Starting phenix.real_space_refine on Wed Aug 27 02:59:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j0b_9760/08_2025/6j0b_9760.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j0b_9760/08_2025/6j0b_9760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6j0b_9760/08_2025/6j0b_9760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j0b_9760/08_2025/6j0b_9760.map" model { file = "/net/cci-nas-00/data/ceres_data/6j0b_9760/08_2025/6j0b_9760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j0b_9760/08_2025/6j0b_9760.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.054 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 156 5.16 5 C 29808 2.51 5 N 7656 2.21 5 O 9168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 468 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46788 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "a" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, b, c, d, e, f, g, h, i, j, k, l Time building chain proxies: 5.32, per 1000 atoms: 0.11 Number of scatterers: 46788 At special positions: 0 Unit cell: (178.239, 180.481, 135.641, 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 156 16.00 O 9168 8.00 N 7656 7.00 C 29808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11208 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 78 sheets defined 28.4% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.857A pdb=" N ALA A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 145' Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 171 through 187 removed outlier: 4.120A pdb=" N VAL A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.689A pdb=" N ALA A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 308' Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 145' Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 171 through 187 removed outlier: 4.120A pdb=" N VAL B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 267 Processing helix chain 'B' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.691A pdb=" N ALA B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 320 through 327 Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU C 58 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.769A pdb=" N ILE C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 111 through 119 removed outlier: 3.794A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL C 117 " --> pdb=" O THR C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 through 145' Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 267 Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.713A pdb=" N ARG C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 removed outlier: 3.691A pdb=" N ALA C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 304 through 308' Processing helix chain 'C' and resid 320 through 327 Processing helix chain 'D' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 3.543A pdb=" N VAL D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.769A pdb=" N ILE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 90 through 95' Processing helix chain 'D' and resid 111 through 119 removed outlier: 3.792A pdb=" N ASP D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL D 117 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 140 through 145' Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 171 through 187 removed outlier: 4.118A pdb=" N VAL D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 Processing helix chain 'D' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 304 through 308' Processing helix chain 'D' and resid 320 through 327 Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU E 58 " --> pdb=" O ASP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL E 70 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 90 through 95' Processing helix chain 'E' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL E 117 " --> pdb=" O THR E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 140 through 145' Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 217 removed outlier: 3.749A pdb=" N GLU E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 267 Processing helix chain 'E' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG E 282 " --> pdb=" O PRO E 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 308 removed outlier: 3.691A pdb=" N ALA E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 304 through 308' Processing helix chain 'E' and resid 320 through 327 Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.525A pdb=" N LEU F 58 " --> pdb=" O ASP F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL F 70 " --> pdb=" O ASP F 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 90 through 95' Processing helix chain 'F' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL F 117 " --> pdb=" O THR F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 145 removed outlier: 3.857A pdb=" N ALA F 144 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 140 through 145' Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL F 175 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 267 Processing helix chain 'F' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG F 282 " --> pdb=" O PRO F 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA F 308 " --> pdb=" O LYS F 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 304 through 308' Processing helix chain 'F' and resid 320 through 327 Processing helix chain 'G' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU G 58 " --> pdb=" O ASP G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 78 removed outlier: 3.543A pdb=" N VAL G 70 " --> pdb=" O ASP G 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 removed outlier: 3.769A pdb=" N ILE G 94 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 90 through 95' Processing helix chain 'G' and resid 111 through 119 removed outlier: 3.794A pdb=" N ASP G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL G 117 " --> pdb=" O THR G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 removed outlier: 3.857A pdb=" N ALA G 144 " --> pdb=" O GLY G 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 140 through 145' Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL G 175 " --> pdb=" O PRO G 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 267 Processing helix chain 'G' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG G 282 " --> pdb=" O PRO G 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 285 " --> pdb=" O GLU G 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR G 290 " --> pdb=" O ALA G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA G 308 " --> pdb=" O LYS G 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 304 through 308' Processing helix chain 'G' and resid 320 through 327 Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU H 58 " --> pdb=" O ASP H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL H 70 " --> pdb=" O ASP H 66 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE H 94 " --> pdb=" O SER H 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 95' Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.794A pdb=" N ASP H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL H 117 " --> pdb=" O THR H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 145 removed outlier: 3.857A pdb=" N ALA H 144 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS H 145 " --> pdb=" O ALA H 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 140 through 145' Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 171 through 187 removed outlier: 4.120A pdb=" N VAL H 175 " --> pdb=" O PRO H 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 217 removed outlier: 3.751A pdb=" N GLU H 215 " --> pdb=" O GLU H 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 267 Processing helix chain 'H' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG H 282 " --> pdb=" O PRO H 278 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA H 285 " --> pdb=" O GLU H 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR H 290 " --> pdb=" O ALA H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA H 308 " --> pdb=" O LYS H 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 304 through 308' Processing helix chain 'H' and resid 320 through 327 Processing helix chain 'I' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU I 58 " --> pdb=" O ASP I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL I 70 " --> pdb=" O ASP I 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 90 through 95' Processing helix chain 'I' and resid 111 through 119 removed outlier: 3.794A pdb=" N ASP I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL I 117 " --> pdb=" O THR I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS I 145 " --> pdb=" O ALA I 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 140 through 145' Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL I 175 " --> pdb=" O PRO I 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY I 178 " --> pdb=" O ALA I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU I 215 " --> pdb=" O GLU I 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR I 216 " --> pdb=" O LEU I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 267 Processing helix chain 'I' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG I 282 " --> pdb=" O PRO I 278 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA I 285 " --> pdb=" O GLU I 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR I 290 " --> pdb=" O ALA I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 308 removed outlier: 3.691A pdb=" N ALA I 308 " --> pdb=" O LYS I 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 304 through 308' Processing helix chain 'I' and resid 320 through 327 Processing helix chain 'J' and resid 51 through 59 removed outlier: 3.525A pdb=" N LEU J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 78 removed outlier: 3.543A pdb=" N VAL J 70 " --> pdb=" O ASP J 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 95 removed outlier: 3.769A pdb=" N ILE J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 90 through 95' Processing helix chain 'J' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL J 117 " --> pdb=" O THR J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS J 145 " --> pdb=" O ALA J 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 140 through 145' Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 171 through 187 removed outlier: 4.120A pdb=" N VAL J 175 " --> pdb=" O PRO J 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY J 178 " --> pdb=" O ALA J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR J 216 " --> pdb=" O LEU J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 267 Processing helix chain 'J' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG J 282 " --> pdb=" O PRO J 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA J 285 " --> pdb=" O GLU J 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR J 290 " --> pdb=" O ALA J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA J 308 " --> pdb=" O LYS J 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 304 through 308' Processing helix chain 'J' and resid 320 through 327 Processing helix chain 'K' and resid 51 through 59 removed outlier: 3.525A pdb=" N LEU K 58 " --> pdb=" O ASP K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 78 removed outlier: 3.543A pdb=" N VAL K 70 " --> pdb=" O ASP K 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN K 78 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE K 94 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 90 through 95' Processing helix chain 'K' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP K 116 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL K 117 " --> pdb=" O THR K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA K 144 " --> pdb=" O GLY K 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS K 145 " --> pdb=" O ALA K 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 140 through 145' Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL K 175 " --> pdb=" O PRO K 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY K 178 " --> pdb=" O ALA K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU K 215 " --> pdb=" O GLU K 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR K 216 " --> pdb=" O LEU K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 267 Processing helix chain 'K' and resid 276 through 297 removed outlier: 3.713A pdb=" N ARG K 282 " --> pdb=" O PRO K 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA K 285 " --> pdb=" O GLU K 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR K 290 " --> pdb=" O ALA K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA K 308 " --> pdb=" O LYS K 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 304 through 308' Processing helix chain 'K' and resid 320 through 327 Processing helix chain 'L' and resid 51 through 59 removed outlier: 3.525A pdb=" N LEU L 58 " --> pdb=" O ASP L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 78 removed outlier: 3.543A pdb=" N VAL L 70 " --> pdb=" O ASP L 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 95 removed outlier: 3.769A pdb=" N ILE L 94 " --> pdb=" O SER L 90 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 90 through 95' Processing helix chain 'L' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL L 117 " --> pdb=" O THR L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA L 144 " --> pdb=" O GLY L 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 140 through 145' Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 171 through 187 removed outlier: 4.120A pdb=" N VAL L 175 " --> pdb=" O PRO L 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY L 178 " --> pdb=" O ALA L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 217 removed outlier: 3.749A pdb=" N GLU L 215 " --> pdb=" O GLU L 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR L 216 " --> pdb=" O LEU L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 267 Processing helix chain 'L' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG L 282 " --> pdb=" O PRO L 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA L 285 " --> pdb=" O GLU L 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR L 290 " --> pdb=" O ALA L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 308 removed outlier: 3.691A pdb=" N ALA L 308 " --> pdb=" O LYS L 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 304 through 308' Processing helix chain 'L' and resid 320 through 327 Processing helix chain 'a' and resid 4 through 12 removed outlier: 3.825A pdb=" N ALA a 9 " --> pdb=" O THR a 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL a 10 " --> pdb=" O SER a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE a 81 " --> pdb=" O LEU a 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA b 9 " --> pdb=" O THR b 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL b 10 " --> pdb=" O SER b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE b 81 " --> pdb=" O LEU b 77 " (cutoff:3.500A) Processing helix chain 'c' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA c 9 " --> pdb=" O THR c 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL c 10 " --> pdb=" O SER c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE c 81 " --> pdb=" O LEU c 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA d 9 " --> pdb=" O THR d 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL d 10 " --> pdb=" O SER d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 83 removed outlier: 3.560A pdb=" N ILE d 81 " --> pdb=" O LEU d 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 4 through 12 removed outlier: 3.825A pdb=" N ALA e 9 " --> pdb=" O THR e 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL e 10 " --> pdb=" O SER e 6 " (cutoff:3.500A) Processing helix chain 'e' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE e 81 " --> pdb=" O LEU e 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA f 9 " --> pdb=" O THR f 5 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL f 10 " --> pdb=" O SER f 6 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE f 81 " --> pdb=" O LEU f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA g 9 " --> pdb=" O THR g 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL g 10 " --> pdb=" O SER g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE g 81 " --> pdb=" O LEU g 77 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA h 9 " --> pdb=" O THR h 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL h 10 " --> pdb=" O SER h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE h 81 " --> pdb=" O LEU h 77 " (cutoff:3.500A) Processing helix chain 'i' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA i 9 " --> pdb=" O THR i 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL i 10 " --> pdb=" O SER i 6 " (cutoff:3.500A) Processing helix chain 'i' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE i 81 " --> pdb=" O LEU i 77 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 83 removed outlier: 3.560A pdb=" N ILE j 81 " --> pdb=" O LEU j 77 " (cutoff:3.500A) Processing helix chain 'k' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA k 9 " --> pdb=" O THR k 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL k 10 " --> pdb=" O SER k 6 " (cutoff:3.500A) Processing helix chain 'k' and resid 77 through 83 removed outlier: 3.560A pdb=" N ILE k 81 " --> pdb=" O LEU k 77 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA l 9 " --> pdb=" O THR l 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL l 10 " --> pdb=" O SER l 6 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 83 removed outlier: 3.560A pdb=" N ILE l 81 " --> pdb=" O LEU l 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 5.993A pdb=" N TYR A 11 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE F 348 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE L 310 " --> pdb=" O GLY L 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA A 106 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP A 130 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 155 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN A 223 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A 156 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 312 removed outlier: 3.506A pdb=" N PHE A 310 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.507A pdb=" N PHE G 310 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA B 106 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP B 130 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 155 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN B 223 