Starting phenix.real_space_refine on Tue Sep 24 00:28:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/09_2024/6mrt_9212.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/09_2024/6mrt_9212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/09_2024/6mrt_9212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/09_2024/6mrt_9212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/09_2024/6mrt_9212.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/09_2024/6mrt_9212.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 26832 atoms to isotropic. 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 60 5.16 5 C 17148 2.51 5 N 4320 2.21 5 O 5340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 26868 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 5.31, per 1000 atoms: 0.20 Number of scatterers: 26868 At special positions: 0 Unit cell: (131.61, 131.61, 159.43, 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 60 16.00 O 5340 8.00 N 4320 7.00 C 17148 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: 5.43 Conformation dependent library (CDL) restraints added in 2.7 seconds 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 94.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 8 through 35 removed outlier: 3.664A pdb=" N GLN A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 101 removed outlier: 3.562A pdb=" N PHE A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 139 removed outlier: 3.728A pdb=" N LYS A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 181 removed outlier: 3.838A pdb=" N LEU A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 188 through 206 removed outlier: 3.578A pdb=" N SER A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 265 removed outlier: 3.590A pdb=" N LYS A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 removed outlier: 3.631A pdb=" N ASN A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 35 removed outlier: 3.665A pdb=" N GLN B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 101 removed outlier: 3.561A pdb=" N PHE B 40 " --> pdb=" O PRO B 36 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 50 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 139 removed outlier: 3.729A pdb=" N LYS B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 181 removed outlier: 3.838A pdb=" N LEU B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 188 through 206 removed outlier: 3.577A pdb=" N SER B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 265 removed outlier: 3.590A pdb=" N LYS B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 292 removed outlier: 3.630A pdb=" N ASN B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 35 removed outlier: 3.664A pdb=" N GLN C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 101 removed outlier: 3.562A pdb=" N PHE C 40 " --> pdb=" O PRO C 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 139 removed outlier: 3.729A pdb=" N LYS C 113 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 181 removed outlier: 3.838A pdb=" N LEU C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER C 160 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 171 " --> pdb=" O GLN C 167 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 188 through 206 removed outlier: 3.577A pdb=" N SER C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 265 removed outlier: 3.590A pdb=" N LYS C 234 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 292 removed outlier: 3.630A pdb=" N ASN C 283 " --> pdb=" O LYS C 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 35 removed outlier: 3.665A pdb=" N GLN D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 101 removed outlier: 3.562A pdb=" N PHE D 40 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 50 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 139 removed outlier: 3.728A pdb=" N LYS D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 181 removed outlier: 3.839A pdb=" N LEU D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP D 171 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 188 through 206 removed outlier: 3.578A pdb=" N SER D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 265 removed outlier: 3.590A pdb=" N LYS D 234 " --> pdb=" O LYS D 230 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 292 removed outlier: 3.631A pdb=" N ASN D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 35 removed outlier: 3.664A pdb=" N GLN E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 101 removed outlier: 3.562A pdb=" N PHE E 40 " --> pdb=" O PRO E 36 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE E 50 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN E 52 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA E 95 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 139 removed outlier: 3.729A pdb=" N LYS E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 181 removed outlier: 3.839A pdb=" N LEU E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER E 160 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'E' and resid 188 through 206 removed outlier: 3.577A pdb=" N SER E 195 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 265 removed outlier: 3.590A pdb=" N LYS E 234 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP E 265 " --> pdb=" O ARG E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 292 removed outlier: 3.630A pdb=" N ASN E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 35 removed outlier: 3.664A pdb=" N GLN F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 101 removed outlier: 3.561A pdb=" N PHE F 40 " --> pdb=" O PRO F 36 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE F 50 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN F 52 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 139 removed outlier: 3.729A pdb=" N LYS F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 125 " --> pdb=" O ASP F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 181 removed outlier: 3.838A pdb=" N LEU F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP F 171 " --> pdb=" O GLN F 167 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 188 through 206 removed outlier: 3.577A pdb=" N SER F 195 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 265 removed outlier: 3.589A pdb=" N LYS F 234 " --> pdb=" O LYS F 230 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP F 265 " --> pdb=" O ARG F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 292 removed outlier: 3.630A pdb=" N ASN F 283 " --> pdb=" O LYS F 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 35 removed outlier: 3.665A pdb=" N