 0.8795 (tttp) cc_final: 0.8572 (ttmm) REVERT: O 291 GLN cc_start: 0.8262 (tp40) cc_final: 0.8021 (tp40) REVERT: O 380 MET cc_start: 0.7031 (ttp) cc_final: 0.6568 (tmm) REVERT: P 84 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8250 (mtmm) REVERT: P 90 TYR cc_start: 0.9044 (t80) cc_final: 0.8827 (t80) REVERT: Q 56 ASN cc_start: 0.8567 (t0) cc_final: 0.8144 (t0) REVERT: Q 79 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8634 (m) REVERT: Q 117 GLU cc_start: 0.7041 (pm20) cc_final: 0.6782 (pm20) REVERT: Q 140 GLU cc_start: 0.7707 (tp30) cc_final: 0.7406 (tt0) REVERT: Q 291 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8148 (tp40) REVERT: Q 362 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5625 (ttt180) REVERT: Q 366 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7506 (mtm-85) REVERT: R 112 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8002 (mp) REVERT: S 15 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6712 (tm-30) REVERT: T 110 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7891 (mp) REVERT: U 15 GLN cc_start: 0.7230 (tm-30) cc_final: 0.6973 (tm-30) REVERT: U 65 MET cc_start: 0.8382 (mtp) cc_final: 0.8077 (mtt) REVERT: U 66 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: U 77 GLU cc_start: 0.8675 (mm-30) cc_final: 0.7742 (mm-30) REVERT: U 78 MET cc_start: 0.8941 (mmt) cc_final: 0.8549 (mmt) REVERT: U 99 SER cc_start: 0.7139 (p) cc_final: 0.6781 (m) REVERT: U 170 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: U 293 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8108 (mt-10) REVERT: W 41 THR cc_start: 0.8292 (p) cc_final: 0.8086 (p) REVERT: W 56 ASN cc_start: 0.8581 (t0) cc_final: 0.8275 (t0) REVERT: W 66 ASP cc_start: 0.8062 (m-30) cc_final: 0.7552 (m-30) REVERT: W 111 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7294 (mm-30) REVERT: W 298 LYS cc_start: 0.8466 (mmtp) cc_final: 0.8054 (mttt) REVERT: W 366 ARG cc_start: 0.7586 (mtm110) cc_final: 0.7288 (mtm-85) REVERT: X 27 LYS cc_start: 0.6767 (tptt) cc_final: 0.6405 (mmmt) REVERT: X 112 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6950 (mm) outliers start: 150 outliers final: 124 residues processed: 1063 average time/residue: 0.5528 time to fit residues: 933.9536 Evaluate side-chains 1097 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 958 time to evaluate : 4.200 ------------------------------------------------------------------------------- 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 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 A residue 380 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain C residue 16 GLN 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 202 ARG Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 380 MET 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 54 GLN Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 74 LEU 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 58 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 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 384 ILE 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 I residue 14 THR 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 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 58 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 114 LEU 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 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 67 LEU Chi-restraints excluded: chain N residue 112 LEU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 114 LEU 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 114 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 291 GLN 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 R residue 112 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 276 GLN Chi-restraints excluded: chain S residue 333 SER Chi-restraints excluded: chain S residue 384 ILE Chi-restraints excluded: chain S residue 399 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 110 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain U residue 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 170 GLU 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 V residue 123 ASN 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 229 ILE Chi-restraints excluded: chain W residue 235 ARG Chi-restraints excluded: chain W residue 253 ARG Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 425 optimal weight: 5.9990 chunk 487 optimal weight: 0.9990 chunk 393 optimal weight: 1.9990 chunk 269 optimal weight: 0.2980 chunk 360 optimal weight: 0.1980 chunk 354 optimal weight: 5.9990 chunk 607 optimal weight: 1.9990 chunk 498 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 181 optimal weight: 0.9980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN G 276 GLN ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN Q 10 ASN ** Q 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN S 10 ASN T 12 GLN U 10 ASN U 382 GLN W 382 GLN X 12 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.151856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.120494 restraints weight = 63917.882| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.91 r_work: 0.3180 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.7606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 51576 Z= 0.199 Angle : 0.602 11.865 70128 Z= 0.304 Chirality : 0.040 0.276 7800 Planarity : 0.007 0.356 9252 Dihedral : 7.152 178.285 7080 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.88 % Favored : 94.93 % Rotamer: Outliers : 2.81 % Allowed : 17.62 % Favored : 79.57 % 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: 1.66 (0.11), residues: 6456 helix: 2.59 (0.09), residues: 3156 sheet: 1.17 (0.22), residues: 492 loop : -0.70 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP B 138 HIS 0.007 0.001 HIS C 155 PHE 0.077 0.003 PHE I 274 TYR 0.020 0.001 TYR R 90 ARG 0.011 0.001 ARG K 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27224.28 seconds wall clock time: 466 minutes 12.65 seconds (27972.65 seconds total)