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL B 156 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AA9, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AB1, first strand: chain 'B' and resid 309 through 312 removed outlier: 3.507A pdb=" N PHE B 310 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.506A pdb=" N PHE H 310 " --> pdb=" O GLY H 334 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA C 106 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP C 130 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 155 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN C 223 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL C 156 " --> pdb=" O ASN C 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AB5, first strand: chain 'C' and resid 225 through 228 Processing sheet with id=AB6, first strand: chain 'C' and resid 309 through 312 removed outlier: 3.507A pdb=" N PHE C 310 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.507A pdb=" N PHE I 310 " --> pdb=" O GLY I 334 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA D 106 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP D 130 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 155 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN D 223 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL D 156 " --> pdb=" O ASN D 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AC1, first strand: chain 'D' and resid 225 through 228 Processing sheet with id=AC2, first strand: chain 'D' and resid 309 through 312 removed outlier: 3.506A pdb=" N PHE D 310 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 343 through 349 removed outlier: 3.506A pdb=" N PHE J 310 " --> pdb=" O GLY J 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA E 106 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP E 130 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E 155 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN E 223 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL E 156 " --> pdb=" O ASN E 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 161 through 163 Processing sheet with id=AC6, first strand: chain 'E' and resid 225 through 228 Processing sheet with id=AC7, first strand: chain 'E' and resid 309 through 312 removed outlier: 3.507A pdb=" N PHE E 310 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.507A pdb=" N PHE K 310 " --> pdb=" O GLY K 334 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 47 through 49 removed outlier: 3.587A pdb=" N ALA F 106 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP F 130 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA F 155 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN F 223 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL F 156 " --> pdb=" O ASN F 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 161 through 163 Processing sheet with id=AD2, first strand: chain 'F' and resid 225 through 228 Processing sheet with id=AD3, first strand: chain 'F' and resid 309 through 312 removed outlier: 3.506A pdb=" N PHE F 310 " --> pdb=" O GLY F 334 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 11 Processing sheet with id=AD5, first strand: chain 'G' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA G 106 " --> pdb=" O VAL G 128 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP G 130 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA G 155 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN G 223 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL G 156 " --> pdb=" O ASN G 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 161 through 163 Processing sheet with id=AD7, first strand: chain 'G' and resid 225 through 228 Processing sheet with id=AD8, first strand: chain 'G' and resid 344 through 345 removed outlier: 6.716A pdb=" N ILE G 344 " --> pdb=" O TYR H 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'H' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA H 106 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP H 130 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA H 155 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN H 223 " --> pdb=" O ALA H 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL H 156 " --> pdb=" O ASN H 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 161 through 163 Processing sheet with id=AE2, first strand: chain 'H' and resid 225 through 228 Processing sheet with id=AE3, first strand: chain 'H' and resid 344 through 345 removed outlier: 6.722A pdb=" N ILE H 344 " --> pdb=" O TYR I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'I' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA I 106 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP I 130 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 155 " --> pdb=" O ALA I 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN I 223 " --> pdb=" O ALA I 154 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL I 156 " --> pdb=" O ASN I 223 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 161 through 163 Processing sheet with id=AE6, first strand: chain 'I' and resid 225 through 228 Processing sheet with id=AE7, first strand: chain 'I' and resid 344 through 345 removed outlier: 6.735A pdb=" N ILE I 344 " --> pdb=" O TYR J 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'J' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA J 106 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP J 130 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA J 155 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN J 223 " --> pdb=" O ALA J 154 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL J 156 " --> pdb=" O ASN J 223 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 161 through 163 Processing sheet with id=AF1, first strand: chain 'J' and resid 225 through 228 Processing sheet with id=AF2, first strand: chain 'J' and resid 344 through 345 removed outlier: 6.713A pdb=" N ILE J 344 " --> pdb=" O TYR K 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'K' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA K 106 " --> pdb=" O VAL K 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP K 130 " --> pdb=" O ALA K 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA K 155 " --> pdb=" O ALA K 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN K 223 " --> pdb=" O ALA K 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL K 156 " --> pdb=" O ASN K 223 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 161 through 163 Processing sheet with id=AF5, first strand: chain 'K' and resid 225 through 228 Processing sheet with id=AF6, first strand: chain 'K' and resid 344 through 345 removed outlier: 6.630A pdb=" N ILE K 344 " --> pdb=" O TYR L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'L' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA L 106 " --> pdb=" O VAL L 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP L 130 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA L 155 " --> pdb=" O ALA L 127 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN L 223 " --> pdb=" O ALA L 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL L 156 " --> pdb=" O ASN L 223 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 161 through 163 Processing sheet with id=AF9, first strand: chain 'L' and resid 225 through 228 Processing sheet with id=AG1, first strand: chain 'a' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS a 92 " --> pdb=" O SER a 113 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER a 113 " --> pdb=" O LYS a 92 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE a 94 " --> pdb=" O ASN a 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN a 111 " --> pdb=" O ILE a 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE a 96 " --> pdb=" O THR a 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR a 109 " --> pdb=" O ILE a 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU a 98 " --> pdb=" O LEU a 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER a 113 " --> pdb=" O ARG a 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG a 143 " --> pdb=" O SER a 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA a 115 " --> pdb=" O ALA a 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA a 141 " --> pdb=" O ALA a 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU a 139 " --> pdb=" O PRO a 117 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER a 119 " --> pdb=" O ILE a 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE a 137 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR a 121 " --> pdb=" O GLN a 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN a 135 " --> pdb=" O THR a 121 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 40 through 46 removed outlier: 5.091A pdb=" N ASP a 41 " --> pdb=" O GLY a 57 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 125 through 126 removed outlier: 4.579A pdb=" N GLN f 135 " --> pdb=" O THR f 121 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR f 121 " --> pdb=" O GLN f 135 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE f 137 " --> pdb=" O SER f 119 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER f 119 " --> pdb=" O ILE f 137 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU f 139 " --> pdb=" O PRO f 117 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA f 141 " --> pdb=" O ALA f 115 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA f 115 " --> pdb=" O ALA f 141 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG f 143 " --> pdb=" O SER f 113 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER f 113 " --> pdb=" O ARG f 143 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU f 98 " --> pdb=" O LEU f 107 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR f 109 " --> pdb=" O ILE f 96 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE f 96 " --> pdb=" O THR f 109 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN f 111 " --> pdb=" O ILE f 94 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE f 94 " --> pdb=" O ASN f 111 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER f 113 " --> pdb=" O LYS f 92 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS f 92 " --> pdb=" O SER f 113 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS b 92 " --> pdb=" O SER b 113 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER b 113 " --> pdb=" O LYS b 92 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE b 94 " --> pdb=" O ASN b 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN b 111 " --> pdb=" O ILE b 94 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE b 96 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR b 109 " --> pdb=" O ILE b 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU b 98 " --> pdb=" O LEU b 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER b 113 " --> pdb=" O ARG b 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG b 143 " --> pdb=" O SER b 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA b 115 " --> pdb=" O ALA b 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA b 141 " --> pdb=" O ALA b 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU b 139 " --> pdb=" O PRO b 117 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER b 119 " --> pdb=" O ILE b 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE b 137 " --> pdb=" O SER b 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR b 121 " --> pdb=" O GLN b 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN b 135 " --> pdb=" O THR b 121 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 40 through 46 removed outlier: 5.091A pdb=" N ASP b 41 " --> pdb=" O GLY b 57 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS c 92 " --> pdb=" O SER c 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER c 113 " --> pdb=" O LYS c 92 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE c 94 " --> pdb=" O ASN c 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN c 111 " --> pdb=" O ILE c 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE c 96 " --> pdb=" O THR c 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR c 109 " --> pdb=" O ILE c 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU c 98 " --> pdb=" O LEU c 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER c 113 " --> pdb=" O ARG c 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG c 143 " --> pdb=" O SER c 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA c 115 " --> pdb=" O ALA c 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA c 141 " --> pdb=" O ALA c 115 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU c 139 " --> pdb=" O PRO c 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER c 119 " --> pdb=" O ILE c 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE c 137 " --> pdb=" O SER c 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR c 121 " --> pdb=" O GLN c 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN c 135 " --> pdb=" O THR c 121 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP c 41 " --> pdb=" O GLY c 57 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 19 through 23 removed outlier: 6.877A pdb=" N LYS d 92 " --> pdb=" O SER d 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER d 113 " --> pdb=" O LYS d 92 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE d 94 " --> pdb=" O ASN d 111 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN d 111 " --> pdb=" O ILE d 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE d 96 " --> pdb=" O THR d 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR d 109 " --> pdb=" O ILE d 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU d 98 " --> pdb=" O LEU d 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER d 113 " --> pdb=" O ARG d 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG d 143 " --> pdb=" O SER d 113 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA d 115 " --> pdb=" O ALA d 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA d 141 " --> pdb=" O ALA d 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU d 139 " --> pdb=" O PRO d 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER d 119 " --> pdb=" O ILE d 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE d 137 " --> pdb=" O SER d 119 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR d 121 " --> pdb=" O GLN d 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN d 135 " --> pdb=" O THR d 121 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'd' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP d 41 " --> pdb=" O GLY d 57 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'e' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS e 92 " --> pdb=" O SER e 113 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER e 113 " --> pdb=" O LYS e 92 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE e 94 " --> pdb=" O ASN e 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN e 111 " --> pdb=" O ILE e 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE e 96 " --> pdb=" O THR e 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR e 109 " --> pdb=" O ILE e 96 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU e 98 " --> pdb=" O LEU e 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER e 113 " --> pdb=" O ARG e 143 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ARG e 143 " --> pdb=" O SER e 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA e 115 " --> pdb=" O ALA e 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA e 141 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU e 139 " --> pdb=" O PRO e 117 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER e 119 " --> pdb=" O ILE e 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE e 137 " --> pdb=" O SER e 119 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR e 121 " --> pdb=" O GLN e 135 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN e 135 " --> pdb=" O THR e 121 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'e' and resid 40 through 46 removed outlier: 5.091A pdb=" N ASP e 41 " --> pdb=" O GLY e 57 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'f' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP f 41 " --> pdb=" O GLY f 57 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'g' and resid 19 through 23 removed outlier: 6.877A pdb=" N LYS g 92 " --> pdb=" O SER g 113 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER g 113 " --> pdb=" O LYS g 92 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE g 94 " --> pdb=" O ASN g 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN g 111 " --> pdb=" O ILE g 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE g 96 " --> pdb=" O THR g 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR g 109 " --> pdb=" O ILE g 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU g 98 " --> pdb=" O LEU g 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER g 113 " --> pdb=" O ARG g 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG g 143 " --> pdb=" O SER g 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA g 115 " --> pdb=" O ALA g 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA g 141 " --> pdb=" O ALA g 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU g 139 " --> pdb=" O PRO g 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER g 119 " --> pdb=" O ILE g 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE g 137 " --> pdb=" O SER g 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR g 121 " --> pdb=" O GLN g 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN g 135 " --> pdb=" O THR g 121 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'g' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP g 41 " --> pdb=" O GLY g 57 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'g' and resid 125 through 126 removed outlier: 4.579A pdb=" N GLN l 135 " --> pdb=" O THR l 121 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR l 121 " --> pdb=" O GLN l 135 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE l 137 " --> pdb=" O SER l 119 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER l 119 " --> pdb=" O ILE l 137 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU l 139 " --> pdb=" O PRO l 117 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA l 141 " --> pdb=" O ALA l 115 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA l 115 " --> pdb=" O ALA l 141 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG l 143 " --> pdb=" O SER l 113 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER l 113 " --> pdb=" O ARG l 143 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU l 98 " --> pdb=" O LEU l 107 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR l 109 " --> pdb=" O