GLN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 101 removed outlier: 3.563A pdb=" N PHE G 40 " --> pdb=" O PRO G 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA G 95 " --> pdb=" O THR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 139 removed outlier: 3.729A pdb=" N LYS G 113 " --> pdb=" O ALA G 109 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR G 125 " --> pdb=" O ASP G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 181 removed outlier: 3.839A pdb=" N LEU G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP G 171 " --> pdb=" O GLN G 167 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'G' and resid 188 through 206 removed outlier: 3.577A pdb=" N SER G 195 " --> pdb=" O GLY G 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 265 removed outlier: 3.590A pdb=" N LYS G 234 " --> pdb=" O LYS G 230 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU G 256 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP G 265 " --> pdb=" O ARG G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 292 removed outlier: 3.630A pdb=" N ASN G 283 " --> pdb=" O LYS G 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 35 removed outlier: 3.664A pdb=" N GLN H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 101 removed outlier: 3.561A pdb=" N PHE H 40 " --> pdb=" O PRO H 36 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE H 50 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN H 52 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL H 60 " --> pdb=" O GLN H 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 139 removed outlier: 3.728A pdb=" N LYS H 113 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR H 125 " --> pdb=" O ASP H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 181 removed outlier: 3.838A pdb=" N LEU H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN H 154 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER H 160 " --> pdb=" O THR H 156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP H 171 " --> pdb=" O GLN H 167 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 188 through 206 removed outlier: 3.578A pdb=" N SER H 195 " --> pdb=" O GLY H 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE H 198 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 265 removed outlier: 3.590A pdb=" N LYS H 234 " --> pdb=" O LYS H 230 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE H 253 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 292 removed outlier: 3.630A pdb=" N ASN H 283 " --> pdb=" O LYS H 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 35 removed outlier: 3.664A pdb=" N GLN I 33 " --> pdb=" O LYS I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 101 removed outlier: 3.561A pdb=" N PHE I 40 " --> pdb=" O PRO I 36 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN I 52 " --> pdb=" O SER I 48 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL I 60 " --> pdb=" O GLN I 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA I 95 " --> pdb=" O THR I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 139 removed outlier: 3.729A pdb=" N LYS I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR I 125 " --> pdb=" O ASP I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 181 removed outlier: 3.839A pdb=" N LEU I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN I 154 " --> pdb=" O ALA I 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER I 160 " --> pdb=" O THR I 156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN I 167 " --> pdb=" O SER I 163 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP I 171 " --> pdb=" O GLN I 167 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS I 172 " --> pdb=" O SER I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 184 No H-bonds generated for 'chain 'I' and resid 182 through 184' Processing helix chain 'I' and resid 188 through 206 removed outlier: 3.577A pdb=" N SER I 195 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE I 198 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU I 204 " --> pdb=" O ALA I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 265 removed outlier: 3.589A pdb=" N LYS I 234 " --> pdb=" O LYS I 230 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE I 253 " --> pdb=" O ALA I 249 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU I 256 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP I 265 " --> pdb=" O ARG I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 292 removed outlier: 3.630A pdb=" N ASN I 283 " --> pdb=" O LYS I 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 35 removed outlier: 3.665A pdb=" N GLN J 33 " --> pdb=" O LYS J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 101 removed outlier: 3.562A pdb=" N PHE J 40 " --> pdb=" O PRO J 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE J 50 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN J 52 " --> pdb=" O SER J 48 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL J 60 " --> pdb=" O GLN J 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN J 92 " --> pdb=" O GLY J 88 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA J 95 " --> pdb=" O THR J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 139 removed outlier: 3.729A pdb=" N LYS J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP J 114 " --> pdb=" O SER J 110 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR J 125 " --> pdb=" O ASP J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 181 removed outlier: 3.839A pdb=" N LEU J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN J 154 " --> pdb=" O ALA J 150 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER J 160 " --> pdb=" O THR J 156 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP J 171 " --> pdb=" O GLN J 167 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS J 172 " --> pdb=" O SER J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 184 No H-bonds generated for 'chain 'J' and resid 182 through 184' Processing helix chain 'J' and resid 188 through 206 removed outlier: 3.577A pdb=" N SER J 195 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE J 198 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU J 204 " --> pdb=" O ALA J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 265 removed outlier: 3.589A pdb=" N LYS J 234 " --> pdb=" O LYS J 230 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE J 253 " --> pdb=" O ALA J 249 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU J 256 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP J 265 " --> pdb=" O ARG J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 292 removed outlier: 3.630A