ILE l 96 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE l 96 " --> pdb=" O THR l 109 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN l 111 " --> pdb=" O ILE l 94 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE l 94 " --> pdb=" O ASN l 111 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER l 113 " --> pdb=" O LYS l 92 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS l 92 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 19 through 23 removed outlier: 6.877A pdb=" N LYS h 92 " --> pdb=" O SER h 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER h 113 " --> pdb=" O LYS h 92 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE h 94 " --> pdb=" O ASN h 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN h 111 " --> pdb=" O ILE h 94 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE h 96 " --> pdb=" O THR h 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR h 109 " --> pdb=" O ILE h 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU h 98 " --> pdb=" O LEU h 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER h 113 " --> pdb=" O ARG h 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG h 143 " --> pdb=" O SER h 113 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA h 115 " --> pdb=" O ALA h 141 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA h 141 " --> pdb=" O ALA h 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU h 139 " --> pdb=" O PRO h 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER h 119 " --> pdb=" O ILE h 137 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE h 137 " --> pdb=" O SER h 119 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR h 121 " --> pdb=" O GLN h 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN h 135 " --> pdb=" O THR h 121 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'h' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP h 41 " --> pdb=" O GLY h 57 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'i' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS i 92 " --> pdb=" O SER i 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER i 113 " --> pdb=" O LYS i 92 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE i 94 " --> pdb=" O ASN i 111 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN i 111 " --> pdb=" O ILE i 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE i 96 " --> pdb=" O THR i 109 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR i 109 " --> pdb=" O ILE i 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU i 98 " --> pdb=" O LEU i 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER i 113 " --> pdb=" O ARG i 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG i 143 " --> pdb=" O SER i 113 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA i 115 " --> pdb=" O ALA i 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA i 141 " --> pdb=" O ALA i 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU i 139 " --> pdb=" O PRO i 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER i 119 " --> pdb=" O ILE i 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE i 137 " --> pdb=" O SER i 119 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR i 121 " --> pdb=" O GLN i 135 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN i 135 " --> pdb=" O THR i 121 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'i' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP i 41 " --> pdb=" O GLY i 57 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'j' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS j 92 " --> pdb=" O SER j 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER j 113 " --> pdb=" O LYS j 92 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE j 94 " --> pdb=" O ASN j 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN j 111 " --> pdb=" O ILE j 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE j 96 " --> pdb=" O THR j 109 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR j 109 " --> pdb=" O ILE j 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU j 98 " --> pdb=" O LEU j 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER j 113 " --> pdb=" O ARG j 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG j 143 " --> pdb=" O SER j 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA j 115 " --> pdb=" O ALA j 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA j 141 " --> pdb=" O ALA j 115 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU j 139 " --> pdb=" O PRO j 117 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER j 119 " --> pdb=" O ILE j 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE j 137 " --> pdb=" O SER j 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR j 121 " --> pdb=" O GLN j 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN j 135 " --> pdb=" O THR j 121 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'j' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP j 41 " --> pdb=" O GLY j 57 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'k' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS k 92 " --> pdb=" O SER k 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER k 113 " --> pdb=" O LYS k 92 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE k 94 " --> pdb=" O ASN k 111 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN k 111 " --> pdb=" O ILE k 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE k 96 " --> pdb=" O THR k 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR k 109 " --> pdb=" O ILE k 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU k 98 " --> pdb=" O LEU k 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER k 113 " --> pdb=" O ARG k 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG k 143 " --> pdb=" O SER k 113 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA k 115 " --> pdb=" O ALA k 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA k 141 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU k 139 " --> pdb=" O PRO k 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER k 119 " --> pdb=" O ILE k 137 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE k 137 " --> pdb=" O SER k 119 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR k 121 " --> pdb=" O GLN k 135 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN k 135 " --> pdb=" O THR k 121 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'k' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP k 41 " --> pdb=" O GLY k 57 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'l' and resid 40 through 46 removed outlier: 5.091A pdb=" N ASP l 41 " --> pdb=" O GLY l 57 " (cutoff:3.500A) 1467 hydrogen bonds defined for protein. 4131 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: 11.83 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 14676 1.33 - 1.45: 7223 1.45 - 1.57: 25597 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 47784 Sorted by residual: bond pdb=" CB VAL k 144 " pdb=" CG2 VAL k 144 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.33e+00 bond pdb=" CB VAL f 144 " pdb=" CG2 VAL f 144 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.31e+00 bond pdb=" CG MET E 267 " pdb=" SD MET E 267 " ideal model delta sigma weight residual 1.803 1.745 0.058 2.50e-02 1.60e+03 5.31e+00 bond pdb=" CB VAL i 144 " pdb=" CG2 VAL i 144 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.30e+00 bond pdb=" CG MET B 267 " pdb=" SD MET B 267 " ideal model delta sigma weight residual 1.803 1.745 0.058 2.50e-02 1.60e+03 5.29e+00 ... (remaining 47779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 62776 2.14 - 4.29: 1824 4.29 - 6.43: 368 6.43 - 8.57: 144 8.57 - 10.72: 24 Bond angle restraints: 65136 Sorted by residual: angle pdb=" N LEU k 86 " pdb=" CA LEU k 86 " pdb=" CB LEU k 86 " ideal model delta sigma weight residual 110.49 103.02 7.47 1.69e+00 3.50e-01 1.95e+01 angle pdb=" N LEU g 86 " pdb=" CA LEU g 86 " pdb=" CB LEU g 86 " ideal model delta sigma weight residual 110.49 103.03 7.46 1.69e+00 3.50e-01 1.95e+01 angle pdb=" N LEU j 86 " pdb=" CA LEU j 86 " pdb=" CB LEU j 86 " ideal model delta sigma weight residual 110.49 103.03 7.46 1.69e+00 3.50e-01 1.95e+01 angle pdb=" N LEU i 86 " pdb=" CA LEU i 86 " pdb=" CB LEU i 86 " ideal model delta sigma weight residual 110.49 103.06 7.43 1.69e+00 3.50e-01 1.93e+01 angle pdb=" N LEU l 86 " pdb=" CA LEU l 86 " pdb=" CB LEU l 86 " ideal model delta sigma weight residual 110.49 103.07 7.42 1.69e+00 3.50e-01 1.93e+01 ... (remaining 65131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 25298 17.83 - 35.66: 2350 35.66 - 53.48: 540 53.48 - 71.31: 120 71.31 - 89.14: 48 Dihedral angle restraints: 28356 sinusoidal: 10932 harmonic: 17424 Sorted by residual: dihedral pdb=" CA GLN g 85 " pdb=" C GLN g 85 " pdb=" N LEU g 86 " pdb=" CA LEU g 86 " ideal model delta harmonic sigma weight residual -180.00 -142.22 -37.78 0 5.00e+00 4.00e-02 5.71e+01 dihedral pdb=" CA GLN h 85 " pdb=" C GLN h 85 " pdb=" N LEU h 86 " pdb=" CA LEU h 86 " ideal model delta harmonic sigma weight residual 180.00 -142.25 -37.75 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA GLN l 85 " pdb=" C GLN l 85 " pdb=" N LEU l 86 " pdb=" CA LEU l 86 " ideal model delta harmonic sigma weight residual -180.00 -142.25 -37.75 0 5.00e+00 4.00e-02 5.70e+01 ... (remaining 28353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 5589 0.057 - 0.114: 1379 0.114 - 0.172: 401 0.172 - 0.229: 45 0.229 - 0.286: 14 Chirality restraints: 7428 Sorted by residual: chirality pdb=" CA ASN E 195 " pdb=" N ASN E 195 " pdb=" C ASN E 195 " pdb=" CB ASN E 195 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASN K 195 " pdb=" N ASN K 195 " pdb=" C ASN K 195 " pdb=" CB ASN K 195 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ASN G 195 " pdb=" N ASN G 195 " pdb=" C ASN G 195 " pdb=" CB ASN G 195 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 7425 not shown) Planarity restraints: 8424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN j 85 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C GLN j 85 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN j 85 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU j 86 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN i 85 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C GLN i 85 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN i 85 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU i 86 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN h 85 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C GLN h 85 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN h 85 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU h 86 " -0.019 2.00e-02 2.50e+03 ... (remaining 8421 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 15006 2.83 - 3.35: 39029 3.35 - 3.86: 77998 3.86 - 4.38: 88805 4.38 - 4.90: 155308 Nonbonded interactions: 376146 Sorted by model distance: nonbonded pdb=" O THR k 75 " pdb=" OG1 THR k 75 " model vdw 2.311 3.040 nonbonded pdb=" O THR b 75 " pdb=" OG1 THR b 75 " model vdw 2.311 3.040 nonbonded pdb=" O THR f 75 " pdb=" OG1 THR f 75 " model vdw 2.311 3.040 nonbonded pdb=" O THR c 75 " pdb=" OG1 THR c 75 " model vdw 2.311 3.040 nonbonded pdb=" O THR d 75 " pdb=" OG1 THR d 75 " model vdw 2.311 3.040 ... (remaining 376141 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } 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: 1.690 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: 0.040 Extract box with map and model: 0.660 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 40.030 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.008 0.089 47784 Z= 0.303 Angle : 0.957 10.718 65136 Z= 0.513 Chirality : 0.057 0.286 7428 Planarity : 0.007 0.057 8424 Dihedral : 15.441 89.140 17148 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.83 % Favored : 95.97 % Rotamer: Outliers : 4.01 % Allowed : 11.65 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.73 (0.08), residues: 5952 helix: -4.13 (0.06), residues: 1536 sheet: -0.97 (0.13), residues: 1452 loop : -2.29 (0.08), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 261 TYR 0.015 0.002 TYR K 158 PHE 0.042 0.003 PHE C 269 TRP 0.008 0.001 TRP E 165 Details of bonding type rmsd covalent geometry : bond 0.00754 (47784) covalent geometry : angle 0.95672 (65136) hydrogen bonds : bond 0.27951 ( 1467) hydrogen bonds : angle 8.79445 ( 4131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1688 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 1484 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8939 (mt) cc_final: 0.8726 (mm) REVERT: A 35 ASP cc_start: 0.7490 (p0) cc_final: 0.7201 (p0) REVERT: A 54 ASP cc_start: 0.8232 (t0) cc_final: 0.8032 (t0) REVERT: A 212 LEU cc_start: 0.8852 (tt) cc_final: 0.8601 (tm) REVERT: A 264 LYS cc_start: 0.8041 (mttt) cc_final: 0.7810 (tptt) REVERT: A 325 ASP cc_start: 0.7551 (m-30) cc_final: 0.7314 (m-30) REVERT: A 332 LYS cc_start: 0.8541 (mttp) cc_final: 0.8283 (mtpm) REVERT: B 15 LEU cc_start: 0.8564 (pp) cc_final: 0.8104 (pp) REVERT: B 24 ASN cc_start: 0.8045 (m-40) cc_final: 0.7819 (m-40) REVERT: B 41 ILE cc_start: 0.8500 (pt) cc_final: 0.8271 (pt) REVERT: B 54 ASP cc_start: 0.7986 (t0) cc_final: 0.7714 (t0) REVERT: B 87 LYS cc_start: 0.8226 (mttt) cc_final: 0.7924 (tppt) REVERT: B 103 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8772 (mt) REVERT: B 112 LYS cc_start: 0.8466 (mttp) cc_final: 0.7685 (ttmt) REVERT: B 195 ASN cc_start: 0.8254 (p0) cc_final: 0.7573 (t0) REVERT: B 243 ASP cc_start: 0.7357 (t0) cc_final: 0.7102 (t70) REVERT: B 325 ASP cc_start: 0.7680 (m-30) cc_final: 0.7432 (m-30) REVERT: B 332 LYS cc_start: 0.8300 (mttp) cc_final: 0.8004 (mtpp) REVERT: C 54 ASP cc_start: 0.8031 (t0) cc_final: 0.7809 (m-30) REVERT: C 67 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7996 (ttmt) REVERT: C 112 LYS cc_start: 0.8435 (mttp) cc_final: 0.8132 (ttmt) REVERT: C 116 ASP cc_start: 0.8236 (m-30) cc_final: 0.7985 (m-30) REVERT: C 195 ASN cc_start: 0.7993 (p0) cc_final: 0.7406 (t0) REVERT: C 203 GLU cc_start: 0.7735 (pt0) cc_final: 0.7528 (pt0) REVERT: C 212 LEU cc_start: 0.8755 (tt) cc_final: 0.8519 (tp) REVERT: C 325 ASP cc_start: 0.7563 (m-30) cc_final: 0.7124 (m-30) REVERT: C 332 LYS cc_start: 0.8403 (mttp) cc_final: 0.8087 (mtpp) REVERT: D 40 TYR cc_start: 0.7862 (m-80) cc_final: 0.7621 (m-80) REVERT: D 54 ASP cc_start: 0.7989 (t0) cc_final: 0.7740 (t0) REVERT: D 117 VAL cc_start: 0.8238 (m) cc_final: 0.8007 (p) REVERT: D 212 LEU cc_start: 0.8756 (tt) cc_final: 0.8376 (tm) REVERT: D 281 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7418 (mm-30) REVERT: D 332 LYS cc_start: 0.8540 (mttp) cc_final: 0.8254 (mtpp) REVERT: E 15 LEU cc_start: 0.8602 (pp) cc_final: 0.8283 (pp) REVERT: E 24 ASN cc_start: 0.8109 (m-40) cc_final: 0.7863 (m-40) REVERT: E 35 ASP cc_start: 0.7497 (p0) cc_final: 0.7147 (p0) REVERT: E 41 ILE cc_start: 0.8528 (pt) cc_final: 0.8285 (pt) REVERT: E 54 ASP cc_start: 0.7979 (t0) cc_final: 0.7366 (m-30) REVERT: E 103 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8668 (mt) REVERT: E 130 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: E 195 ASN cc_start: 0.8092 (p0) cc_final: 0.7602 (t0) REVERT: E 212 LEU cc_start: 0.8811 (tt) cc_final: 0.8561 (tm) REVERT: E 325 ASP cc_start: 0.7730 (m-30) cc_final: 0.7363 (m-30) REVERT: E 332 LYS cc_start: 0.8481 (mttp) cc_final: 0.8218 (mtpp) REVERT: F 67 LYS cc_start: 0.8334 (ttmt) cc_final: 0.8124 (tttt) REVERT: F 112 LYS cc_start: 0.8369 (mttp) cc_final: 0.8095 (ttmt) REVERT: F 182 SER cc_start: 0.8871 (t) cc_final: 0.8285 (p) REVERT: F 195 ASN cc_start: 0.7969 (p0) cc_final: 0.7627 (t0) REVERT: F 203 GLU cc_start: 0.7837 (pt0) cc_final: 0.7622 (pt0) REVERT: F 325 ASP cc_start: 0.7618 (m-30) cc_final: 0.7150 (m-30) REVERT: F 332 LYS cc_start: 0.8412 (mttp) cc_final: 0.8176 (mtpp) REVERT: G 15 LEU cc_start: 0.8392 (pp) cc_final: 0.7612 (pp) REVERT: G 100 ASP cc_start: 0.7620 (p0) cc_final: 0.6888 (p0) REVERT: G 117 VAL cc_start: 0.8482 (m) cc_final: 0.8260 (p) REVERT: G 167 ASN cc_start: 0.8119 (t0) cc_final: 0.7716 (m-40) REVERT: G 175 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.8951 (t) REVERT: H 40 TYR cc_start: 0.7705 (m-80) cc_final: 0.7424 (m-80) REVERT: H 87 LYS cc_start: 0.8024 (mttt) cc_final: 0.7809 (mttp) REVERT: H 100 ASP cc_start: 0.7497 (p0) cc_final: 0.7106 (p0) REVERT: H 113 THR cc_start: 0.8323 (p) cc_final: 0.8086 (m) REVERT: H 130 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: H 195 ASN cc_start: 0.8329 (p0) cc_final: 0.8032 (t0) REVERT: I 54 ASP cc_start: 0.7774 (t0) cc_final: 0.7520 (m-30) REVERT: I 112 LYS cc_start: 0.8518 (mttp) cc_final: 0.8206 (mttm) REVERT: I 117 VAL cc_start: 0.8384 (m) cc_final: 0.8174 (p) REVERT: I 130 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: I 145 LYS cc_start: 0.8298 (mtmt) cc_final: 0.8070 (mtmm) REVERT: I 195 ASN cc_start: 0.8262 (p0) cc_final: 0.7901 (t0) REVERT: J 35 ASP cc_start: 0.7328 (p0) cc_final: 0.6890 (p0) REVERT: J 117 VAL cc_start: 0.8216 (m) cc_final: 0.8011 (p) REVERT: J 130 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: J 167 ASN cc_start: 0.8095 (t0) cc_final: 0.7888 (m110) REVERT: J 176 MET cc_start: 0.8632 (mmm) cc_final: 0.8399 (mmm) REVERT: K 40 TYR cc_start: 0.7698 (m-80) cc_final: 0.7477 (m-80) REVERT: K 103 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8477 (mt) REVERT: K 167 ASN cc_start: 0.8194 (t0) cc_final: 0.7862 (m-40) REVERT: K 261 ARG cc_start: 0.7246 (ttt180) cc_final: 0.7037 (ttm110) REVERT: L 67 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8057 (ttpt) REVERT: L 100 ASP cc_start: 0.7716 (p0) cc_final: 0.7466 (p0) REVERT: L 145 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8030 (mtmm) REVERT: L 167 ASN cc_start: 0.8351 (t0) cc_final: 0.7923 (m-40) REVERT: L 195 ASN cc_start: 0.8097 (p0) cc_final: 0.7776 (t0) REVERT: a 55 MET cc_start: 0.8476 (mtm) cc_final: 0.8014 (mtt) REVERT: b 93 ASP cc_start: 0.7709 (m-30) cc_final: 0.7355 (m-30) REVERT: c 34 SER cc_start: 0.8441 (t) cc_final: 0.8231 (m) REVERT: d 55 MET cc_start: 0.8559 (mtm) cc_final: 0.8215 (mtp) REVERT: d 105 GLU cc_start: 0.7501 (tp30) cc_final: 0.7130 (tp30) REVERT: e 93 ASP cc_start: 0.7523 (m-30) cc_final: 0.7226 (m-30) REVERT: g 88 GLN cc_start: 0.8358 (mt0) cc_final: 0.8075 (mt0) REVERT: g 143 ARG cc_start: 0.7370 (ttt-90) cc_final: 0.6454 (ttt180) REVERT: i 6 SER cc_start: 0.8811 (p) cc_final: 0.8524 (t) REVERT: i 143 ARG cc_start: 0.7244 (ttt-90) cc_final: 0.6367 (ttt180) REVERT: l 6 SER cc_start: 0.8821 (p) cc_final: 0.8563 (t) REVERT: l 88 GLN cc_start: 0.8330 (mt0) cc_final: 0.8002 (mt0) REVERT: l 143 ARG cc_start: 0.7283 (ttt-90) cc_final: 0.6380 (ttt180) outliers start: 204 outliers final: 34 residues processed: 1612 average time/residue: 0.6953 time to fit residues: 1405.4684 Evaluate side-chains 927 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 885 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain l residue 16 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 0.0470 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 0.8980 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 20.0000 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 289 ASN A 321 GLN B 16 ASN B 213 GLN B 289 ASN B 321 GLN C 195 ASN C 213 GLN C 289 ASN C 321 GLN D 16 ASN D 213 GLN D 289 ASN D 321 GLN E 16 ASN E 167 ASN E 195 ASN E 213 GLN E 289 ASN E 296 GLN E 321 GLN F 195 ASN F 213 GLN F 289 ASN F 296 GLN F 321 GLN G 16 ASN G 45 ASN G 195 ASN G 213 GLN G 289 ASN G 296 GLN H 16 ASN H 213 GLN H 289 ASN H 296 GLN H 321 GLN I 45 ASN I 78 ASN I 195 ASN I 213 GLN I 289 ASN I 321 GLN J 16 ASN J 45 ASN J 195 ASN J 213 GLN J 230 ASN J 289 ASN J 296 GLN K 16 ASN K 45 ASN K 195 ASN K 213 GLN K 289 ASN K 321 GLN L 16 ASN L 78 ASN L 213 GLN L 289 ASN L 296 GLN L 321 GLN a 7 GLN a 114 ASN b 7 GLN b 60 GLN b 114 ASN c 7 GLN c 58 GLN c 114 ASN d 7 GLN d 31 ASN d 60 GLN d 111 ASN d 114 ASN e 7 GLN e 60 GLN e 114 ASN f 7 GLN f 60 GLN f 114 ASN g 31 ASN g 60 GLN g 130 ASN h 7 GLN h 31 ASN h 60 GLN h 130 ASN h 147 GLN i 7 GLN i 31 ASN i 60 GLN i 130 ASN j 31 ASN j 58 GLN j 60 GLN j 63 ASN j 130 ASN k 7 GLN k 60 GLN k 130 ASN l 60 GLN l 130 ASN Total number of N/Q/H flips: 104 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113679 restraints weight = 55955.377| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.79 r_work: 0.3152 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 47784 Z= 0.155 Angle : 0.647 10.672 65136 Z= 0.334 Chirality : 0.047 0.220 7428 Planarity : 0.005 0.034 8424 Dihedral : 6.477 46.329 6489 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.34 % Favored : 96.49 % Rotamer: Outliers : 5.88 % Allowed : 19.48 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.09), residues: 5952 helix: -2.00 (0.10), residues: 1512 sheet: -0.05 (0.14), residues: 1248 loop : -2.14 (0.08), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 187 TYR 0.011 0.001 TYR G 157 PHE 0.026 0.002 PHE E 269 TRP 0.006 0.001 TRP L 190 Details of bonding type rmsd covalent geometry : bond 0.00352 (47784) covalent geometry : angle 0.64717 (65136) hydrogen bonds : bond 0.04285 ( 1467) hydrogen bonds : angle 5.16797 ( 4131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 299 poor density : 962 time to evaluate : 2.026 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8243 (t0) cc_final: 0.8008 (t0) REVERT: A 195 ASN cc_start: 0.7599 (p0) cc_final: 0.7329 (t0) REVERT: A 212 LEU cc_start: 0.8754 (tt) cc_final: 0.8399 (tm) REVERT: A 245 ASP cc_start: 0.7973 (m-30) cc_final: 0.7721 (m-30) REVERT: A 261 ARG cc_start: 0.7681 (ttt180) cc_final: 0.7261 (ttm110) REVERT: B 24 ASN cc_start: 0.8452 (m-40) cc_final: 0.8009 (m-40) REVERT: B 54 ASP cc_start: 0.8206 (t0) cc_final: 0.7385 (m-30) REVERT: B 112 LYS cc_start: 0.8093 (mttp) cc_final: 0.7744 (ttmt) REVERT: B 130 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: B 195 ASN cc_start: 0.7701 (p0) cc_final: 0.7496 (t0) REVERT: B 245 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7652 (m-30) REVERT: C 54 ASP cc_start: 0.8149 (t0) cc_final: 0.7591 (m-30) REVERT: C 130 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: C 146 GLN cc_start: 0.7925 (tp40) cc_final: 0.7711 (tp40) REVERT: C 195 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7496 (t0) REVERT: C 203 GLU cc_start: 0.8223 (pt0) cc_final: 0.7952 (pt0) REVERT: C 321 GLN cc_start: 0.8075 (tp40) cc_final: 0.7767 (tp40) REVERT: C 325 ASP cc_start: 0.7478 (m-30) cc_final: 0.6775 (m-30) REVERT: D 54 ASP cc_start: 0.8164 (t0) cc_final: 0.7716 (m-30) REVERT: D 195 ASN cc_start: 0.7737 (p0) cc_final: 0.7261 (t0) REVERT: D 212 LEU cc_start: 0.8680 (tt) cc_final: 0.8288 (tm) REVERT: D 261 ARG cc_start: 0.7835 (ttt180) cc_final: 0.7382 (ttm110) REVERT: D 265 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7384 (mpt-90) REVERT: D 281 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8178 (mm-30) REVERT: D 315 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8501 (tptt) REVERT: E 24 ASN cc_start: 0.8463 (m-40) cc_final: 0.8010 (m-40) REVERT: E 54 ASP cc_start: 0.8169 (t0) cc_final: 0.7323 (m-30) REVERT: E 130 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: E 195 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7397 (t0) REVERT: E 212 LEU cc_start: 0.8758 (tt) cc_final: 0.8344 (tm) REVERT: E 233 THR cc_start: 0.9177 (t) cc_final: 0.8951 (m) REVERT: E 261 ARG cc_start: 0.7727 (ttt180) cc_final: 0.7253 (ttm-80) REVERT: E 321 GLN cc_start: 0.8076 (tp40) cc_final: 0.7693 (tp40) REVERT: E 325 ASP cc_start: 0.7685 (m-30) cc_final: 0.7192 (m-30) REVERT: F 54 ASP cc_start: 0.8176 (m-30) cc_final: 0.7926 (m-30) REVERT: F 195 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7618 (t0) REVERT: F 203 GLU cc_start: 0.8256 (pt0) cc_final: 0.7827 (mt-10) REVERT: F 212 LEU cc_start: 0.8587 (tt) cc_final: 0.8308 (tm) REVERT: F 242 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7619 (tp30) REVERT: F 267 MET cc_start: 0.8184 (mmp) cc_final: 0.7975 (mmp) REVERT: F 271 MET cc_start: 0.8962 (mmp) cc_final: 0.8613 (mmm) REVERT: F 273 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: F 321 GLN cc_start: 0.8020 (tp40) cc_final: 0.7644 (tp40) REVERT: F 325 ASP cc_start: 0.7676 (m-30) cc_final: 0.7048 (m-30) REVERT: G 100 ASP cc_start: 0.8026 (p0) cc_final: 0.7431 (p0) REVERT: G 167 ASN cc_start: 0.8140 (t0) cc_final: 0.7686 (m-40) REVERT: G 182 SER cc_start: 0.8859 (t) cc_final: 0.8648 (p) REVERT: G 195 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7614 (t0) REVERT: G 211 GLU cc_start: 0.7948 (mp0) cc_final: 0.7703 (pm20) REVERT: G 245 ASP cc_start: 0.8251 (m-30) cc_final: 0.8048 (m-30) REVERT: G 296 GLN cc_start: 0.8342 (mt0) cc_final: 0.8100 (mt0) REVERT: G 315 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8471 (tmmt) REVERT: G 325 ASP cc_start: 0.8101 (m-30) cc_final: 0.7818 (m-30) REVERT: H 40 TYR cc_start: 0.7755 (m-80) cc_final: 0.7446 (m-80) REVERT: H 53 MET cc_start: 0.8606 (ttp) cc_final: 0.8368 (ttp) REVERT: H 100 ASP cc_start: 0.7970 (p0) cc_final: 0.7459 (p0) REVERT: H 136 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6016 (pp) REVERT: H 146 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7591 (tt0) REVERT: H 176 MET cc_start: 0.8621 (mmm) cc_final: 0.8368 (mmm) REVERT: H 195 ASN cc_start: 0.8327 (p0) cc_final: 0.7836 (t0) REVERT: H 211 GLU cc_start: 0.8140 (mp0) cc_final: 0.7730 (pm20) REVERT: H 262 ASP cc_start: 0.7924 (m-30) cc_final: 0.7690 (m-30) REVERT: H 307 ASP cc_start: 0.7343 (m-30) cc_final: 0.7128 (m-30) REVERT: I 54 ASP cc_start: 0.7839 (t0) cc_final: 0.7367 (m-30) REVERT: I 130 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: I 136 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5438 (pp) REVERT: I 182 SER cc_start: 0.8858 (t) cc_final: 0.8461 (p) REVERT: I 195 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7744 (t0) REVERT: I 211 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: I 224 MET cc_start: 0.8738 (mtt) cc_final: 0.8187 (mtt) REVERT: I 262 ASP cc_start: 0.7977 (m-30) cc_final: 0.7660 (m-30) REVERT: J 130 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7316 (m-30) REVERT: J 146 GLN cc_start: 0.8149 (tt0) cc_final: 0.7575 (mm-40) REVERT: J 182 SER cc_start: 0.8905 (t) cc_final: 0.8431 (p) REVERT: J 195 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7480 (t0) REVERT: J 245 ASP cc_start: 0.8154 (t0) cc_final: 0.7941 (m-30) REVERT: J 262 ASP cc_start: 0.7933 (m-30) cc_final: 0.7573 (m-30) REVERT: K 40 TYR cc_start: 0.7757 (m-80) cc_final: 0.7364 (m-80) REVERT: K 149 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6468 (t) REVERT: K 167 ASN cc_start: 0.8336 (t0) cc_final: 0.7886 (m-40) REVERT: K 176 MET cc_start: 0.8677 (mmm) cc_final: 0.8476 (mmm) REVERT: K 195 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7536 (t0) REVERT: K 261 ARG cc_start: 0.7557 (ttt180) cc_final: 0.6668 (ttm110) REVERT: K 282 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7937 (mtp85) REVERT: L 66 ASP cc_start: 0.7681 (t0) cc_final: 0.7294 (t0) REVERT: L 136 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5769 (pp) REVERT: L 149 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6420 (p) REVERT: L 167 ASN cc_start: 0.8362 (t0) cc_final: 0.7957 (m-40) REVERT: L 182 SER cc_start: 0.8915 (t) cc_final: 0.8624 (p) REVERT: L 195 ASN cc_start: 0.7868 (p0) cc_final: 0.7655 (t0) REVERT: L 211 GLU cc_start: 0.8000 (mp0) cc_final: 0.7523 (pm20) REVERT: L 261 ARG cc_start: 0.7667 (ttt180) cc_final: 0.7029 (ttm110) REVERT: L 262 ASP cc_start: 0.8032 (m-30) cc_final: 0.7752 (m-30) REVERT: L 304 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7660 (ttmm) REVERT: a 67 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.8021 (ttm-80) REVERT: a 136 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7699 (mp0) REVERT: b 90 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: b 93 ASP cc_start: 0.8430 (m-30) cc_final: 0.8072 (m-30) REVERT: b 147 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7732 (tp-100) REVERT: d 136 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7734 (mp0) REVERT: e 11 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7931 (mp0) REVERT: e 93 ASP cc_start: 0.8414 (m-30) cc_final: 0.8097 (m-30) REVERT: f 90 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: g 37 ASP cc_start: 0.8323 (p0) cc_final: 0.8034 (p0) REVERT: h 27 LYS cc_start: 0.8475 (pttm) cc_final: 0.8240 (ptmm) REVERT: h 37 ASP cc_start: 0.8259 (p0) cc_final: 0.7953 (p0) REVERT: h 136 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8125 (mt-10) REVERT: i 6 SER cc_start: 0.8752 (p) cc_final: 0.8479 (t) REVERT: i 74 LYS cc_start: 0.7067 (mppt) cc_final: 0.6807 (mmtt) REVERT: j 6 SER cc_start: 0.8956 (p) cc_final: 0.8615 (t) REVERT: j 58 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8467 (mm-40) REVERT: j 74 LYS cc_start: 0.7050 (mppt) cc_final: 0.6739 (mtpt) REVERT: j 136 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8063 (mt-10) REVERT: k 37 ASP cc_start: 0.8305 (p0) cc_final: 0.8097 (p0) REVERT: k 101 ASP cc_start: 0.7704 (m-30) cc_final: 0.7318 (m-30) REVERT: l 6 SER cc_start: 0.8891 (p) cc_final: 0.8590 (t) REVERT: l 88 GLN cc_start: 0.8546 (mt0) cc_final: 0.8182 (mt0) REVERT: l 126 ASP cc_start: 0.8979 (t0) cc_final: 0.8636 (t0) REVERT: l 140 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8260 (ttm) outliers start: 299 outliers final: 117 residues processed: 1172 average time/residue: 0.5766 time to fit residues: 867.8585 Evaluate side-chains 946 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 800 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 282 ARG Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 64 ILE Chi-restraints excluded: chain b residue 90 GLU Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 75 THR Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 90 GLU Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain h residue 140 MET Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 58 GLN Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 95 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 247 optimal weight: 9.9990 chunk 468 optimal weight: 5.9990 chunk 512 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 561 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 392 optimal weight: 9.9990 chunk 363 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 354 optimal weight: 8.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 296 GLN E 195 ASN F 195 ASN G 16 ASN G 195 ASN G 227 ASN G 230 ASN H 296 GLN I 321 GLN J 16 ASN J 230 ASN K 195 ASN K 321 GLN L 321 GLN b 31 ASN ** b 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 60 GLN e 60 GLN ** e 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 60 GLN g 31 ASN g 114 ASN h 7 GLN h 114 ASN h 147 GLN i 58 GLN i 114 ASN j 31 ASN j 114 ASN k 114 ASN l 114 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109169 restraints weight = 56185.549| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.76 r_work: 0.3091 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 47784 Z= 0.224 Angle : 0.663 10.037 65136 Z= 0.341 Chirality : 0.049 0.216 7428 Planarity : 0.005 0.033 8424 Dihedral : 6.379 53.425 6476 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.86 % Favored : 96.02 % Rotamer: Outliers : 6.49 % Allowed : 20.05 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.09), residues: 5952 helix: -0.61 (0.13), residues: 1440 sheet: -0.05 (0.13), residues: 1476 loop : -2.04 (0.09), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 265 TYR 0.011 0.002 TYR K 157 PHE 0.022 0.002 PHE B 129 TRP 0.007 0.001 TRP D 165 Details of bonding type rmsd covalent geometry : bond 0.00551 (47784) covalent geometry : angle 0.66302 (65136) hydrogen bonds : bond 0.04519 ( 1467) hydrogen bonds : angle 4.93723 ( 4131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 330 poor density : 890 time to evaluate : 1.858 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8198 (pt0) cc_final: 0.7871 (pp20) REVERT: A 27 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 54 ASP cc_start: 0.8184 (t0) cc_final: 0.7972 (t0) REVERT: A 67 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7599 (ttmt) REVERT: A 93 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7980 (mtpt) REVERT: A 129 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7144 (p90) REVERT: A 195 ASN cc_start: 0.7669 (p0) cc_final: 0.7352 (t0) REVERT: A 203 GLU cc_start: 0.8334 (pt0) cc_final: 0.8073 (pt0) REVERT: A 212 LEU cc_start: 0.8635 (tt) cc_final: 0.8225 (tm) REVERT: A 245 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: A 261 ARG cc_start: 0.7797 (ttt180) cc_final: 0.7416 (ttm110) REVERT: B 24 ASN cc_start: 0.8417 (m-40) cc_final: 0.8030 (m-40) REVERT: B 54 ASP cc_start: 0.8105 (t0) cc_final: 0.7424 (m-30) REVERT: B 112 LYS cc_start: 0.8079 (mttp) cc_final: 0.7740 (ttmt) REVERT: B 130 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: B 195 ASN cc_start: 0.7870 (p0) cc_final: 0.7659 (t0) REVERT: B 224 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8600 (mtt) REVERT: B 233 THR cc_start: 0.9145 (t) cc_final: 0.8925 (m) REVERT: B 245 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: C 130 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: C 146 GLN cc_start: 0.7929 (tp40) cc_final: 0.7687 (tp40) REVERT: C 195 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7508 (t0) REVERT: C 203 GLU cc_start: 0.8212 (pt0) cc_final: 0.7947 (pt0) REVERT: C 242 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: C 244 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7643 (mtpt) REVERT: C 273 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: C 315 LYS cc_start: 0.8649 (tmtt) cc_final: 0.8382 (tppp) REVERT: C 321 GLN cc_start: 0.8127 (tp40) cc_final: 0.7704 (tp40) REVERT: C 325 ASP cc_start: 0.7849 (m-30) cc_final: 0.7214 (m-30) REVERT: D 54 ASP cc_start: 0.8138 (t0) cc_final: 0.7916 (t0) REVERT: D 67 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7731 (ttmt) REVERT: D 129 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7375 (p90) REVERT: D 146 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7558 (tp40) REVERT: D 212 LEU cc_start: 0.8618 (tt) cc_final: 0.8201 (tm) REVERT: D 224 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8392 (mmm) REVERT: D 261 ARG cc_start: 0.7903 (ttt180) cc_final: 0.7395 (ttm110) REVERT: D 304 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8068 (ttmm) REVERT: E 24 ASN cc_start: 0.8481 (m-40) cc_final: 0.8078 (m-40) REVERT: E 54 ASP cc_start: 0.8203 (t0) cc_final: 0.7502 (m-30) REVERT: E 129 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7086 (p90) REVERT: E 195 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7346 (t0) REVERT: E 233 THR cc_start: 0.9155 (t) cc_final: 0.8901 (m) REVERT: E 261 ARG cc_start: 0.7829 (ttt180) cc_final: 0.7470 (ttm-80) REVERT: F 129 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7014 (p90) REVERT: F 195 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7569 (t0) REVERT: F 203 GLU cc_start: 0.8221 (pt0) cc_final: 0.7861 (mt-10) REVERT: F 242 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: F 261 ARG cc_start: 0.7895 (ttt180) cc_final: 0.7377 (ttm110) REVERT: F 321 GLN cc_start: 0.8081 (tp40) cc_final: 0.7528 (tp40) REVERT: F 325 ASP cc_start: 0.7749 (m-30) cc_final: 0.7047 (m-30) REVERT: G 66 ASP cc_start: 0.7641 (t0) cc_final: 0.7239 (t0) REVERT: G 100 ASP cc_start: 0.8294 (p0) cc_final: 0.7597 (p0) REVERT: G 146 GLN cc_start: 0.8121 (tt0) cc_final: 0.7549 (mm-40) REVERT: G 167 ASN cc_start: 0.8158 (t0) cc_final: 0.7667 (m-40) REVERT: G 182 SER cc_start: 0.8893 (t) cc_final: 0.8554 (p) REVERT: G 245 ASP cc_start: 0.8150 (m-30) cc_final: 0.7947 (m-30) REVERT: G 325 ASP cc_start: 0.8099 (m-30) cc_final: 0.7893 (m-30) REVERT: H 12 ILE cc_start: 0.9055 (mm) cc_final: 0.8829 (mp) REVERT: H 40 TYR cc_start: 0.7762 (m-80) cc_final: 0.7273 (m-80) REVERT: H 53 MET cc_start: 0.8580 (ttp) cc_final: 0.8288 (ttp) REVERT: H 66 ASP cc_start: 0.7770 (t0) cc_final: 0.7358 (t70) REVERT: H 100 ASP cc_start: 0.8193 (p0) cc_final: 0.7662 (p0) REVERT: H 130 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7698 (m-30) REVERT: H 195 ASN cc_start: 0.8217 (p0) cc_final: 0.7888 (t0) REVERT: H 224 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.7692 (mtt) REVERT: H 262 ASP cc_start: 0.7922 (m-30) cc_final: 0.7590 (m-30) REVERT: I 66 ASP cc_start: 0.7775 (t0) cc_final: 0.7367 (t0) REVERT: I 130 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: I 136 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.5761 (pp) REVERT: I 182 SER cc_start: 0.8945 (t) cc_final: 0.8423 (p) REVERT: I 211 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: I 262 ASP cc_start: 0.8072 (m-30) cc_final: 0.7824 (m-30) REVERT: J 12 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8894 (mp) REVERT: J 18 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8682 (tm) REVERT: J 66 ASP cc_start: 0.7372 (t0) cc_final: 0.7021 (t0) REVERT: J 129 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7459 (p90) REVERT: J 130 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: J 146 GLN cc_start: 0.8202 (tt0) cc_final: 0.7604 (mm-40) REVERT: J 182 SER cc_start: 0.8968 (t) cc_final: 0.8381 (p) REVERT: J 350 GLN cc_start: 0.9104 (tp-100) cc_final: 0.8704 (tp40) REVERT: K 40 TYR cc_start: 0.7732 (m-80) cc_final: 0.7363 (m-80) REVERT: K 66 ASP cc_start: 0.7911 (t0) cc_final: 0.7558 (t70) REVERT: K 149 THR cc_start: 0.7083 (OUTLIER) cc_final: 0.6784 (t) REVERT: K 167 ASN cc_start: 0.8343 (t0) cc_final: 0.7897 (m-40) REVERT: K 195 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7743 (t0) REVERT: K 224 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.7515 (mtt) REVERT: K 261 ARG cc_start: 0.7506 (ttt180) cc_final: 0.6820 (ttm110) REVERT: K 282 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8420 (mtp85) REVERT: L 66 ASP cc_start: 0.8107 (t0) cc_final: 0.7614 (t0) REVERT: L 136 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6001 (pp) REVERT: L 167 ASN cc_start: 0.8344 (t0) cc_final: 0.7957 (m-40) REVERT: L 182 SER cc_start: 0.8942 (t) cc_final: 0.8518 (p) REVERT: L 224 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8176 (mtt) REVERT: L 261 ARG cc_start: 0.7562 (ttt180) cc_final: 0.7184 (ttm110) REVERT: L 262 ASP cc_start: 0.8092 (m-30) cc_final: 0.7873 (m-30) REVERT: L 304 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7670 (ttmm) REVERT: b 93 ASP cc_start: 0.8464 (m-30) cc_final: 0.8097 (m-30) REVERT: d 11 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7773 (mp0) REVERT: d 136 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7722 (mp0) REVERT: e 58 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8686 (mt0) REVERT: e 93 ASP cc_start: 0.8490 (m-30) cc_final: 0.8153 (m-30) REVERT: f 28 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7752 (mt) REVERT: f 44 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: f 86 LEU cc_start: 0.8562 (tp) cc_final: 0.8238 (tp) REVERT: f 90 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: g 74 LYS cc_start: 0.7142 (mppt) cc_final: 0.6838 (mtpt) REVERT: h 27 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8288 (ptmm) REVERT: h 37 ASP cc_start: 0.8328 (p0) cc_final: 0.8075 (p0) REVERT: h 74 LYS cc_start: 0.7156 (mppt) cc_final: 0.6862 (mmmm) REVERT: h 136 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8160 (mt-10) REVERT: i 6 SER cc_start: 0.8728 (p) cc_final: 0.8520 (t) REVERT: i 58 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8345 (mt0) REVERT: i 74 LYS cc_start: 0.7138 (mppt) cc_final: 0.6831 (mtpt) REVERT: i 136 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8073 (mt-10) REVERT: j 6 SER cc_start: 0.8902 (p) cc_final: 0.8653 (t) REVERT: j 74 LYS cc_start: 0.7194 (mppt) cc_final: 0.6822 (mtpt) REVERT: j 136 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8091 (mt-10) REVERT: k 37 ASP cc_start: 0.8411 (p0) cc_final: 0.8210 (p0) REVERT: k 51 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8061 (p0) REVERT: k 101 ASP cc_start: 0.7765 (m-30) cc_final: 0.7367 (m-30) REVERT: l 88 GLN cc_start: 0.8652 (mt0) cc_final: 0.8345 (mt0) REVERT: l 136 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8091 (mt-10) REVERT: l 143 ARG cc_start: 0.7608 (ttt-90) cc_final: 0.6289 (ttt180) outliers start: 330 outliers final: 164 residues processed: 1116 average time/residue: 0.4994 time to fit residues: 717.0444 Evaluate side-chains 1013 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 804 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 224 MET Chi-restraints excluded: chain K residue 227 ASN Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 282 ARG Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 189 VAL Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 20 ILE Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 58 GLN Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 90 GLU Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 34 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 88 GLN Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 27 LYS Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 58 GLN Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 140 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 51 ASN Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 378 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 401 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 393 optimal weight: 10.0000 chunk 426 optimal weight: 0.9980 chunk 373 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 561 optimal weight: 3.9990 chunk 538 optimal weight: 1.9990 chunk 576 optimal weight: 0.0980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN D 167 ASN E 195 ASN F 195 ASN G 16 ASN H 296 GLN I 195 ASN J 16 ASN J 195 ASN J 230 ASN K 195 ASN a 31 ASN b 60 GLN ** b 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 31 ASN c 60 GLN e 60 GLN ** e 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 31 ASN f 60 GLN g 31 ASN h 7 GLN j 31 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.110155 restraints weight = 56005.852| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.74 r_work: 0.3126 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47784 Z= 0.131 Angle : 0.595 10.278 65136 Z= 0.302 Chirality : 0.045 0.189 7428 Planarity : 0.004 0.033 8424 Dihedral : 6.015 56.770 6476 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.44 % Rotamer: Outliers : 5.56 % Allowed : 21.70 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.10), residues: 5952 helix: -0.04 (0.13), residues: 1440 sheet: 0.09 (0.13), residues: 1476 loop : -1.98 (0.09), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 265 TYR 0.011 0.001 TYR H 157 PHE 0.026 0.001 PHE A 269 TRP 0.006 0.001 TRP J 165 Details of bonding type rmsd covalent geometry : bond 0.00311 (47784) covalent geometry : angle 0.59483 (65136) hydrogen bonds : bond 0.03515 ( 1467) hydrogen bonds : angle 4.64378 ( 4131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 283 poor density : 881 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8167 (t0) cc_final: 0.7940 (t0) REVERT: A 67 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7539 (ttmt) REVERT: A 129 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7046 (p90) REVERT: A 130 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7570 (m-30) REVERT: A 212 LEU cc_start: 0.8516 (tt) cc_final: 0.8138 (tm) REVERT: A 244 LYS cc_start: 0.7660 (mttm) cc_final: 0.7404 (mttm) REVERT: A 245 ASP cc_start: 0.7781 (m-30) cc_final: 0.7500 (m-30) REVERT: A 261 ARG cc_start: 0.7766 (ttt180) cc_final: 0.7372 (ttm110) REVERT: B 24 ASN cc_start: 0.8375 (m-40) cc_final: 0.7976 (m-40) REVERT: B 54 ASP cc_start: 0.8059 (t0) cc_final: 0.7382 (m-30) REVERT: B 129 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.6940 (p90) REVERT: B 130 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: B 203 GLU cc_start: 0.8384 (pt0) cc_final: 0.8167 (pt0) REVERT: B 224 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8556 (mtt) REVERT: B 233 THR cc_start: 0.9138 (t) cc_final: 0.8885 (m) REVERT: B 245 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: C 43 GLU cc_start: 0.7706 (mp0) cc_final: 0.7300 (mp0) REVERT: C 130 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7429 (p0) REVERT: C 146 GLN cc_start: 0.7902 (tp40) cc_final: 0.7683 (tp40) REVERT: C 242 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: C 244 LYS cc_start: 0.8007 (mtmm) cc_final: 0.7621 (mtpt) REVERT: C 315 LYS cc_start: 0.8694 (tmtt) cc_final: 0.8381 (tppp) REVERT: C 321 GLN cc_start: 0.8073 (tp40) cc_final: 0.7586 (tp40) REVERT: C 325 ASP cc_start: 0.7634 (m-30) cc_final: 0.6987 (m-30) REVERT: D 54 ASP cc_start: 0.8123 (t0) cc_final: 0.7893 (t0) REVERT: D 67 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7642 (ttmt) REVERT: D 117 VAL cc_start: 0.7912 (m) cc_final: 0.7693 (p) REVERT: D 129 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7375 (p90) REVERT: D 212 LEU cc_start: 0.8562 (tt) cc_final: 0.8168 (tm) REVERT: D 224 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8416 (mmm) REVERT: D 244 LYS cc_start: 0.7936 (mttm) cc_final: 0.7721 (mttp) REVERT: D 261 ARG cc_start: 0.7715 (ttt180) cc_final: 0.7189 (ttm110) REVERT: E 24 ASN cc_start: 0.8436 (m-40) cc_final: 0.8029 (m-40) REVERT: E 54 ASP cc_start: 0.8030 (t0) cc_final: 0.7378 (m-30) REVERT: E 129 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.6999 (p90) REVERT: E 224 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8032 (mtt) REVERT: E 233 THR cc_start: 0.9129 (t) cc_final: 0.8892 (m) REVERT: E 245 ASP cc_start: 0.8225 (m-30) cc_final: 0.7880 (m-30) REVERT: E 261 ARG cc_start: 0.7813 (ttt180) cc_final: 0.7375 (ttm-80) REVERT: E 325 ASP cc_start: 0.7762 (m-30) cc_final: 0.7277 (m-30) REVERT: F 129 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7065 (p90) REVERT: F 203 GLU cc_start: 0.8153 (pt0) cc_final: 0.7840 (mt-10) REVERT: F 242 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: F 261 ARG cc_start: 0.7868 (ttt180) cc_final: 0.7302 (ttm110) REVERT: F 269 PHE cc_start: 0.8519 (p90) cc_final: 0.7919 (p90) REVERT: F 282 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7668 (mtp85) REVERT: F 313 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8868 (tt) REVERT: F 321 GLN cc_start: 0.7860 (tp40) cc_final: 0.7375 (tp-100) REVERT: F 325 ASP cc_start: 0.7715 (m-30) cc_final: 0.7003 (m-30) REVERT: G 66 ASP cc_start: 0.7750 (t0) cc_final: 0.7311 (t0) REVERT: G 100 ASP cc_start: 0.8327 (p0) cc_final: 0.7685 (p0) REVERT: G 118 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7889 (tt) REVERT: G 142 GLU cc_start: 0.8408 (pt0) cc_final: 0.7755 (tp30) REVERT: G 146 GLN cc_start: 0.8163 (tt0) cc_final: 0.7508 (mm-40) REVERT: G 167 ASN cc_start: 0.8067 (t0) cc_final: 0.7657 (m-40) REVERT: G 182 SER cc_start: 0.8839 (t) cc_final: 0.8532 (p) REVERT: G 211 GLU cc_start: 0.7867 (mp0) cc_final: 0.7657 (pm20) REVERT: G 245 ASP cc_start: 0.8172 (m-30) cc_final: 0.7964 (m-30) REVERT: G 269 PHE cc_start: 0.8655 (p90) cc_final: 0.8443 (p90) REVERT: G 315 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7752 (tmmt) REVERT: G 325 ASP cc_start: 0.8091 (m-30) cc_final: 0.7875 (m-30) REVERT: H 40 TYR cc_start: 0.7687 (m-80) cc_final: 0.7220 (m-80) REVERT: H 53 MET cc_start: 0.8532 (ttp) cc_final: 0.8229 (ttp) REVERT: H 66 ASP cc_start: 0.7863 (t0) cc_final: 0.7435 (t70) REVERT: H 100 ASP cc_start: 0.8236 (p0) cc_final: 0.7749 (p0) REVERT: H 118 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7871 (tt) REVERT: H 130 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: H 211 GLU cc_start: 0.7933 (mp0) cc_final: 0.7510 (pm20) REVERT: H 224 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7559 (mtt) REVERT: H 262 ASP cc_start: 0.7800 (m-30) cc_final: 0.7474 (m-30) REVERT: I 66 ASP cc_start: 0.8005 (t0) cc_final: 0.7559 (t0) REVERT: I 130 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: I 136 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.5609 (pp) REVERT: I 182 SER cc_start: 0.8882 (t) cc_final: 0.8417 (p) REVERT: I 211 GLU cc_start: 0.8143 (mp0) cc_final: 0.7770 (pm20) REVERT: I 224 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8032 (mtt) REVERT: I 262 ASP cc_start: 0.7994 (m-30) cc_final: 0.7683 (m-30) REVERT: J 18 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8649 (tm) REVERT: J 66 ASP cc_start: 0.7384 (t0) cc_final: 0.6951 (t0) REVERT: J 118 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7925 (tt) REVERT: J 129 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7352 (p90) REVERT: J 130 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: J 146 GLN cc_start: 0.8258 (tt0) cc_final: 0.7630 (mm-40) REVERT: J 169 ASP cc_start: 0.8237 (m-30) cc_final: 0.8006 (m-30) REVERT: J 182 SER cc_start: 0.8936 (t) cc_final: 0.8517 (p) REVERT: J 350 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8702 (tp40) REVERT: K 40 TYR cc_start: 0.7690 (m-80) cc_final: 0.7394 (m-80) REVERT: K 66 ASP cc_start: 0.7885 (t0) cc_final: 0.7546 (t70) REVERT: K 149 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6639 (t) REVERT: K 167 ASN cc_start: 0.8333 (t0) cc_final: 0.7755 (m-40) REVERT: K 224 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7457 (mtt) REVERT: K 261 ARG cc_start: 0.7457 (ttt180) cc_final: 0.6765 (ttm110) REVERT: L 66 ASP cc_start: 0.8065 (t0) cc_final: 0.7569 (t0) REVERT: L 136 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.5954 (pp) REVERT: L 182 SER cc_start: 0.8893 (t) cc_final: 0.8523 (p) REVERT: L 211 GLU cc_start: 0.8032 (mp0) cc_final: 0.7565 (pm20) REVERT: L 224 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8118 (mtt) REVERT: L 261 ARG cc_start: 0.7544 (ttt180) cc_final: 0.7227 (ttm110) REVERT: L 262 ASP cc_start: 0.8002 (m-30) cc_final: 0.7780 (m-30) REVERT: L 304 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7676 (ttmm) REVERT: a 106 LEU cc_start: 0.9074 (mp) cc_final: 0.8807 (mp) REVERT: c 90 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: d 11 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7639 (mp0) REVERT: d 136 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7616 (mp0) REVERT: e 93 ASP cc_start: 0.8497 (m-30) cc_final: 0.8147 (m-30) REVERT: f 86 LEU cc_start: 0.8485 (tp) cc_final: 0.8109 (tp) REVERT: g 37 ASP cc_start: 0.8502 (p0) cc_final: 0.8190 (p0) REVERT: g 74 LYS cc_start: 0.7129 (mppt) cc_final: 0.6783 (mtpt) REVERT: g 140 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8700 (ttm) REVERT: h 27 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8374 (ptmm) REVERT: h 37 ASP cc_start: 0.8318 (p0) cc_final: 0.8098 (p0) REVERT: h 74 LYS cc_start: 0.7196 (mppt) cc_final: 0.6926 (mmmm) REVERT: h 136 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8135 (mt-10) REVERT: i 49 VAL cc_start: 0.9318 (m) cc_final: 0.8989 (t) REVERT: i 58 GLN cc_start: 0.8780 (mm110) cc_final: 0.8561 (mt0) REVERT: i 74 LYS cc_start: 0.7129 (mppt) cc_final: 0.6782 (mtpt) REVERT: j 6 SER cc_start: 0.8863 (p) cc_final: 0.8657 (t) REVERT: j 74 LYS cc_start: 0.7121 (mppt) cc_final: 0.6777 (mtpt) REVERT: j 140 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8703 (ttm) REVERT: k 51 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8034 (p0) REVERT: k 101 ASP cc_start: 0.7776 (m-30) cc_final: 0.7357 (m-30) REVERT: l 58 GLN cc_start: 0.8709 (mm110) cc_final: 0.8430 (mt0) REVERT: l 140 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8522 (ttm) outliers start: 283 outliers final: 139 residues processed: 1081 average time/residue: 0.4251 time to fit residues: 589.1165 Evaluate side-chains 979 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 799 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 224 MET Chi-restraints excluded: chain K residue 227 ASN Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 90 GLU Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 34 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 27 LYS Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 140 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 51 ASN Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 42 optimal weight: 5.9990 chunk 206 optimal weight: 0.6980 chunk 491 optimal weight: 5.9990 chunk 557 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 436 optimal weight: 4.9990 chunk 393 optimal weight: 9.9990 chunk 463 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 ASN H 296 GLN c 60 GLN e 58 GLN e 60 GLN f 60 GLN g 31 ASN h 7 GLN i 58 GLN j 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.112532 restraints weight = 56006.863| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.74 r_work: 0.3127 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 47784 Z= 0.124 Angle : 0.579 10.837 65136 Z= 0.292 Chirality : 0.045 0.252 7428 Planarity : 0.004 0.046 8424 Dihedral : 5.760 58.665 6476 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 5.66 % Allowed : 21.93 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.10), residues: 5952 helix: 0.24 (0.13), residues: 1476 sheet: 0.34 (0.14), residues: 1404 loop : -1.90 (0.09), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 265 TYR 0.010 0.001 TYR K 157 PHE 0.019 0.001 PHE E 269 TRP 0.007 0.001 TRP J 165 Details of bonding type rmsd covalent geometry : bond 0.00296 (47784) covalent geometry : angle 0.57880 (65136) hydrogen bonds : bond 0.03300 ( 1467) hydrogen bonds : angle 4.44064 ( 4131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 288 poor density : 863 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8175 (t0) cc_final: 0.7948 (t0) REVERT: A 67 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7508 (ttmt) REVERT: A 129 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7197 (p90) REVERT: A 130 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: A 212 LEU cc_start: 0.8477 (tt) cc_final: 0.8098 (tm) REVERT: A 261 ARG cc_start: 0.7781 (ttt180) cc_final: 0.7287 (ttm110) REVERT: B 24 ASN cc_start: 0.8394 (m-40) cc_final: 0.7979 (m-40) REVERT: B 54 ASP cc_start: 0.8042 (t0) cc_final: 0.7349 (m-30) REVERT: B 129 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.6973 (p90) REVERT: B 130 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: B 203 GLU cc_start: 0.8315 (pt0) cc_final: 0.8092 (pt0) REVERT: B 224 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8507 (mtt) REVERT: B 245 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: B 325 ASP cc_start: 0.7838 (m-30) cc_final: 0.7319 (m-30) REVERT: C 43 GLU cc_start: 0.7580 (mp0) cc_final: 0.7238 (mp0) REVERT: C 66 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6411 (t0) REVERT: C 130 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7440 (p0) REVERT: C 242 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7426 (tp30) REVERT: C 244 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7506 (mtpt) REVERT: C 315 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8389 (tppp) REVERT: C 321 GLN cc_start: 0.7848 (tp40) cc_final: 0.7381 (tp40) REVERT: C 325 ASP cc_start: 0.7644 (m-30) cc_final: 0.6981 (m-30) REVERT: D 54 ASP cc_start: 0.8128 (t0) cc_final: 0.7905 (t0) REVERT: D 67 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7574 (ttmt) REVERT: D 117 VAL cc_start: 0.7868 (m) cc_final: 0.7647 (p) REVERT: D 129 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7476 (p90) REVERT: D 212 LEU cc_start: 0.8467 (tt) cc_final: 0.8040 (tm) REVERT: D 224 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8389 (mmm) REVERT: D 244 LYS cc_start: 0.7886 (mttm) cc_final: 0.7677 (mttm) REVERT: D 261 ARG cc_start: 0.7731 (ttt180) cc_final: 0.7180 (ttm110) REVERT: E 24 ASN cc_start: 0.8408 (m-40) cc_final: 0.7988 (m-40) REVERT: E 39 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: E 54 ASP cc_start: 0.8038 (t0) cc_final: 0.7407 (m-30) REVERT: E 129 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7023 (p90) REVERT: E 130 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: E 187 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7829 (mtp180) REVERT: E 224 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7962 (mtt) REVERT: E 245 ASP cc_start: 0.8240 (m-30) cc_final: 0.7941 (m-30) REVERT: E 261 ARG cc_start: 0.7816 (ttt180) cc_final: 0.7350 (ttm-80) REVERT: E 315 LYS cc_start: 0.8932 (tptp) cc_final: 0.8667 (tptm) REVERT: E 325 ASP cc_start: 0.7750 (m-30) cc_final: 0.7286 (m-30) REVERT: F 129 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7241 (p90) REVERT: F 203 GLU cc_start: 0.8251 (pt0) cc_final: 0.7969 (mt-10) REVERT: F 205 LYS cc_start: 0.8332 (mtpt) cc_final: 0.8028 (mtpp) REVERT: F 224 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7783 (mtt) REVERT: F 261 ARG cc_start: 0.7799 (ttt180) cc_final: 0.7385 (ttm110) REVERT: F 269 PHE cc_start: 0.8588 (p90) cc_final: 0.8123 (p90) REVERT: F 282 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7671 (mtp85) REVERT: F 313 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8844 (tt) REVERT: F 321 GLN cc_start: 0.7780 (tp40) cc_final: 0.7370 (tp40) REVERT: F 325 ASP cc_start: 0.7716 (m-30) cc_final: 0.7066 (m-30) REVERT: G 66 ASP cc_start: 0.7739 (t0) cc_final: 0.7294 (t0) REVERT: G 100 ASP cc_start: 0.8393 (p0) cc_final: 0.7859 (p0) REVERT: G 118 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8004 (tt) REVERT: G 142 GLU cc_start: 0.8401 (pt0) cc_final: 0.7822 (tp30) REVERT: G 146 GLN cc_start: 0.8173 (tt0) cc_final: 0.7411 (mm-40) REVERT: G 167 ASN cc_start: 0.8018 (t0) cc_final: 0.7675 (m-40) REVERT: G 182 SER cc_start: 0.8895 (t) cc_final: 0.8574 (p) REVERT: G 211 GLU cc_start: 0.7857 (mp0) cc_final: 0.7599 (pm20) REVERT: G 315 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7748 (tmmt) REVERT: G 325 ASP cc_start: 0.8066 (m-30) cc_final: 0.7836 (m-30) REVERT: H 40 TYR cc_start: 0.7672 (m-80) cc_final: 0.7175 (m-80) REVERT: H 53 MET cc_start: 0.8539 (ttp) cc_final: 0.8232 (ttp) REVERT: H 66 ASP cc_start: 0.7947 (t0) cc_final: 0.7586 (t70) REVERT: H 100 ASP cc_start: 0.8390 (p0) cc_final: 0.7952 (p0) REVERT: H 118 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7892 (tt) REVERT: H 146 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7640 (mm-40) REVERT: H 211 GLU cc_start: 0.8072 (mp0) cc_final: 0.7689 (pm20) REVERT: H 262 ASP cc_start: 0.7805 (m-30) cc_final: 0.7467 (m-30) REVERT: I 66 ASP cc_start: 0.8007 (t0) cc_final: 0.7511 (t0) REVERT: I 130 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7293 (m-30) REVERT: I 136 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.5713 (pp) REVERT: I 182 SER cc_start: 0.8865 (t) cc_final: 0.8415 (p) REVERT: I 211 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7796 (pm20) REVERT: I 262 ASP cc_start: 0.7962 (m-30) cc_final: 0.7649 (m-30) REVERT: J 66 ASP cc_start: 0.7350 (t0) cc_final: 0.6943 (t0) REVERT: J 129 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7364 (p90) REVERT: J 130 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: J 146 GLN cc_start: 0.8249 (tt0) cc_final: 0.7634 (mm-40) REVERT: J 169 ASP cc_start: 0.8238 (m-30) cc_final: 0.7969 (m-30) REVERT: J 182 SER cc_start: 0.8932 (t) cc_final: 0.8462 (p) REVERT: K 40 TYR cc_start: 0.7717 (m-80) cc_final: 0.7421 (m-80) REVERT: K 66 ASP cc_start: 0.7837 (t0) cc_final: 0.7449 (t70) REVERT: K 103 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8346 (mt) REVERT: K 118 LEU cc_start: 0.8416 (tt) cc_final: 0.8181 (tt) REVERT: K 182 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8316 (m) REVERT: K 261 ARG cc_start: 0.7523 (ttt180) cc_final: 0.6767 (ttm110) REVERT: L 66 ASP cc_start: 0.7990 (t0) cc_final: 0.7454 (t0) REVERT: L 136 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.5981 (pp) REVERT: L 182 SER cc_start: 0.8875 (t) cc_final: 0.8402 (p) REVERT: L 211 GLU cc_start: 0.8033 (mp0) cc_final: 0.7552 (pm20) REVERT: L 224 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8172 (mtt) REVERT: L 261 ARG cc_start: 0.7550 (ttt180) cc_final: 0.7226 (ttm110) REVERT: L 262 ASP cc_start: 0.7957 (m-30) cc_final: 0.7658 (m-30) REVERT: L 304 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7702 (ttmm) REVERT: a 106 LEU cc_start: 0.9097 (mp) cc_final: 0.8789 (mp) REVERT: b 90 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7903 (tt0) REVERT: c 20 ILE cc_start: 0.8707 (mt) cc_final: 0.8425 (pt) REVERT: c 74 LYS cc_start: 0.7529 (mptt) cc_final: 0.7291 (mppt) REVERT: c 90 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: d 11 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7633 (mp0) REVERT: f 20 ILE cc_start: 0.8723 (mt) cc_final: 0.8419 (pt) REVERT: f 74 LYS cc_start: 0.7526 (mptt) cc_final: 0.7299 (mppt) REVERT: f 86 LEU cc_start: 0.8480 (tp) cc_final: 0.8100 (tp) REVERT: g 27 LYS cc_start: 0.8577 (pttm) cc_final: 0.8270 (ptmm) REVERT: g 58 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8487 (mm-40) REVERT: g 74 LYS cc_start: 0.7037 (mppt) cc_final: 0.6765 (mtpt) REVERT: g 140 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8674 (ttm) REVERT: h 74 LYS cc_start: 0.7251 (mppt) cc_final: 0.7007 (mmtm) REVERT: h 136 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8074 (mt-10) REVERT: i 58 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8499 (mt0) REVERT: i 74 LYS cc_start: 0.7061 (mppt) cc_final: 0.6707 (mmtp) REVERT: i 140 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8553 (ttm) REVERT: j 74 LYS cc_start: 0.7093 (mppt) cc_final: 0.6688 (mtpt) REVERT: j 140 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8731 (ttm) REVERT: k 101 ASP cc_start: 0.7771 (m-30) cc_final: 0.7368 (m-30) REVERT: l 58 GLN cc_start: 0.8784 (mm110) cc_final: 0.8465 (mt0) REVERT: l 126 ASP cc_start: 0.9073 (t0) cc_final: 0.8706 (t0) REVERT: l 140 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8390 (ttm) outliers start: 288 outliers final: 148 residues processed: 1067 average time/residue: 0.4223 time to fit residues: 578.0216 Evaluate side-chains 985 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 795 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 187 ARG Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 90 GLU Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 34 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 58 GLN Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 140 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 319 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 393 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 352 optimal weight: 9.9990 chunk 583 optimal weight: 0.8980 chunk 315 optimal weight: 10.0000 chunk 495 optimal weight: 0.0670 chunk 471 optimal weight: 4.9990 overall best weight: 3.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 296 GLN J 230 ASN J 296 GLN L 296 GLN c 60 GLN e 60 GLN g 31 ASN h 7 GLN h 60 GLN j 31 ASN k 60 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108073 restraints weight = 56243.832| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.76 r_work: 0.3092 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 47784 Z= 0.195 Angle : 0.631 10.720 65136 Z= 0.320 Chirality : 0.047 0.258 7428 Planarity : 0.004 0.043 8424 Dihedral : 5.961 56.120 6475 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 6.05 % Allowed : 21.86 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.10), residues: 5952 helix: 0.44 (0.14), residues: 1440 sheet: 0.27 (0.14), residues: 1476 loop : -1.95 (0.09), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 265 TYR 0.010 0.001 TYR K 157 PHE 0.022 0.002 PHE A 269 TRP 0.005 0.001 TRP J 165 Details of bonding type rmsd covalent geometry : bond 0.00482 (47784) covalent geometry : angle 0.63148 (65136) hydrogen bonds : bond 0.03838 ( 1467) hydrogen bonds : angle 4.57310 ( 4131) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 308 poor density : 824 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8179 (t0) cc_final: 0.7968 (t0) REVERT: A 67 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7578 (ttmt) REVERT: A 129 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7350 (p90) REVERT: A 130 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: A 261 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7310 (ttm110) REVERT: A 269 PHE cc_start: 0.8607 (p90) cc_final: 0.8191 (p90) REVERT: A 273 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: B 24 ASN cc_start: 0.8407 (m-40) cc_final: 0.7988 (m-40) REVERT: B 54 ASP cc_start: 0.8160 (t0) cc_final: 0.7422 (m-30) REVERT: B 129 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7469 (p90) REVERT: B 130 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: B 224 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8547 (mtt) REVERT: B 245 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7688 (m-30) REVERT: B 325 ASP cc_start: 0.7813 (m-30) cc_final: 0.7272 (m-30) REVERT: C 43 GLU cc_start: 0.7560 (mp0) cc_final: 0.7198 (mp0) REVERT: C 129 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7168 (p90) REVERT: C 130 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7832 (p0) REVERT: C 146 GLN cc_start: 0.7883 (tp40) cc_final: 0.7620 (tp40) REVERT: C 242 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: C 244 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7509 (mtpt) REVERT: C 269 PHE cc_start: 0.8632 (p90) cc_final: 0.8386 (p90) REVERT: C 271 MET cc_start: 0.9264 (mmm) cc_final: 0.8797 (mmt) REVERT: C 273 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: C 315 LYS cc_start: 0.8698 (tmtt) cc_final: 0.8366 (tppp) REVERT: C 321 GLN cc_start: 0.7857 (tp40) cc_final: 0.7397 (tp40) REVERT: C 325 ASP cc_start: 0.7624 (m-30) cc_final: 0.6930 (m-30) REVERT: D 13 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: D 15 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8089 (pt) REVERT: D 54 ASP cc_start: 0.8140 (t0) cc_final: 0.7932 (t0) REVERT: D 67 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7606 (ttmt) REVERT: D 129 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7494 (p90) REVERT: D 212 LEU cc_start: 0.8497 (tt) cc_final: 0.8260 (tp) REVERT: D 224 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8475 (mmm) REVERT: D 244 LYS cc_start: 0.7893 (mttm) cc_final: 0.7690 (mttm) REVERT: D 261 ARG cc_start: 0.7803 (ttt180) cc_final: 0.7231 (ttm110) REVERT: E 24 ASN cc_start: 0.8415 (m-40) cc_final: 0.7993 (m-40) REVERT: E 54 ASP cc_start: 0.8155 (t0) cc_final: 0.7450 (m-30) REVERT: E 65 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6875 (mt-10) REVERT: E 129 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7364 (p90) REVERT: E 130 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: E 187 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7848 (mtp180) REVERT: E 245 ASP cc_start: 0.8292 (m-30) cc_final: 0.8008 (m-30) REVERT: E 261 ARG cc_start: 0.7944 (ttt180) cc_final: 0.7368 (ttm110) REVERT: E 271 MET cc_start: 0.7491 (mmt) cc_final: 0.7255 (mmt) REVERT: E 273 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: E 315 LYS cc_start: 0.8938 (tptp) cc_final: 0.8675 (tptm) REVERT: F 43 GLU cc_start: 0.7556 (mp0) cc_final: 0.7164 (mp0) REVERT: F 129 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7028 (p90) REVERT: F 203 GLU cc_start: 0.8264 (pt0) cc_final: 0.7988 (mt-10) REVERT: F 205 LYS cc_start: 0.8383 (mtpt) cc_final: 0.8054 (mtpp) REVERT: F 242 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7653 (tp30) REVERT: F 261 ARG cc_start: 0.7867 (ttt180) cc_final: 0.7408 (ttm110) REVERT: F 282 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7925 (mtp85) REVERT: F 313 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8847 (tt) REVERT: F 321 GLN cc_start: 0.7838 (tp40) cc_final: 0.7456 (tp40) REVERT: F 325 ASP cc_start: 0.7802 (m-30) cc_final: 0.7200 (m-30) REVERT: G 66 ASP cc_start: 0.7732 (t0) cc_final: 0.7281 (t0) REVERT: G 118 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7965 (tt) REVERT: G 130 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: G 142 GLU cc_start: 0.8379 (pt0) cc_final: 0.7941 (tp30) REVERT: G 146 GLN cc_start: 0.8204 (tt0) cc_final: 0.7560 (mm-40) REVERT: G 167 ASN cc_start: 0.8194 (t0) cc_final: 0.7785 (m-40) REVERT: G 182 SER cc_start: 0.8973 (t) cc_final: 0.8642 (p) REVERT: G 211 GLU cc_start: 0.7895 (mp0) cc_final: 0.7613 (pm20) REVERT: G 245 ASP cc_start: 0.8247 (m-30) cc_final: 0.7917 (m-30) REVERT: G 315 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.7849 (tmmt) REVERT: H 40 TYR cc_start: 0.7669 (m-80) cc_final: 0.7240 (m-80) REVERT: H 53 MET cc_start: 0.8573 (ttp) cc_final: 0.8277 (ttp) REVERT: H 130 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: H 146 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7589 (mm-40) REVERT: H 262 ASP cc_start: 0.7803 (m-30) cc_final: 0.7480 (m-30) REVERT: I 66 ASP cc_start: 0.7986 (t0) cc_final: 0.7457 (t0) REVERT: I 130 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: I 136 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6340 (pp) REVERT: I 182 SER cc_start: 0.8905 (t) cc_final: 0.8478 (p) REVERT: I 211 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: I 262 ASP cc_start: 0.7988 (m-30) cc_final: 0.7691 (m-30) REVERT: J 15 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8159 (pt) REVERT: J 18 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8685 (tm) REVERT: J 66 ASP cc_start: 0.7313 (t0) cc_final: 0.6909 (t0) REVERT: J 129 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7531 (p90) REVERT: J 130 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: J 146 GLN cc_start: 0.8270 (tt0) cc_final: 0.7676 (mm-40) REVERT: J 169 ASP cc_start: 0.8303 (m-30) cc_final: 0.8019 (m-30) REVERT: K 40 TYR cc_start: 0.7717 (m-80) cc_final: 0.7431 (m-80) REVERT: K 66 ASP cc_start: 0.7860 (t0) cc_final: 0.7436 (t70) REVERT: K 182 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8293 (m) REVERT: K 261 ARG cc_start: 0.7536 (ttt180) cc_final: 0.6902 (ttm110) REVERT: L 130 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: L 136 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6546 (pp) REVERT: L 182 SER cc_start: 0.8912 (t) cc_final: 0.8487 (p) REVERT: L 211 GLU cc_start: 0.8097 (mp0) cc_final: 0.7684 (pm20) REVERT: L 224 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8141 (mtt) REVERT: L 261 ARG cc_start: 0.7591 (ttt180) cc_final: 0.7292 (ttm110) REVERT: L 262 ASP cc_start: 0.7962 (m-30) cc_final: 0.7675 (m-30) REVERT: L 304 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7802 (ttmm) REVERT: b 76 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: b 93 ASP cc_start: 0.8550 (m-30) cc_final: 0.8243 (m-30) REVERT: c 28 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7741 (mp) REVERT: d 11 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7799 (mp0) REVERT: e 44 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8269 (mm-30) REVERT: e 90 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: e 93 ASP cc_start: 0.8554 (m-30) cc_final: 0.8218 (m-30) REVERT: f 28 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7958 (mp) REVERT: f 86 LEU cc_start: 0.8651 (tp) cc_final: 0.8318 (tp) REVERT: g 27 LYS cc_start: 0.8762 (pttm) cc_final: 0.8319 (ptmm) REVERT: g 74 LYS cc_start: 0.7098 (mppt) cc_final: 0.6825 (mtpt) REVERT: g 95 THR cc_start: 0.8808 (p) cc_final: 0.8541 (m) REVERT: h 74 LYS cc_start: 0.7308 (mppt) cc_final: 0.7085 (mmtm) REVERT: h 136 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8147 (mt-10) REVERT: i 49 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.8958 (t) REVERT: i 58 GLN cc_start: 0.8806 (mm110) cc_final: 0.8494 (mt0) REVERT: i 74 LYS cc_start: 0.7003 (mppt) cc_final: 0.6750 (mtpt) REVERT: i 136 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8093 (mt-10) REVERT: j 74 LYS cc_start: 0.7074 (mppt) cc_final: 0.6802 (mtpt) REVERT: k 101 ASP cc_start: 0.7830 (m-30) cc_final: 0.7469 (m-30) REVERT: l 58 GLN cc_start: 0.8838 (mm110) cc_final: 0.8551 (mt0) outliers start: 308 outliers final: 177 residues processed: 1030 average time/residue: 0.3984 time to fit residues: 529.6012 Evaluate side-chains 1004 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 779 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 187 ARG Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 319 MET Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 55 MET Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 90 GLU Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 34 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 55 MET Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 140 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 428 optimal weight: 3.9990 chunk 422 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 556 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 537 optimal weight: 4.9990 chunk 423 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 474 optimal weight: 1.9990 chunk 460 optimal weight: 2.9990 chunk 559 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 277 GLN G 230 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN g 31 ASN h 7 GLN h 60 GLN i 58 GLN j 31 ASN k 60 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109351 restraints weight = 56402.751| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.72 r_work: 0.3080 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 47784 Z= 0.193 Angle : 0.634 9.852 65136 Z= 0.321 Chirality : 0.047 0.227 7428 Planarity : 0.004 0.035 8424 Dihedral : 5.997 56.702 6475 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 6.31 % Allowed : 22.19 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.10), residues: 5952 helix: 0.35 (0.14), residues: 1476 sheet: 0.29 (0.14), residues: 1476 loop : -1.97 (0.09), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 265 TYR 0.011 0.001 TYR f 17 PHE 0.020 0.002 PHE A 269 TRP 0.006 0.001 TRP J 165 Details of bonding type rmsd covalent geometry : bond 0.00478 (47784) covalent geometry : angle 0.63424 (65136) hydrogen bonds : bond 0.03813 ( 1467) hydrogen bonds : angle 4.59187 ( 4131) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 321 poor density : 797 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8234 (t0) cc_final: 0.7985 (t0) REVERT: A 67 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7578 (ttmt) REVERT: A 129 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7410 (p90) REVERT: A 130 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: A 224 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8172 (mpt) REVERT: A 261 ARG cc_start: 0.7864 (ttt180) cc_final: 0.7297 (ttm110) REVERT: B 24 ASN cc_start: 0.8450 (m-40) cc_final: 0.8011 (m-40) REVERT: B 54 ASP cc_start: 0.8101 (t0) cc_final: 0.7334 (m-30) REVERT: B 129 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7546 (p90) REVERT: B 130 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.7923 (m-30) REVERT: B 224 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8605 (mtt) REVERT: B 245 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: B 325 ASP cc_start: 0.7781 (m-30) cc_final: 0.7278 (m-30) REVERT: C 43 GLU cc_start: 0.7681 (mp0) cc_final: 0.7310 (mp0) REVERT: C 129 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7175 (p90) REVERT: C 130 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7930 (p0) REVERT: C 242 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: C 244 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7496 (mtpt) REVERT: C 269 PHE cc_start: 0.8647 (p90) cc_final: 0.8392 (p90) REVERT: C 271 MET cc_start: 0.9288 (mmm) cc_final: 0.8767 (mmt) REVERT: C 273 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: C 315 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8373 (tppp) REVERT: C 321 GLN cc_start: 0.7857 (tp40) cc_final: 0.7391 (tp40) REVERT: C 325 ASP cc_start: 0.7583 (m-30) cc_final: 0.6870 (m-30) REVERT: D 13 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7987 (pt0) REVERT: D 15 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8049 (pt) REVERT: D 54 ASP cc_start: 0.8156 (t0) cc_final: 0.7925 (t0) REVERT: D 67 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7591 (ttmt) REVERT: D 129 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7290 (p90) REVERT: D 205 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8105 (tttm) REVERT: D 212 LEU cc_start: 0.8474 (tt) cc_final: 0.8248 (tp) REVERT: D 224 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8457 (mmm) REVERT: D 244 LYS cc_start: 0.7953 (mttm) cc_final: 0.7752 (mttp) REVERT: D 261 ARG cc_start: 0.7789 (ttt180) cc_final: 0.7246 (ttm110) REVERT: E 24 ASN cc_start: 0.8415 (m-40) cc_final: 0.7979 (m-40) REVERT: E 39 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: E 54 ASP cc_start: 0.8005 (t0) cc_final: 0.7298 (m-30) REVERT: E 129 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7425 (p90) REVERT: E 130 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.7959 (m-30) REVERT: E 187 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7783 (mtp180) REVERT: E 245 ASP cc_start: 0.8300 (m-30) cc_final: 0.8025 (m-30) REVERT: E 261 ARG cc_start: 0.7977 (ttt180) cc_final: 0.7489 (ttm110) REVERT: E 315 LYS cc_start: 0.8954 (tptp) cc_final: 0.8652 (tptm) REVERT: F 43 GLU cc_start: 0.7585 (mp0) cc_final: 0.7210 (mp0) REVERT: F 129 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7241 (p90) REVERT: F 203 GLU cc_start: 0.8240 (pt0) cc_final: 0.7985 (mt-10) REVERT: F 205 LYS cc_start: 0.8380 (mtpt) cc_final: 0.8062 (mtpp) REVERT: F 242 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7662 (tp30) REVERT: F 261 ARG cc_start: 0.7881 (ttt180) cc_final: 0.7420 (ttm110) REVERT: F 269 PHE cc_start: 0.8696 (p90) cc_final: 0.8290 (p90) REVERT: F 271 MET cc_start: 0.9209 (mmm) cc_final: 0.8790 (mmt) REVERT: F 273 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: F 282 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7974 (mtp85) REVERT: F 321 GLN cc_start: 0.7817 (tp40) cc_final: 0.7471 (tp40) REVERT: F 325 ASP cc_start: 0.7680 (m-30) cc_final: 0.7126 (m-30) REVERT: G 54 ASP cc_start: 0.8111 (t0) cc_final: 0.7902 (t0) REVERT: G 118 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7983 (tt) REVERT: G 129 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7452 (p90) REVERT: G 130 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: G 142 GLU cc_start: 0.8347 (pt0) cc_final: 0.7995 (tp30) REVERT: G 146 GLN cc_start: 0.8251 (tt0) cc_final: 0.7619 (mm-40) REVERT: G 167 ASN cc_start: 0.8199 (t0) cc_final: 0.7727 (m-40) REVERT: G 211 GLU cc_start: 0.7925 (mp0) cc_final: 0.7648 (pm20) REVERT: G 245 ASP cc_start: 0.8270 (m-30) cc_final: 0.7911 (m-30) REVERT: G 315 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7881 (tmmt) REVERT: H 40 TYR cc_start: 0.7663 (m-80) cc_final: 0.7306 (m-80) REVERT: H 53 MET cc_start: 0.8581 (ttp) cc_final: 0.8305 (ttp) REVERT: H 93 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8258 (mtmm) REVERT: H 130 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: H 146 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7601 (mm-40) REVERT: H 211 GLU cc_start: 0.7931 (mp0) cc_final: 0.7587 (pm20) REVERT: H 262 ASP cc_start: 0.7816 (m-30) cc_final: 0.7479 (m-30) REVERT: I 66 ASP cc_start: 0.8149 (t0) cc_final: 0.7548 (t0) REVERT: I 130 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: I 136 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6569 (pp) REVERT: I 182 SER cc_start: 0.8876 (t) cc_final: 0.8451 (p) REVERT: I 189 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8787 (p) REVERT: I 211 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: I 262 ASP cc_start: 0.7973 (m-30) cc_final: 0.7700 (m-30) REVERT: J 18 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8586 (tm) REVERT: J 66 ASP cc_start: 0.7526 (t0) cc_final: 0.7148 (t70) REVERT: J 129 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7426 (p90) REVERT: J 130 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: J 146 GLN cc_start: 0.8207 (tt0) cc_final: 0.7619 (mm-40) REVERT: J 169 ASP cc_start: 0.8269 (m-30) cc_final: 0.7976 (m-30) REVERT: J 305 GLU cc_start: 0.7969 (tt0) cc_final: 0.7497 (pt0) REVERT: J 306 GLU cc_start: 0.7781 (mp0) cc_final: 0.7543 (mp0) REVERT: K 40 TYR cc_start: 0.7696 (m-80) cc_final: 0.7434 (m-80) REVERT: K 66 ASP cc_start: 0.7859 (t0) cc_final: 0.7436 (t70) REVERT: K 182 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8283 (m) REVERT: K 261 ARG cc_start: 0.7464 (ttt180) cc_final: 0.6775 (ttm110) REVERT: L 130 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: L 136 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6666 (pp) REVERT: L 182 SER cc_start: 0.8888 (t) cc_final: 0.8469 (p) REVERT: L 211 GLU cc_start: 0.8115 (mp0) cc_final: 0.7698 (pm20) REVERT: L 261 ARG cc_start: 0.7532 (ttt180) cc_final: 0.7239 (ttm110) REVERT: L 262 ASP cc_start: 0.7917 (m-30) cc_final: 0.7656 (m-30) REVERT: L 304 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7886 (mtpp) REVERT: a 106 LEU cc_start: 0.9124 (mp) cc_final: 0.8798 (mp) REVERT: b 93 ASP cc_start: 0.8562 (m-30) cc_final: 0.8262 (m-30) REVERT: c 28 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8101 (mp) REVERT: d 11 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7813 (mp0) REVERT: e 11 GLU cc_start: 0.8251 (mp0) cc_final: 0.8047 (mt-10) REVERT: e 44 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8304 (mm-30) REVERT: e 76 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: e 90 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: e 93 ASP cc_start: 0.8540 (m-30) cc_final: 0.8224 (m-30) REVERT: f 28 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8202 (mp) REVERT: f 44 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8404 (mt-10) REVERT: f 86 LEU cc_start: 0.8659 (tp) cc_final: 0.8338 (tp) REVERT: g 27 LYS cc_start: 0.8780 (pttm) cc_final: 0.8313 (ptmm) REVERT: g 74 LYS cc_start: 0.7142 (mppt) cc_final: 0.6895 (mtpt) REVERT: g 95 THR cc_start: 0.8807 (p) cc_final: 0.8582 (m) REVERT: h 74 LYS cc_start: 0.7342 (mppt) cc_final: 0.7119 (mmtp) REVERT: h 130 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8620 (t0) REVERT: h 136 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8149 (mt-10) REVERT: i 58 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8678 (mt0) REVERT: i 74 LYS cc_start: 0.7024 (mppt) cc_final: 0.6722 (mmtt) REVERT: i 136 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8105 (mt-10) REVERT: j 74 LYS cc_start: 0.7106 (mppt) cc_final: 0.6824 (mtpt) REVERT: k 101 ASP cc_start: 0.7829 (m-30) cc_final: 0.7458 (m-30) REVERT: l 58 GLN cc_start: 0.8847 (mm110) cc_final: 0.8581 (mt0) outliers start: 321 outliers final: 191 residues processed: 1018 average time/residue: 0.3914 time to fit residues: 515.7508 Evaluate side-chains 1001 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 760 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 187 ARG Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 93 LYS Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 20 ILE Chi-restraints excluded: chain a residue 55 MET Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 90 GLU Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 34 SER Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain h residue 130 ASN Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 55 MET Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 140 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 262 optimal weight: 0.4980 chunk 271 optimal weight: 1.9990 chunk 329 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 492 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 284 optimal weight: 0.1980 chunk 201 optimal weight: 7.9990 chunk 575 optimal weight: 3.9990 chunk 129 optimal weight: 0.3980 chunk 99 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 78 ASN L 61 ASN a 111 ASN b 60 GLN e 60 GLN g 31 ASN g 51 ASN h 7 GLN h 60 GLN j 31 ASN k 60 GLN l 58 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115286 restraints weight = 56178.102| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.80 r_work: 0.3185 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 47784 Z= 0.096 Angle : 0.567 10.234 65136 Z= 0.283 Chirality : 0.043 0.205 7428 Planarity : 0.004 0.032 8424 Dihedral : 5.433 57.587 6475 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.93 % Allowed : 25.00 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.10), residues: 5952 helix: 0.60 (0.14), residues: 1476 sheet: 0.56 (0.14), residues: 1404 loop : -1.82 (0.09), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 265 TYR 0.010 0.001 TYR c 17 PHE 0.025 0.001 PHE D 269 TRP 0.008 0.001 TRP J 165 Details of bonding type rmsd covalent geometry : bond 0.00216 (47784) covalent geometry : angle 0.56722 (65136) hydrogen bonds : bond 0.02774 ( 1467) hydrogen bonds : angle 4.24525 ( 4131) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 842 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8222 (t0) cc_final: 0.7963 (t0) REVERT: A 67 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7594 (ttmt) REVERT: A 142 GLU cc_start: 0.7521 (tp30) cc_final: 0.7224 (tp30) REVERT: A 224 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8111 (mpt) REVERT: A 261 ARG cc_start: 0.7811 (ttt180) cc_final: 0.7264 (ttm110) REVERT: B 24 ASN cc_start: 0.8425 (m-40) cc_final: 0.7949 (m-40) REVERT: B 54 ASP cc_start: 0.7905 (t0) cc_final: 0.7240 (m-30) REVERT: B 130 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: B 224 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8445 (mtt) REVERT: B 245 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: C 43 GLU cc_start: 0.7480 (mp0) cc_final: 0.7139 (mp0) REVERT: C 130 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7568 (p0) REVERT: C 315 LYS cc_start: 0.8742 (tmtt) cc_final: 0.8445 (tppp) REVERT: C 321 GLN cc_start: 0.7713 (tp40) cc_final: 0.7256 (tp40) REVERT: C 325 ASP cc_start: 0.7653 (m-30) cc_final: 0.6969 (m-30) REVERT: D 54 ASP cc_start: 0.8143 (t0) cc_final: 0.7900 (t0) REVERT: D 212 LEU cc_start: 0.8493 (tt) cc_final: 0.8114 (tm) REVERT: D 261 ARG cc_start: 0.7731 (ttt180) cc_final: 0.7180 (ttm110) REVERT: E 24 ASN cc_start: 0.8406 (m-40) cc_final: 0.7930 (m-40) REVERT: E 39 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: E 53 MET cc_start: 0.8597 (ttp) cc_final: 0.8243 (ttp) REVERT: E 54 ASP cc_start: 0.7977 (t0) cc_final: 0.7290 (m-30) REVERT: E 57 ASN cc_start: 0.7457 (m-40) cc_final: 0.7183 (m-40) REVERT: E 117 VAL cc_start: 0.7987 (m) cc_final: 0.7744 (p) REVERT: E 129 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.6976 (p90) REVERT: E 231 THR cc_start: 0.7575 (m) cc_final: 0.7365 (t) REVERT: E 245 ASP cc_start: 0.8281 (m-30) cc_final: 0.8040 (m-30) REVERT: E 261 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7371 (ttm110) REVERT: E 321 GLN cc_start: 0.7613 (tp40) cc_final: 0.7392 (tp-100) REVERT: F 43 GLU cc_start: 0.7479 (mp0) cc_final: 0.7108 (mp0) REVERT: F 129 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7289 (p90) REVERT: F 203 GLU cc_start: 0.8182 (pt0) cc_final: 0.7860 (mt-10) REVERT: F 261 ARG cc_start: 0.7808 (ttt180) cc_final: 0.7340 (ttm110) REVERT: F 271 MET cc_start: 0.9202 (mmm) cc_final: 0.8878 (mmt) REVERT: F 313 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8704 (tt) REVERT: F 321 GLN cc_start: 0.7671 (tp40) cc_final: 0.7434 (tp40) REVERT: F 325 ASP cc_start: 0.7608 (m-30) cc_final: 0.7167 (m-30) REVERT: G 66 ASP cc_start: 0.7871 (t0) cc_final: 0.7400 (t0) REVERT: G 118 LEU cc_start: 0.8234 (tt) cc_final: 0.8008 (tt) REVERT: G 142 GLU cc_start: 0.8332 (pt0) cc_final: 0.8011 (tp30) REVERT: G 146 GLN cc_start: 0.8253 (tt0) cc_final: 0.7583 (mm-40) REVERT: G 167 ASN cc_start: 0.8083 (t0) cc_final: 0.7783 (m-40) REVERT: G 211 GLU cc_start: 0.7757 (mp0) cc_final: 0.7461 (pm20) REVERT: G 224 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8177 (mtm) REVERT: G 245 ASP cc_start: 0.8314 (m-30) cc_final: 0.7994 (m-30) REVERT: G 315 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7712 (tmmt) REVERT: H 40 TYR cc_start: 0.7623 (m-80) cc_final: 0.7203 (m-80) REVERT: H 53 MET cc_start: 0.8527 (ttp) cc_final: 0.8215 (ttp) REVERT: H 93 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8213 (mtmm) REVERT: H 130 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: H 142 GLU cc_start: 0.8010 (pt0) cc_final: 0.7739 (tp30) REVERT: H 146 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7463 (mm-40) REVERT: H 211 GLU cc_start: 0.7832 (mp0) cc_final: 0.7520 (pm20) REVERT: H 262 ASP cc_start: 0.7724 (m-30) cc_final: 0.7363 (m-30) REVERT: I 66 ASP cc_start: 0.8101 (t0) cc_final: 0.7534 (t0) REVERT: I 113 THR cc_start: 0.8299 (m) cc_final: 0.8017 (p) REVERT: I 130 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: I 136 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6321 (pp) REVERT: I 143 GLU cc_start: 0.7404 (tp30) cc_final: 0.7069 (tt0) REVERT: I 182 SER cc_start: 0.8730 (t) cc_final: 0.8345 (p) REVERT: I 211 GLU cc_start: 0.8139 (mp0) cc_final: 0.7778 (pm20) REVERT: I 224 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8078 (mtt) REVERT: I 262 ASP cc_start: 0.7853 (m-30) cc_final: 0.7531 (m-30) REVERT: J 118 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7828 (tt) REVERT: J 129 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7389 (p90) REVERT: J 130 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: J 146 GLN cc_start: 0.8188 (tt0) cc_final: 0.7541 (mm-40) REVERT: J 211 GLU cc_start: 0.8431 (tt0) cc_final: 0.8170 (mp0) REVERT: J 224 MET cc_start: 0.8662 (mtt) cc_final: 0.8201 (mtm) REVERT: J 243 ASP cc_start: 0.7382 (t0) cc_final: 0.6795 (t0) REVERT: J 305 GLU cc_start: 0.7847 (tt0) cc_final: 0.7622 (tt0) REVERT: K 40 TYR cc_start: 0.7718 (m-80) cc_final: 0.7369 (m-80) REVERT: K 66 ASP cc_start: 0.7862 (t0) cc_final: 0.7464 (t70) REVERT: K 130 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: K 142 GLU cc_start: 0.8156 (pt0) cc_final: 0.7816 (tp30) REVERT: K 261 ARG cc_start: 0.7372 (ttt180) cc_final: 0.6719 (ttm110) REVERT: K 296 GLN cc_start: 0.8415 (mt0) cc_final: 0.8153 (mt0) REVERT: L 100 ASP cc_start: 0.8418 (p0) cc_final: 0.8188 (p0) REVERT: L 136 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6359 (pp) REVERT: L 182 SER cc_start: 0.8745 (t) cc_final: 0.8346 (p) REVERT: L 211 GLU cc_start: 0.8149 (mp0) cc_final: 0.7744 (pm20) REVERT: L 224 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8111 (mtt) REVERT: L 261 ARG cc_start: 0.7471 (ttt180) cc_final: 0.7173 (ttm110) REVERT: L 262 ASP cc_start: 0.7892 (m-30) cc_final: 0.7618 (m-30) REVERT: L 320 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7457 (p) REVERT: c 20 ILE cc_start: 0.8535 (mt) cc_final: 0.8302 (pt) REVERT: c 28 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8049 (mp) REVERT: d 11 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7512 (mp0) REVERT: f 20 ILE cc_start: 0.8578 (mt) cc_final: 0.8312 (pt) REVERT: f 28 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8132 (mp) REVERT: f 86 LEU cc_start: 0.8516 (tp) cc_final: 0.8149 (tp) REVERT: g 27 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8310 (ptmm) REVERT: g 58 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8391 (mm-40) REVERT: g 74 LYS cc_start: 0.7094 (mppt) cc_final: 0.6746 (mtpt) REVERT: g 95 THR cc_start: 0.8766 (p) cc_final: 0.8512 (m) REVERT: g 140 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8470 (ttm) REVERT: h 74 LYS cc_start: 0.7293 (mppt) cc_final: 0.7092 (mmtm) REVERT: i 58 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8590 (mt0) REVERT: i 140 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8155 (ttm) REVERT: j 74 LYS cc_start: 0.7025 (mppt) cc_final: 0.6653 (mtpt) REVERT: j 140 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8439 (ttm) REVERT: k 27 LYS cc_start: 0.8517 (ttpp) cc_final: 0.8316 (ttpp) REVERT: k 101 ASP cc_start: 0.7763 (m-30) cc_final: 0.7323 (m-30) REVERT: l 58 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: l 126 ASP cc_start: 0.8944 (t0) cc_final: 0.8625 (t0) outliers start: 200 outliers final: 114 residues processed: 974 average time/residue: 0.4153 time to fit residues: 520.4348 Evaluate side-chains 916 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 770 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 93 LYS Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 64 ILE Chi-restraints excluded: chain b residue 101 ASP Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain g residue 34 SER Chi-restraints excluded: chain g residue 51 ASN Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 140 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 58 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 470 optimal weight: 6.9990 chunk 438 optimal weight: 7.9990 chunk 496 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 468 optimal weight: 6.9990 chunk 54 optimal weight: 0.0370 chunk 297 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 333 optimal weight: 8.9990 chunk 209 optimal weight: 8.9990 chunk 442 optimal weight: 6.9990 overall best weight: 2.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 167 ASN G 61 ASN H 296 GLN J 78 ASN ** b 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 88 GLN c 60 GLN e 31 ASN e 60 GLN ** e 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 60 GLN g 31 ASN h 7 GLN h 60 GLN i 51 ASN j 31 ASN k 60 GLN k 63 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110187 restraints weight = 56051.822| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.75 r_work: 0.3111 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 47784 Z= 0.175 Angle : 0.629 14.709 65136 Z= 0.315 Chirality : 0.047 0.234 7428 Planarity : 0.004 0.041 8424 Dihedral : 5.685 58.944 6472 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 4.42 % Allowed : 24.88 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.10), residues: 5952 helix: 0.60 (0.14), residues: 1476 sheet: 0.69 (0.15), residues: 1296 loop : -1.81 (0.09), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 265 TYR 0.016 0.001 TYR A 148 PHE 0.024 0.002 PHE F 269 TRP 0.007 0.001 TRP D 280 Details of bonding type rmsd covalent geometry : bond 0.00433 (47784) covalent geometry : angle 0.62919 (65136) hydrogen bonds : bond 0.03618 ( 1467) hydrogen bonds : angle 4.37982 ( 4131) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 790 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8262 (t0) cc_final: 0.8028 (t0) REVERT: A 67 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7667 (ttmt) REVERT: A 142 GLU cc_start: 0.7620 (tp30) cc_final: 0.7330 (tp30) REVERT: A 224 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8224 (mpt) REVERT: A 261 ARG cc_start: 0.7907 (ttt180) cc_final: 0.7389 (ttm110) REVERT: B 24 ASN cc_start: 0.8425 (m-40) cc_final: 0.7958 (m-40) REVERT: B 54 ASP cc_start: 0.8140 (t0) cc_final: 0.7499 (m-30) REVERT: B 130 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: B 224 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8549 (mtt) REVERT: B 245 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: C 43 GLU cc_start: 0.7452 (mp0) cc_final: 0.7142 (mp0) REVERT: C 129 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7153 (p90) REVERT: C 130 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8023 (OUTLIER) REVERT: C 244 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7483 (mtpt) REVERT: C 271 MET cc_start: 0.9235 (mmm) cc_final: 0.8937 (mmt) REVERT: C 315 LYS cc_start: 0.8699 (tmtt) cc_final: 0.8385 (tppp) REVERT: C 321 GLN cc_start: 0.7821 (tp40) cc_final: 0.7364 (tp40) REVERT: C 325 ASP cc_start: 0.7619 (m-30) cc_final: 0.6901 (m-30) REVERT: D 54 ASP cc_start: 0.8186 (t0) cc_final: 0.7975 (t0) REVERT: D 212 LEU cc_start: 0.8562 (tt) cc_final: 0.8234 (tm) REVERT: D 261 ARG cc_start: 0.7829 (ttt180) cc_final: 0.7318 (ttm110) REVERT: E 24 ASN cc_start: 0.8396 (m-40) cc_final: 0.7929 (m-40) REVERT: E 39 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: E 54 ASP cc_start: 0.8211 (t0) cc_final: 0.7547 (m-30) REVERT: E 129 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7355 (p90) REVERT: E 130 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: E 207 LEU cc_start: 0.9138 (mm) cc_final: 0.8919 (mp) REVERT: E 224 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: E 245 ASP cc_start: 0.8267 (m-30) cc_final: 0.7980 (m-30) REVERT: E 261 ARG cc_start: 0.7932 (ttt180) cc_final: 0.7438 (ttm110) REVERT: F 43 GLU cc_start: 0.7495 (mp0) cc_final: 0.7136 (mp0) REVERT: F 129 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7323 (p90) REVERT: F 203 GLU cc_start: 0.8227 (pt0) cc_final: 0.7907 (mt-10) REVERT: F 261 ARG cc_start: 0.7910 (ttt180) cc_final: 0.7468 (ttm110) REVERT: F 271 MET cc_start: 0.9270 (mmm) cc_final: 0.8995 (mmt) REVERT: F 321 GLN cc_start: 0.7747 (tp40) cc_final: 0.7432 (tp40) REVERT: F 325 ASP cc_start: 0.7663 (m-30) cc_final: 0.7086 (m-30) REVERT: G 130 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.7755 (m-30) REVERT: G 142 GLU cc_start: 0.8242 (pt0) cc_final: 0.8022 (tp30) REVERT: G 146 GLN cc_start: 0.8268 (tt0) cc_final: 0.7664 (mm-40) REVERT: G 167 ASN cc_start: 0.8104 (t0) cc_final: 0.7838 (m-40) REVERT: G 211 GLU cc_start: 0.7760 (mp0) cc_final: 0.7468 (pm20) REVERT: G 245 ASP cc_start: 0.8288 (m-30) cc_final: 0.7968 (m-30) REVERT: G 315 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7723 (tmmt) REVERT: H 40 TYR cc_start: 0.7679 (m-80) cc_final: 0.7302 (m-80) REVERT: H 53 MET cc_start: 0.8633 (ttp) cc_final: 0.8314 (ttp) REVERT: H 65 GLU cc_start: 0.7875 (mp0) cc_final: 0.7656 (mp0) REVERT: H 93 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8349 (mtmm) REVERT: H 142 GLU cc_start: 0.8051 (pt0) cc_final: 0.7830 (tp30) REVERT: H 146 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7567 (mm-40) REVERT: H 211 GLU cc_start: 0.7856 (mp0) cc_final: 0.7543 (pm20) REVERT: H 262 ASP cc_start: 0.7779 (m-30) cc_final: 0.7438 (m-30) REVERT: I 66 ASP cc_start: 0.8127 (t0) cc_final: 0.7548 (t0) REVERT: I 130 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: I 136 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.6625 (pp) REVERT: I 143 GLU cc_start: 0.7603 (tp30) cc_final: 0.7290 (tt0) REVERT: I 182 SER cc_start: 0.8925 (t) cc_final: 0.8439 (p) REVERT: I 211 GLU cc_start: 0.8149 (mp0) cc_final: 0.7788 (pm20) REVERT: I 262 ASP cc_start: 0.7933 (m-30) cc_final: 0.7649 (m-30) REVERT: J 65 GLU cc_start: 0.7907 (mp0) cc_final: 0.7562 (mp0) REVERT: J 129 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7497 (p90) REVERT: J 130 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: J 146 GLN cc_start: 0.8234 (tt0) cc_final: 0.7623 (mm-40) REVERT: J 211 GLU cc_start: 0.8442 (tt0) cc_final: 0.8228 (mp0) REVERT: J 305 GLU cc_start: 0.7871 (tt0) cc_final: 0.7598 (tt0) REVERT: K 40 TYR cc_start: 0.7721 (m-80) cc_final: 0.7408 (m-80) REVERT: K 142 GLU cc_start: 0.8243 (pt0) cc_final: 0.7840 (tp30) REVERT: K 182 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8358 (m) REVERT: K 261 ARG cc_start: 0.7551 (ttt180) cc_final: 0.6929 (ttm110) REVERT: L 118 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7660 (tt) REVERT: L 136 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6642 (pp) REVERT: L 182 SER cc_start: 0.8910 (t) cc_final: 0.8421 (p) REVERT: L 211 GLU cc_start: 0.8180 (mp0) cc_final: 0.7775 (pm20) REVERT: L 261 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7246 (ttm110) REVERT: L 262 ASP cc_start: 0.7931 (m-30) cc_final: 0.7646 (m-30) REVERT: L 304 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7817 (ttmm) REVERT: b 76 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: c 28 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8255 (mp) REVERT: c 136 GLU cc_start: 0.8049 (mp0) cc_final: 0.7738 (mp0) REVERT: d 11 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7728 (mp0) REVERT: d 37 ASP cc_start: 0.8537 (p0) cc_final: 0.8334 (p0) REVERT: e 76 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.6919 (pm20) REVERT: g 27 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8358 (ptmm) REVERT: g 58 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8463 (mm-40) REVERT: g 74 LYS cc_start: 0.7172 (mppt) cc_final: 0.6809 (mtpt) REVERT: i 31 ASN cc_start: 0.8885 (t0) cc_final: 0.8559 (t0) REVERT: i 58 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8646 (mt0) REVERT: i 74 LYS cc_start: 0.7036 (mppt) cc_final: 0.6757 (mtpt) REVERT: j 74 LYS cc_start: 0.7207 (mppt) cc_final: 0.6851 (mtpt) REVERT: k 27 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8329 (ttpp) REVERT: l 31 ASN cc_start: 0.8927 (t0) cc_final: 0.8652 (t0) REVERT: l 58 GLN cc_start: 0.8709 (mm110) cc_final: 0.8481 (mt0) REVERT: l 126 ASP cc_start: 0.9051 (t0) cc_final: 0.8720 (t0) outliers start: 225 outliers final: 146 residues processed: 948 average time/residue: 0.4048 time to fit residues: 494.9063 Evaluate side-chains 933 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 759 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 93 LYS Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 261 ARG Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 108 MET Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 55 MET Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain g residue 34 SER Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 140 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 128 optimal weight: 5.9990 chunk 347 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 530 optimal weight: 0.7980 chunk 343 optimal weight: 6.9990 chunk 537 optimal weight: 0.7980 chunk 404 optimal weight: 4.9990 chunk 315 optimal weight: 3.9990 chunk 579 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 167 ASN G 296 GLN J 16 ASN K 61 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 60 GLN c 60 GLN ** d 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN g 31 ASN g 51 ASN h 7 GLN h 60 GLN j 31 ASN k 60 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.109476 restraints weight = 56582.915| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.77 r_work: 0.3111 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 47784 Z= 0.191 Angle : 0.645 14.633 65136 Z= 0.323 Chirality : 0.047 0.213 7428 Planarity : 0.004 0.049 8424 Dihedral : 5.756 57.320 6470 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 4.13 % Allowed : 25.29 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.10), residues: 5952 helix: 0.53 (0.14), residues: 1476 sheet: 0.56 (0.14), residues: 1380 loop : -1.86 (0.09), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG h 46 TYR 0.017 0.001 TYR A 148 PHE 0.024 0.002 PHE D 269 TRP 0.007 0.001 TRP A 280 Details of bonding type rmsd covalent geometry : bond 0.00471 (47784) covalent geometry : angle 0.64504 (65136) hydrogen bonds : bond 0.03711 ( 1467) hydrogen bonds : angle 4.47070 ( 4131) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 772 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8231 (t0) cc_final: 0.8024 (t0) REVERT: A 67 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7645 (ttmt) REVERT: A 224 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8267 (mpt) REVERT: A 261 ARG cc_start: 0.7910 (ttt180) cc_final: 0.7373 (ttm110) REVERT: B 24 ASN cc_start: 0.8418 (m-40) cc_final: 0.7960 (m-40) REVERT: B 43 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7557 (mp0) REVERT: B 54 ASP cc_start: 0.8060 (t0) cc_final: 0.7401 (m-30) REVERT: B 130 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: B 189 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8905 (p) REVERT: B 224 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8564 (mtt) REVERT: B 245 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: C 43 GLU cc_start: 0.7468 (mp0) cc_final: 0.7170 (mp0) REVERT: C 129 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7213 (p90) REVERT: C 244 LYS cc_start: 0.7927 (mtmm) cc_final: 0.7557 (mtpt) REVERT: C 271 MET cc_start: 0.9247 (mmm) cc_final: 0.8945 (mmt) REVERT: C 315 LYS cc_start: 0.8684 (tmtt) cc_final: 0.8371 (tppp) REVERT: C 321 GLN cc_start: 0.7863 (tp40) cc_final: 0.7426 (tp40) REVERT: C 325 ASP cc_start: 0.7606 (m-30) cc_final: 0.6876 (m-30) REVERT: D 15 LEU cc_start: 0.8408 (pp) cc_final: 0.8168 (pt) REVERT: D 54 ASP cc_start: 0.8214 (t0) cc_final: 0.7997 (t0) REVERT: D 212 LEU cc_start: 0.8543 (tt) cc_final: 0.8193 (tm) REVERT: D 261 ARG cc_start: 0.7836 (ttt180) cc_final: 0.7318 (ttm110) REVERT: E 24 ASN cc_start: 0.8411 (m-40) cc_final: 0.7947 (m-40) REVERT: E 39 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: E 54 ASP cc_start: 0.8200 (t0) cc_final: 0.7518 (m-30) REVERT: E 129 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7527 (p90) REVERT: E 130 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.7992 (m-30) REVERT: E 142 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6934 (tp30) REVERT: E 207 LEU cc_start: 0.9147 (mm) cc_final: 0.8911 (mp) REVERT: E 245 ASP cc_start: 0.8246 (m-30) cc_final: 0.7986 (m-30) REVERT: E 261 ARG cc_start: 0.7946 (ttt180) cc_final: 0.7434 (ttm110) REVERT: F 43 GLU cc_start: 0.7506 (mp0) cc_final: 0.7150 (mp0) REVERT: F 129 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7305 (p90) REVERT: F 203 GLU cc_start: 0.8201 (pt0) cc_final: 0.7866 (mt-10) REVERT: F 261 ARG cc_start: 0.7919 (ttt180) cc_final: 0.7483 (ttm110) REVERT: F 271 MET cc_start: 0.9264 (mmm) cc_final: 0.8983 (mmt) REVERT: F 321 GLN cc_start: 0.7782 (tp40) cc_final: 0.7444 (tp40) REVERT: F 325 ASP cc_start: 0.7655 (m-30) cc_final: 0.7080 (m-30) REVERT: G 129 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7517 (p90) REVERT: G 130 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: G 142 GLU cc_start: 0.8280 (pt0) cc_final: 0.8014 (tp30) REVERT: G 146 GLN cc_start: 0.8256 (tt0) cc_final: 0.7655 (mm-40) REVERT: G 167 ASN cc_start: 0.8115 (t0) cc_final: 0.7887 (m-40) REVERT: G 175 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8764 (m) REVERT: G 211 GLU cc_start: 0.7780 (mp0) cc_final: 0.7474 (pm20) REVERT: G 224 MET cc_start: 0.8819 (mtt) cc_final: 0.8477 (mtm) REVERT: G 245 ASP cc_start: 0.8276 (m-30) cc_final: 0.8061 (m-30) REVERT: G 315 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7836 (tmmt) REVERT: H 40 TYR cc_start: 0.7693 (m-80) cc_final: 0.7355 (m-80) REVERT: H 53 MET cc_start: 0.8606 (ttp) cc_final: 0.8320 (ttp) REVERT: H 65 GLU cc_start: 0.7878 (mp0) cc_final: 0.7675 (mp0) REVERT: H 93 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8387 (mtmm) REVERT: H 130 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: H 142 GLU cc_start: 0.8237 (pt0) cc_final: 0.7912 (tp30) REVERT: H 146 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7547 (mm-40) REVERT: H 211 GLU cc_start: 0.7834 (mp0) cc_final: 0.7514 (pm20) REVERT: H 262 ASP cc_start: 0.7822 (m-30) cc_final: 0.7482 (m-30) REVERT: I 130 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: I 136 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6700 (pp) REVERT: I 143 GLU cc_start: 0.7606 (tp30) cc_final: 0.7295 (tt0) REVERT: I 182 SER cc_start: 0.8913 (t) cc_final: 0.8420 (p) REVERT: I 211 GLU cc_start: 0.8126 (mp0) cc_final: 0.7754 (pm20) REVERT: I 224 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8157 (mtt) REVERT: I 262 ASP cc_start: 0.7925 (m-30) cc_final: 0.7639 (m-30) REVERT: J 129 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7425 (p90) REVERT: J 130 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: J 146 GLN cc_start: 0.8189 (tt0) cc_final: 0.7617 (mm-40) REVERT: J 211 GLU cc_start: 0.8432 (tt0) cc_final: 0.8113 (mp0) REVERT: J 305 GLU cc_start: 0.7864 (tt0) cc_final: 0.7579 (tt0) REVERT: K 40 TYR cc_start: 0.7757 (m-80) cc_final: 0.7447 (m-80) REVERT: K 130 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: K 142 GLU cc_start: 0.8269 (pt0) cc_final: 0.7858 (tp30) REVERT: K 182 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8348 (m) REVERT: K 261 ARG cc_start: 0.7562 (ttt180) cc_final: 0.6911 (ttm110) REVERT: L 136 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.6648 (pp) REVERT: L 182 SER cc_start: 0.8908 (t) cc_final: 0.8415 (p) REVERT: L 211 GLU cc_start: 0.8115 (mp0) cc_final: 0.7713 (pm20) REVERT: L 224 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8125 (mtt) REVERT: L 261 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7210 (ttm110) REVERT: L 262 ASP cc_start: 0.7889 (m-30) cc_final: 0.7581 (m-30) REVERT: L 304 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7820 (ttmm) REVERT: a 106 LEU cc_start: 0.9092 (mp) cc_final: 0.8794 (mp) REVERT: b 90 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: c 26 GLU cc_start: 0.7941 (pt0) cc_final: 0.7714 (pm20) REVERT: c 136 GLU cc_start: 0.8050 (mp0) cc_final: 0.7697 (mp0) REVERT: d 11 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7746 (mp0) REVERT: d 37 ASP cc_start: 0.8568 (p0) cc_final: 0.8342 (p0) REVERT: e 93 ASP cc_start: 0.8513 (m-30) cc_final: 0.8233 (m-30) REVERT: f 26 GLU cc_start: 0.7920 (pt0) cc_final: 0.7719 (pm20) REVERT: g 27 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8355 (ptmm) REVERT: g 58 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8491 (mm-40) REVERT: g 74 LYS cc_start: 0.7212 (mppt) cc_final: 0.6919 (mtpt) REVERT: h 136 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8055 (mt-10) REVERT: i 31 ASN cc_start: 0.8881 (t0) cc_final: 0.8549 (t0) REVERT: i 58 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8701 (mt0) REVERT: i 74 LYS cc_start: 0.7032 (mppt) cc_final: 0.6773 (mtpt) REVERT: j 74 LYS cc_start: 0.7219 (mppt) cc_final: 0.6934 (mtpt) REVERT: j 140 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8842 (ttm) REVERT: k 27 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8362 (ttpp) REVERT: k 101 ASP cc_start: 0.7788 (m-30) cc_final: 0.7499 (m-30) REVERT: l 31 ASN cc_start: 0.8947 (t0) cc_final: 0.8612 (t0) REVERT: l 58 GLN cc_start: 0.8838 (mm110) cc_final: 0.8514 (mt0) REVERT: l 126 ASP cc_start: 0.9029 (t0) cc_final: 0.8697 (t0) REVERT: l 140 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8343 (ttm) outliers start: 210 outliers final: 151 residues processed: 929 average time/residue: 0.3995 time to fit residues: 478.0794 Evaluate side-chains 931 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 747 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 93 LYS Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 146 GLN Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 261 ARG Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 90 GLU Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 108 MET Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain g residue 34 SER Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 140 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 567 optimal weight: 0.9980 chunk 554 optimal weight: 0.5980 chunk 68 optimal weight: 40.0000 chunk 389 optimal weight: 4.9990 chunk 211 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 418 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 420 optimal weight: 9.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 61 ASN ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN K 61 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 60 GLN e 60 GLN g 31 ASN g 51 ASN h 7 GLN j 31 ASN k 60 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108650 restraints weight = 56334.300| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.74 r_work: 0.3095 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 47784 Z= 0.200 Angle : 0.655 14.466 65136 Z= 0.329 Chirality : 0.048 0.314 7428 Planarity : 0.004 0.049 8424 Dihedral : 5.802 57.245 6468 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 4.58 % Allowed : 24.86 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.10), residues: 5952 helix: 0.62 (0.14), residues: 1440 sheet: 0.52 (0.14), residues: 1380 loop : -1.86 (0.09), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 265 TYR 0.017 0.001 TYR D 148 PHE 0.025 0.002 PHE B 269 TRP 0.010 0.001 TRP L 190 Details of bonding type rmsd covalent geometry : bond 0.00495 (47784) covalent geometry : angle 0.65466 (65136) hydrogen bonds : bond 0.03824 ( 1467) hydrogen bonds : angle 4.54816 ( 4131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13538.33 seconds wall clock time: 230 minutes 4.69 seconds (13804.69 seconds total)