pdb=" N ASN J 283 " --> pdb=" O LYS J 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 35 removed outlier: 3.664A pdb=" N GLN K 33 " --> pdb=" O LYS K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 101 removed outlier: 3.562A pdb=" N PHE K 40 " --> pdb=" O PRO K 36 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE K 50 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL K 60 " --> pdb=" O GLN K 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU K 61 " --> pdb=" O ALA K 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN K 92 " --> pdb=" O GLY K 88 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA K 95 " --> pdb=" O THR K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 139 removed outlier: 3.729A pdb=" N LYS K 113 " --> pdb=" O ALA K 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR K 125 " --> pdb=" O ASP K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 181 removed outlier: 3.839A pdb=" N LEU K 149 " --> pdb=" O SER K 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN K 154 " --> pdb=" O ALA K 150 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER K 160 " --> pdb=" O THR K 156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN K 167 " --> pdb=" O SER K 163 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP K 171 " --> pdb=" O GLN K 167 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS K 172 " --> pdb=" O SER K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 184 No H-bonds generated for 'chain 'K' and resid 182 through 184' Processing helix chain 'K' and resid 188 through 206 removed outlier: 3.578A pdb=" N SER K 195 " --> pdb=" O GLY K 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE K 198 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU K 204 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 265 removed outlier: 3.590A pdb=" N LYS K 234 " --> pdb=" O LYS K 230 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE K 253 " --> pdb=" O ALA K 249 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU K 256 " --> pdb=" O GLU K 252 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP K 265 " --> pdb=" O ARG K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 292 removed outlier: 3.631A pdb=" N ASN K 283 " --> pdb=" O LYS K 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 35 removed outlier: 3.665A pdb=" N GLN L 33 " --> pdb=" O LYS L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 101 removed outlier: 3.562A pdb=" N PHE L 40 " --> pdb=" O PRO L 36 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE L 50 " --> pdb=" O GLU L 46 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN L 52 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL L 60 " --> pdb=" O GLN L 56 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN L 92 " --> pdb=" O GLY L 88 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 139 removed outlier: 3.729A pdb=" N LYS L 113 " --> pdb=" O ALA L 109 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR L 125 " --> pdb=" O ASP L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 181 removed outlier: 3.838A pdb=" N LEU L 149 " --> pdb=" O SER L 145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN L 154 " --> pdb=" O ALA L 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER L 160 " --> pdb=" O THR L 156 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN L 167 " --> pdb=" O SER L 163 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP L 171 " --> pdb=" O GLN L 167 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS L 172 " --> pdb=" O SER L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 184 No H-bonds generated for 'chain 'L' and resid 182 through 184' Processing helix chain 'L' and resid 188 through 206 removed outlier: 3.577A pdb=" N SER L 195 " --> pdb=" O GLY L 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE L 198 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU L 204 " --> pdb=" O ALA L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 265 removed outlier: 3.589A pdb=" N LYS L 234 " --> pdb=" O LYS L 230 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE L 253 " --> pdb=" O ALA L 249 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU L 256 " --> pdb=" O GLU L 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP L 265 " --> pdb=" O ARG L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 292 removed outlier: 3.630A pdb=" N ASN L 283 " --> pdb=" O LYS L 279 " (cutoff:3.500A) 2521 hydrogen bonds defined for protein. 7563 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: 7.14 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7198 1.34 - 1.45: 4216 1.45 - 1.57: 15730 1.57 - 1.68: 0 1.68 - 1.80: 96 Bond restraints: 27240 Sorted by residual: bond pdb=" C ILE I 208 " pdb=" N PRO I 209 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.22e+00 bond pdb=" C ILE E 208 " pdb=" N PRO E 209 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.18e+00 bond pdb=" CB GLN B 131 " pdb=" CG GLN B 131 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" C ILE L 208 " pdb=" N PRO L 209 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.11e+00 bond pdb=" CB GLN C 131 " pdb=" CG GLN C 131 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.11e+00 ... (remaining 27235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 36058 2.49 - 4.99: 638 4.99 - 7.48: 24 7.48 - 9.97: 36 9.97 - 12.47: 24 Bond angle restraints: 36780 Sorted by residual: angle pdb=" CA LEU I 148 " pdb=" CB LEU I 148 " pdb=" CG LEU I 148 " ideal model delta sigma weight residual 116.30 128.77 -12.47 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA LEU B 148 " pdb=" CB LEU B 148 " pdb=" CG LEU B 148 " ideal model delta sigma weight residual 116.30 128.76 -12.46 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA LEU J 148 " pdb=" CB LEU J 148 " pdb=" CG LEU J 148 " ideal model delta sigma weight residual 116.30 128.74 -12.44 3.50e+00 8.16e-02 1.26e+01 angle pdb=" CA LEU H 148 " pdb=" CB LEU H 148 " pdb=" CG LEU H 148 " ideal model delta sigma weight residual 116.30 128.74 -12.44 3.50e+00 8.16e-02 1.26e+01 angle pdb=" CA LEU A 148 " pdb=" CB LEU A 148 " pdb=" CG LEU A 148 " ideal model delta sigma weight residual 116.30 128.73 -12.43 3.50e+00 8.16e-02 1.26e+01 ... (remaining 36775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 15758 16.20 - 32.40: 634 32.40 - 48.60: 216 48.60 - 64.80: 0 64.80 - 81.00: 24 Dihedral angle restraints: 16632 sinusoidal: 6516 harmonic: 10116 Sorted by residual: dihedral pdb=" CA ASP I 102 " pdb=" C ASP I 102 " pdb=" N GLU I 103 " pdb=" CA GLU I 103 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP A 102 " pdb=" C ASP A 102 " pdb=" N GLU A 103 " pdb=" CA GLU A 103 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP B 102 " pdb=" C ASP B 102 " pdb=" N GLU B 103 " pdb=" CA GLU B 103 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 16629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2723 0.042 - 0.085: 1350 0.085 - 0.127: 223 0.127 - 0.170: 12 0.170 - 0.212: 24 Chirality restraints: 4332 Sorted by residual: chirality pdb=" CG LEU E 135 " pdb=" CB LEU E 135 " pdb=" CD1 LEU E 135 " pdb=" CD2 LEU E 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU B 135 " pdb=" CB LEU B 135 " pdb=" CD1 LEU B 135 " pdb=" CD2 LEU B 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU L 135 " pdb=" CB LEU L 135 " pdb=" CD1 LEU L 135 " pdb=" CD2 LEU L 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 4329 not shown) Planarity restraints: 4632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 86 " -0.019 2.00e-02 2.50e+03 1.24e-02 3.84e+00 pdb=" CG TRP D 86 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP D 86 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 86 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 86 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP D 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 86 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 86 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 86 " -0.019 2.00e-02 2.50e+03 1.23e-02 3.78e+00 pdb=" CG TRP K 86 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP K 86 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP K 86 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP K 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 86 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP K 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 86 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 86 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP K 86 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 86 " 0.019 2.00e-02 2.50e+03 1.22e-02 3.74e+00 pdb=" CG TRP I 86 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP I 86 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP I 86 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP I 86 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 86 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP I 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 86 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I 86 " 0.000 2.00e-02 2.50e+03 ... (remaining 4629 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5839 2.79 - 3.32: 25573 3.32 - 3.84: 44717 3.84 - 4.37: 49436 4.37 - 4.90: 88479 Nonbonded interactions: 214044 Sorted by model distance: nonbonded pdb=" OH TYR D 54 " pdb=" OD2 ASP D 158 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR I 54 " pdb=" OD2 ASP I 158 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR L 54 " pdb=" OD2 ASP L 158 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR J 54 " pdb=" OD2 ASP J 158 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR K 54 " pdb=" OD2 ASP K 158 " model vdw 2.261 3.040 ... (remaining 214039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 38.890 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 0.064 27240 Z= 0.494 Angle : 0.899 12.467 36780 Z= 0.468 Chirality : 0.047 0.212 4332 Planarity : 0.006 0.039 4632 Dihedral : 10.675 81.004 10080 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.82 % Allowed : 3.67 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.12), residues: 3396 helix: -0.60 (0.08), residues: 3156 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.006 TRP D 86 HIS 0.006 0.004 HIS A 292 PHE 0.020 0.003 PHE F 101 TYR 0.020 0.003 TYR A 54 ARG 0.006 0.001 ARG L 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 526 time to evaluate : 2.227 Fit side-chains REVERT: A 45 LYS cc_start: 0.8071 (mttm) cc_final: 0.7723 (mtpt) REVERT: A 267 ASP cc_start: 0.8015 (t0) cc_final: 0.7687 (t0) REVERT: A 281 MET cc_start: 0.8508 (mtp) cc_final: 0.8150 (mtp) REVERT: B 15 ASN cc_start: 0.7716 (m-40) cc_final: 0.7296 (m110) REVERT: B 98 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8460 (mt) REVERT: B 102 ASP cc_start: 0.7963 (t0) cc_final: 0.7714 (m-30) REVERT: B 267 ASP cc_start: 0.7984 (t0) cc_final: 0.7671 (t0) REVERT: C 15 ASN cc_start: 0.7713 (m-40) cc_final: 0.7448 (m110) REVERT: C 45 LYS cc_start: 0.8164 (mttm) cc_final: 0.7724 (mtpt) REVERT: C 103 GLU cc_start: 0.7482 (mp0) cc_final: 0.7111 (mp0) REVERT: C 105 ASN cc_start: 0.8265 (t0) cc_final: 0.8061 (t0) REVERT: C 267 ASP cc_start: 0.7732 (t0) cc_final: 0.7397 (t0) REVERT: D 103 GLU cc_start: 0.7480 (mp0) cc_final: 0.7267 (mp0) REVERT: D 267 ASP cc_start: 0.7841 (t0) cc_final: 0.7524 (t0) REVERT: D 270 MET cc_start: 0.9130 (mmm) cc_final: 0.8704 (mmp) REVERT: D 281 MET cc_start: 0.8418 (mtp) cc_final: 0.8100 (mtp) REVERT: E 15 ASN cc_start: 0.7519 (m-40) cc_final: 0.7227 (m110) REVERT: E 98 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8577 (mm) REVERT: E 114 ASP cc_start: 0.7830 (m-30) cc_final: 0.7615 (m-30) REVERT: E 267 ASP cc_start: 0.7697 (t0) cc_final: 0.7379 (t0) REVERT: F 216 LYS cc_start: 0.7916 (tptt) cc_final: 0.7655 (ttmt) REVERT: F 267 ASP cc_start: 0.7683 (t0) cc_final: 0.7376 (t0) REVERT: G 103 GLU cc_start: 0.7560 (mp0) cc_final: 0.7262 (mp0) REVERT: G 216 LYS cc_start: 0.7905 (tptt) cc_final: 0.7663 (ttmt) REVERT: G 267 ASP cc_start: 0.7874 (t0) cc_final: 0.7500 (t0) REVERT: H 15 ASN cc_start: 0.7531 (m-40) cc_final: 0.7312 (m110) REVERT: H 42 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7156 (pt0) REVERT: H 98 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8575 (mm) REVERT: H 114 ASP cc_start: 0.7645 (m-30) cc_final: 0.7440 (m-30) REVERT: H 267 ASP cc_start: 0.7932 (t0) cc_final: 0.7649 (t0) REVERT: I 45 LYS cc_start: 0.8105 (mttm) cc_final: 0.7784 (mtpt) REVERT: I 103 GLU cc_start: 0.7387 (mp0) cc_final: 0.7038 (mp0) REVERT: I 132 LYS cc_start: 0.8359 (mtpp) cc_final: 0.8136 (mtmm) REVERT: I 267 ASP cc_start: 0.7603 (t0) cc_final: 0.7354 (t70) REVERT: J 42 GLU cc_start: 0.7242 (mt-10) cc_final: 0.7028 (pt0) REVERT: J 45 LYS cc_start: 0.8063 (mttm) cc_final: 0.7751 (mtpt) REVERT: J 267 ASP cc_start: 0.7840 (t0) cc_final: 0.7543 (t0) REVERT: J 270 MET cc_start: 0.9151 (mmm) cc_final: 0.8709 (mmp) REVERT: J 281 MET cc_start: 0.8485 (mtp) cc_final: 0.8086 (mtp) REVERT: K 15 ASN cc_start: 0.7768 (m-40) cc_final: 0.7396 (m110) REVERT: K 102 ASP cc_start: 0.7960 (t0) cc_final: 0.7621 (m-30) REVERT: K 114 ASP cc_start: 0.7901 (m-30) cc_final: 0.7682 (m-30) REVERT: K 267 ASP cc_start: 0.7638 (t0) cc_final: 0.7313 (t0) REVERT: L 15 ASN cc_start: 0.7790 (m-40) cc_final: 0.7482 (m110) REVERT: L 42 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7171 (mm-30) REVERT: L 267 ASP cc_start: 0.7824 (t0) cc_final: 0.7510 (t0) outliers start: 24 outliers final: 0 residues processed: 550 average time/residue: 1.3243 time to fit residues: 824.1265 Evaluate side-chains 274 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 271 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 112 GLN B 52 GLN B 112 GLN C 28 ASN C 52 GLN D 28 ASN D 52 GLN D 112 GLN E 28 ASN E 52 GLN E 112 GLN F 28 ASN F 52 GLN G 52 GLN G 112 GLN H 52 GLN H 112 GLN I 28 ASN I 52 GLN J 28 ASN J 52 GLN J 112 GLN K 52 GLN K 112 GLN L 28 ASN L 52 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 27240 Z= 0.263 Angle : 0.546 7.611 36780 Z= 0.284 Chirality : 0.035 0.152 4332 Planarity : 0.003 0.032 4632 Dihedral : 3.750 35.300 3618 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 3.47 % Allowed : 6.84 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.14), residues: 3396 helix: 1.69 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.33 (0.26), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 86 HIS 0.004 0.002 HIS L 292 PHE 0.011 0.002 PHE C 101 TYR 0.017 0.002 TYR H 54 ARG 0.002 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 323 time to evaluate : 2.320 Fit side-chains REVERT: A 45 LYS cc_start: 0.8017 (mttm) cc_final: 0.7662 (mtpt) REVERT: A 129 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6911 (mm-30) REVERT: A 210 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6876 (mm-30) REVERT: A 234 LYS cc_start: 0.7940 (mttp) cc_final: 0.7684 (mtmt) REVERT: A 267 ASP cc_start: 0.8087 (t0) cc_final: 0.7686 (t0) REVERT: B 15 ASN cc_start: 0.7611 (m-40) cc_final: 0.7215 (m110) REVERT: B 98 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8316 (mt) REVERT: B 102 ASP cc_start: 0.7963 (t0) cc_final: 0.7689 (m-30) REVERT: B 216 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7638 (tptp) REVERT: B 267 ASP cc_start: 0.8112 (t0) cc_final: 0.7775 (t0) REVERT: C 15 ASN cc_start: 0.7764 (m-40) cc_final: 0.7439 (m110) REVERT: C 18 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: C 45 LYS cc_start: 0.8137 (mttm) cc_final: 0.7725 (mtpt) REVERT: C 129 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7024 (mm-30) REVERT: C 210 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7032 (mm-30) REVERT: C 216 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7783 (tmtm) REVERT: C 267 ASP cc_start: 0.7814 (t0) cc_final: 0.7482 (t0) REVERT: D 129 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6892 (mm-30) REVERT: D 210 GLU cc_start: 0.7184 (tp30) cc_final: 0.6731 (mm-30) REVERT: D 267 ASP cc_start: 0.7928 (t0) cc_final: 0.7551 (t0) REVERT: E 15 ASN cc_start: 0.7518 (m-40) cc_final: 0.7206 (m110) REVERT: E 114 ASP cc_start: 0.7760 (m-30) cc_final: 0.7550 (m-30) REVERT: E 216 LYS cc_start: 0.7945 (tptt) cc_final: 0.7743 (tptp) REVERT: E 267 ASP cc_start: 0.8033 (t0) cc_final: 0.7714 (t0) REVERT: F 56 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: F 129 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6980 (mm-30) REVERT: F 267 ASP cc_start: 0.7811 (t0) cc_final: 0.7487 (t0) REVERT: G 18 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6748 (mt-10) REVERT: G 103 GLU cc_start: 0.7468 (mp0) cc_final: 0.7199 (mp0) REVERT: G 129 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6877 (mm-30) REVERT: G 210 GLU cc_start: 0.7174 (tp30) cc_final: 0.6717 (mm-30) REVERT: G 216 LYS cc_start: 0.7880 (tptt) cc_final: 0.7558 (ttmm) REVERT: G 267 ASP cc_start: 0.8013 (t0) cc_final: 0.7655 (t0) REVERT: H 15 ASN cc_start: 0.7734 (m-40) cc_final: 0.7402 (m110) REVERT: H 114 ASP cc_start: 0.7632 (m-30) cc_final: 0.7416 (m-30) REVERT: H 267 ASP cc_start: 0.8062 (t0) cc_final: 0.7759 (t0) REVERT: I 45 LYS cc_start: 0.8167 (mttm) cc_final: 0.7718 (mtpt) REVERT: I 129 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7007 (mm-30) REVERT: I 210 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: I 216 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7742 (tmtm) REVERT: I 267 ASP cc_start: 0.7818 (t0) cc_final: 0.7514 (t0) REVERT: J 45 LYS cc_start: 0.8006 (mttm) cc_final: 0.7620 (mtpt) REVERT: J 107 LYS cc_start: 0.8661 (tttp) cc_final: 0.8388 (mtmt) REVERT: J 210 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6969 (mm-30) REVERT: J 216 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7335 (tmtm) REVERT: J 267 ASP cc_start: 0.7903 (t0) cc_final: 0.7537 (t70) REVERT: K 15 ASN cc_start: 0.7692 (m-40) cc_final: 0.7279 (m110) REVERT: K 18 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6959 (mt-10) REVERT: K 102 ASP cc_start: 0.8024 (t0) cc_final: 0.7630 (m-30) REVERT: K 114 ASP cc_start: 0.7765 (m-30) cc_final: 0.7557 (m-30) REVERT: K 216 LYS cc_start: 0.7943 (tptt) cc_final: 0.7740 (tptp) REVERT: K 267 ASP cc_start: 0.7878 (t0) cc_final: 0.7548 (t0) REVERT: L 15 ASN cc_start: 0.7729 (m-40) cc_final: 0.7378 (m110) REVERT: L 18 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: L 129 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6991 (mm-30) REVERT: L 216 LYS cc_start: 0.7977 (tttp) cc_final: 0.7590 (tmtm) REVERT: L 267 ASP cc_start: 0.7837 (t0) cc_final: 0.7523 (t0) outliers start: 102 outliers final: 15 residues processed: 379 average time/residue: 1.3489 time to fit residues: 579.5211 Evaluate side-chains 299 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 271 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 197 SER Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 210 GLU Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 118 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 0.7980 chunk 330 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 245 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 52 GLN D 52 GLN E 52 GLN G 52 GLN H 52 GLN J 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 27240 Z= 0.151 Angle : 0.417 5.122 36780 Z= 0.226 Chirality : 0.032 0.129 4332 Planarity : 0.003 0.028 4632 Dihedral : 3.303 36.293 3614 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.67 % Allowed : 9.32 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.14), residues: 3396 helix: 3.01 (0.09), residues: 3096 sheet: None (None), residues: 0 loop : -1.50 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 86 HIS 0.002 0.001 HIS E 292 PHE 0.010 0.001 PHE E 50 TYR 0.015 0.001 TYR B 54 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 324 time to evaluate : 2.297 Fit side-chains REVERT: A 45 LYS cc_start: 0.7942 (mttm) cc_final: 0.7578 (mtpt) REVERT: A 210 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6753 (mm-30) REVERT: A 216 LYS cc_start: 0.7904 (tmtm) cc_final: 0.7480 (ttmm) REVERT: A 267 ASP cc_start: 0.8054 (t0) cc_final: 0.7701 (t0) REVERT: B 15 ASN cc_start: 0.7464 (m-40) cc_final: 0.7098 (m110) REVERT: B 18 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6722 (mt-10) REVERT: B 102 ASP cc_start: 0.7933 (t0) cc_final: 0.7562 (m-30) REVERT: B 267 ASP cc_start: 0.8110 (t0) cc_final: 0.7765 (t0) REVERT: C 45 LYS cc_start: 0.8083 (mttm) cc_final: 0.7706 (mtpt) REVERT: C 107 LYS cc_start: 0.8586 (tttp) cc_final: 0.8355 (tttt) REVERT: C 129 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6942 (mm-30) REVERT: C 132 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8419 (mttp) REVERT: C 216 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7566 (tmtm) REVERT: C 267 ASP cc_start: 0.7807 (t0) cc_final: 0.7476 (t0) REVERT: D 267 ASP cc_start: 0.8057 (t0) cc_final: 0.7633 (t0) REVERT: E 15 ASN cc_start: 0.7337 (m-40) cc_final: 0.7019 (m110) REVERT: E 107 LYS cc_start: 0.8548 (tptm) cc_final: 0.8298 (tttt) REVERT: E 114 ASP cc_start: 0.7595 (m-30) cc_final: 0.7374 (m-30) REVERT: E 118 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8020 (mtmm) REVERT: E 267 ASP cc_start: 0.8062 (t0) cc_final: 0.7725 (t0) REVERT: F 129 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7016 (mm-30) REVERT: F 132 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8310 (mtmp) REVERT: F 216 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7510 (tmtm) REVERT: F 267 ASP cc_start: 0.7796 (t0) cc_final: 0.7473 (t0) REVERT: G 18 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6685 (mt-10) REVERT: G 129 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6912 (mm-30) REVERT: G 216 LYS cc_start: 0.7773 (tptt) cc_final: 0.7502 (ttmm) REVERT: G 267 ASP cc_start: 0.8045 (t0) cc_final: 0.7680 (t0) REVERT: H 15 ASN cc_start: 0.7652 (m-40) cc_final: 0.7317 (m110) REVERT: H 18 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6884 (mt-10) REVERT: H 106 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7128 (pm20) REVERT: H 267 ASP cc_start: 0.8114 (t0) cc_final: 0.7770 (t0) REVERT: I 45 LYS cc_start: 0.8019 (mttm) cc_final: 0.7577 (mtpt) REVERT: I 129 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6983 (mm-30) REVERT: I 216 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7562 (tmtm) REVERT: I 267 ASP cc_start: 0.7779 (t0) cc_final: 0.7446 (t0) REVERT: J 45 LYS cc_start: 0.7947 (mttm) cc_final: 0.7564 (mtpt) REVERT: J 56 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.6864 (tm130) REVERT: J 62 VAL cc_start: 0.7709 (t) cc_final: 0.7502 (t) REVERT: J 210 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6858 (mm-30) REVERT: J 216 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7502 (ttmm) REVERT: J 267 ASP cc_start: 0.7937 (t0) cc_final: 0.7573 (t0) REVERT: K 15 ASN cc_start: 0.7500 (m-40) cc_final: 0.7117 (m110) REVERT: K 18 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6819 (mt-10) REVERT: K 102 ASP cc_start: 0.7989 (t0) cc_final: 0.7578 (m-30) REVERT: K 114 ASP cc_start: 0.7596 (m-30) cc_final: 0.7373 (m-30) REVERT: K 118 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8024 (mtmm) REVERT: K 234 LYS cc_start: 0.7864 (mttm) cc_final: 0.7654 (mtmt) REVERT: K 267 ASP cc_start: 0.8041 (t0) cc_final: 0.7704 (t0) REVERT: L 118 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7479 (tttt) REVERT: L 129 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7005 (mm-30) REVERT: L 267 ASP cc_start: 0.7776 (t0) cc_final: 0.7457 (t0) outliers start: 49 outliers final: 13 residues processed: 357 average time/residue: 1.3154 time to fit residues: 534.5353 Evaluate side-chains 281 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 255 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain I residue 197 SER Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain J residue 56 GLN Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 210 GLU Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 118 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 290 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN C 52 GLN E 28 ASN G 28 ASN I 56 GLN L 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 27240 Z= 0.242 Angle : 0.488 6.885 36780 Z= 0.260 Chirality : 0.034 0.148 4332 Planarity : 0.003 0.029 4632 Dihedral : 3.287 15.742 3612 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 2.14 % Allowed : 11.50 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.24 (0.14), residues: 3396 helix: 3.15 (0.09), residues: 3084 sheet: None (None), residues: 0 loop : -1.40 (0.29), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 86 HIS 0.004 0.002 HIS I 292 PHE 0.012 0.002 PHE D 50 TYR 0.018 0.002 TYR C 54 ARG 0.001 0.000 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 266 time to evaluate : 2.337 Fit side-chains REVERT: A 45 LYS cc_start: 0.7941 (mttm) cc_final: 0.7574 (mtpt) REVERT: A 46 GLU cc_start: 0.7717 (tp30) cc_final: 0.7506 (tp30) REVERT: A 210 GLU cc_start: 0.7437 (tp30) cc_final: 0.6934 (mm-30) REVERT: A 267 ASP cc_start: 0.8109 (t0) cc_final: 0.7736 (t0) REVERT: B 15 ASN cc_start: 0.7612 (m-40) cc_final: 0.7228 (m110) REVERT: B 18 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6842 (mt-10) REVERT: B 102 ASP cc_start: 0.7950 (t0) cc_final: 0.7579 (m-30) REVERT: B 129 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: B 216 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7646 (tptp) REVERT: B 267 ASP cc_start: 0.8122 (t0) cc_final: 0.7791 (t0) REVERT: C 18 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6664 (mt-10) REVERT: C 45 LYS cc_start: 0.8040 (mttm) cc_final: 0.7671 (mtpt) REVERT: C 129 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6979 (mm-30) REVERT: C 132 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8481 (mtmt) REVERT: C 219 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: C 267 ASP cc_start: 0.7981 (t0) cc_final: 0.7645 (t0) REVERT: D 210 GLU cc_start: 0.7151 (tp30) cc_final: 0.6740 (mm-30) REVERT: D 267 ASP cc_start: 0.8087 (t0) cc_final: 0.7710 (t0) REVERT: E 15 ASN cc_start: 0.7486 (m-40) cc_final: 0.7124 (m110) REVERT: E 114 ASP cc_start: 0.7673 (m-30) cc_final: 0.7473 (m-30) REVERT: E 267 ASP cc_start: 0.8072 (t0) cc_final: 0.7750 (t0) REVERT: F 45 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7624 (mtpt) REVERT: F 129 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6984 (mm-30) REVERT: F 132 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8453 (mtmt) REVERT: F 216 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7746 (tmtm) REVERT: F 267 ASP cc_start: 0.7983 (t0) cc_final: 0.7636 (t0) REVERT: G 18 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: G 129 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6906 (mm-30) REVERT: G 210 GLU cc_start: 0.7115 (tp30) cc_final: 0.6712 (mm-30) REVERT: G 216 LYS cc_start: 0.7820 (tptt) cc_final: 0.7530 (ttmm) REVERT: G 267 ASP cc_start: 0.8101 (t0) cc_final: 0.7731 (t0) REVERT: H 15 ASN cc_start: 0.7683 (m-40) cc_final: 0.7321 (m110) REVERT: H 18 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6905 (mt-10) REVERT: H 106 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: H 267 ASP cc_start: 0.8127 (t0) cc_final: 0.7772 (t0) REVERT: I 45 LYS cc_start: 0.8102 (mttm) cc_final: 0.7774 (mtpt) REVERT: I 129 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7009 (mm-30) REVERT: I 267 ASP cc_start: 0.8011 (t0) cc_final: 0.7672 (t0) REVERT: J 45 LYS cc_start: 0.7902 (mttm) cc_final: 0.7518 (mtpt) REVERT: J 193 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6590 (tp) REVERT: J 210 GLU cc_start: 0.7398 (tp30) cc_final: 0.6888 (mm-30) REVERT: J 216 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7485 (tmtm) REVERT: J 267 ASP cc_start: 0.8102 (t0) cc_final: 0.7740 (t0) REVERT: K 15 ASN cc_start: 0.7646 (m-40) cc_final: 0.7257 (m110) REVERT: K 18 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6918 (mt-10) REVERT: K 102 ASP cc_start: 0.7932 (t0) cc_final: 0.7583 (m-30) REVERT: K 129 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: K 267 ASP cc_start: 0.8084 (t0) cc_final: 0.7768 (t0) REVERT: L 15 ASN cc_start: 0.7767 (m-40) cc_final: 0.7311 (m110) REVERT: L 18 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: L 56 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: L 118 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7633 (tttt) REVERT: L 129 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7046 (mm-30) REVERT: L 216 LYS cc_start: 0.7918 (tttp) cc_final: 0.7618 (tmtm) REVERT: L 267 ASP cc_start: 0.7980 (t0) cc_final: 0.7639 (t0) outliers start: 63 outliers final: 15 residues processed: 301 average time/residue: 1.5478 time to fit residues: 522.7748 Evaluate side-chains 289 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 258 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 118 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 241 optimal weight: 0.0370 chunk 134 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 291 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN D 28 ASN G 28 ASN J 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 27240 Z= 0.136 Angle : 0.388 5.088 36780 Z= 0.213 Chirality : 0.031 0.128 4332 Planarity : 0.002 0.026 4632 Dihedral : 3.088 14.287 3612 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.63 % Allowed : 12.28 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.09 (0.14), residues: 3396 helix: 3.65 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.88 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 86 HIS 0.001 0.001 HIS L 292 PHE 0.011 0.001 PHE K 50 TYR 0.015 0.001 TYR I 54 ARG 0.000 0.000 ARG D 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 293 time to evaluate : 4.885 Fit side-chains REVERT: A 45 LYS cc_start: 0.7946 (mttm) cc_final: 0.7558 (mtpt) REVERT: A 129 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6668 (pt0) REVERT: A 210 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6779 (mm-30) REVERT: A 216 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7327 (tmtm) REVERT: A 267 ASP cc_start: 0.8058 (t0) cc_final: 0.7697 (t0) REVERT: B 15 ASN cc_start: 0.7513 (m-40) cc_final: 0.7160 (m110) REVERT: B 18 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6648 (mt-10) REVERT: B 102 ASP cc_start: 0.7916 (t0) cc_final: 0.7516 (m-30) REVERT: B 267 ASP cc_start: 0.8083 (t0) cc_final: 0.7756 (t0) REVERT: C 18 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6626 (mt-10) REVERT: C 45 LYS cc_start: 0.7948 (mttm) cc_final: 0.7580 (mtpt) REVERT: C 129 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7034 (mm-30) REVERT: C 132 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8330 (mttp) REVERT: C 267 ASP cc_start: 0.7903 (t0) cc_final: 0.7563 (t0) REVERT: D 129 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6657 (pt0) REVERT: D 267 ASP cc_start: 0.8054 (t0) cc_final: 0.7703 (t0) REVERT: E 15 ASN cc_start: 0.7367 (m-40) cc_final: 0.7055 (m110) REVERT: E 118 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7908 (mtmm) REVERT: E 267 ASP cc_start: 0.8059 (t0) cc_final: 0.7738 (t0) REVERT: F 45 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7612 (mtpt) REVERT: F 129 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7057 (mm-30) REVERT: F 132 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8287 (mttp) REVERT: F 167 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7753 (tp40) REVERT: F 216 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7561 (tmtm) REVERT: F 267 ASP cc_start: 0.7900 (t0) cc_final: 0.7570 (t0) REVERT: G 18 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6695 (mt-10) REVERT: G 118 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7786 (ttmt) REVERT: G 216 LYS cc_start: 0.7786 (tptt) cc_final: 0.7545 (ttmt) REVERT: G 267 ASP cc_start: 0.8046 (t0) cc_final: 0.7707 (t0) REVERT: H 15 ASN cc_start: 0.7515 (m-40) cc_final: 0.7191 (m110) REVERT: H 18 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6714 (mt-10) REVERT: H 106 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7070 (pm20) REVERT: I 45 LYS cc_start: 0.7985 (mttm) cc_final: 0.7597 (mtpt) REVERT: I 129 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6922 (mm-30) REVERT: I 267 ASP cc_start: 0.7894 (t0) cc_final: 0.7556 (t0) REVERT: J 45 LYS cc_start: 0.7953 (mttm) cc_final: 0.7554 (mtpt) REVERT: J 118 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7764 (ttmt) REVERT: J 210 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6788 (mm-30) REVERT: J 216 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7492 (ttmm) REVERT: J 258 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7180 (mt-10) REVERT: J 267 ASP cc_start: 0.8032 (t0) cc_final: 0.7677 (t0) REVERT: K 15 ASN cc_start: 0.7520 (m-40) cc_final: 0.7161 (m110) REVERT: K 18 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6693 (mt-10) REVERT: K 102 ASP cc_start: 0.7887 (t0) cc_final: 0.7539 (m-30) REVERT: K 118 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7908 (mtmm) REVERT: K 267 ASP cc_start: 0.8071 (t0) cc_final: 0.7748 (t0) REVERT: L 18 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6630 (mt-10) REVERT: L 118 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7416 (tttt) REVERT: L 129 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7007 (mm-30) REVERT: L 219 GLN cc_start: 0.7614 (mt0) cc_final: 0.7319 (mt0) REVERT: L 267 ASP cc_start: 0.7940 (t0) cc_final: 0.7621 (t0) outliers start: 48 outliers final: 8 residues processed: 331 average time/residue: 1.4330 time to fit residues: 538.7617 Evaluate side-chains 273 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 251 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 210 GLU Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.7980 chunk 292 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 325 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 170 optimal weight: 0.0050 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 27240 Z= 0.130 Angle : 0.382 4.899 36780 Z= 0.209 Chirality : 0.031 0.135 4332 Planarity : 0.002 0.025 4632 Dihedral : 2.988 13.831 3612 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.70 % Allowed : 12.89 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.48 (0.14), residues: 3396 helix: 3.91 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.90 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 86 HIS 0.001 0.000 HIS A 292 PHE 0.013 0.001 PHE J 50 TYR 0.012 0.001 TYR E 54 ARG 0.000 0.000 ARG K 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 274 time to evaluate : 2.305 Fit side-chains REVERT: A 129 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6727 (pt0) REVERT: A 216 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7294 (tmtm) REVERT: A 267 ASP cc_start: 0.8017 (t0) cc_final: 0.7658 (t0) REVERT: B 15 ASN cc_start: 0.7515 (m-40) cc_final: 0.7166 (m110) REVERT: B 18 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6657 (mt-10) REVERT: C 18 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6616 (mt-10) REVERT: C 45 LYS cc_start: 0.7950 (mttm) cc_final: 0.7578 (mtpt) REVERT: C 118 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7453 (tttt) REVERT: C 129 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6958 (mm-30) REVERT: C 132 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8260 (mttp) REVERT: C 267 ASP cc_start: 0.7939 (t0) cc_final: 0.7641 (t0) REVERT: D 129 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6713 (pt0) REVERT: D 267 ASP cc_start: 0.8016 (t0) cc_final: 0.7663 (t0) REVERT: E 15 ASN cc_start: 0.7436 (m-40) cc_final: 0.7120 (m110) REVERT: F 45 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7605 (mtpt) REVERT: F 118 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7453 (tttt) REVERT: F 129 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6974 (mm-30) REVERT: F 132 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8376 (mttp) REVERT: F 216 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7512 (tmtm) REVERT: F 267 ASP cc_start: 0.7938 (t0) cc_final: 0.7645 (t0) REVERT: G 18 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6699 (mt-10) REVERT: G 129 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6758 (pt0) REVERT: G 267 ASP cc_start: 0.8046 (t0) cc_final: 0.7702 (t0) REVERT: H 15 ASN cc_start: 0.7561 (m-40) cc_final: 0.7247 (m110) REVERT: H 106 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: I 45 LYS cc_start: 0.7965 (mttm) cc_final: 0.7588 (mtpt) REVERT: I 129 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6962 (mm-30) REVERT: I 267 ASP cc_start: 0.7924 (t0) cc_final: 0.7616 (t0) REVERT: J 216 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7536 (ttmt) REVERT: J 258 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7165 (mt-10) REVERT: J 267 ASP cc_start: 0.8047 (t0) cc_final: 0.7709 (t0) REVERT: K 15 ASN cc_start: 0.7520 (m-40) cc_final: 0.7167 (m110) REVERT: K 102 ASP cc_start: 0.7866 (t0) cc_final: 0.7483 (m-30) REVERT: L 18 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6618 (mt-10) REVERT: L 56 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7526 (mm-40) REVERT: L 118 LYS cc_start: 0.7843 (ttpt) cc_final: 0.7364 (tttt) REVERT: L 129 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7055 (mm-30) REVERT: L 267 ASP cc_start: 0.7990 (t0) cc_final: 0.7697 (t0) outliers start: 50 outliers final: 20 residues processed: 312 average time/residue: 1.3524 time to fit residues: 478.9033 Evaluate side-chains 275 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 143 ASN Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 185 optimal weight: 0.4980 chunk 237 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 273 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 323 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 197 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 27240 Z= 0.140 Angle : 0.388 4.893 36780 Z= 0.212 Chirality : 0.031 0.137 4332 Planarity : 0.002 0.025 4632 Dihedral : 2.974 13.872 3612 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.53 % Allowed : 13.13 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.57 (0.14), residues: 3396 helix: 3.97 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.90 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 86 HIS 0.001 0.001 HIS H 292 PHE 0.013 0.001 PHE A 50 TYR 0.014 0.001 TYR L 54 ARG 0.000 0.000 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 262 time to evaluate : 2.323 Fit side-chains REVERT: A 45 LYS cc_start: 0.7942 (mttm) cc_final: 0.7560 (mtpt) REVERT: A 129 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6723 (pt0) REVERT: A 216 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7299 (tmtm) REVERT: A 267 ASP cc_start: 0.8092 (t0) cc_final: 0.7751 (t0) REVERT: B 15 ASN cc_start: 0.7517 (m-40) cc_final: 0.7180 (m110) REVERT: B 18 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6695 (mt-10) REVERT: B 102 ASP cc_start: 0.7873 (t0) cc_final: 0.7507 (t0) REVERT: C 18 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6624 (mt-10) REVERT: C 45 LYS cc_start: 0.8024 (mttm) cc_final: 0.7659 (mtpt) REVERT: C 129 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6970 (mm-30) REVERT: C 132 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8334 (mttp) REVERT: C 267 ASP cc_start: 0.7997 (t0) cc_final: 0.7696 (t0) REVERT: D 129 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6710 (pt0) REVERT: D 267 ASP cc_start: 0.8115 (t0) cc_final: 0.7761 (t0) REVERT: E 15 ASN cc_start: 0.7492 (m-40) cc_final: 0.7182 (m110) REVERT: F 129 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6961 (mm-30) REVERT: F 132 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8357 (mttp) REVERT: F 216 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7516 (tmtm) REVERT: F 267 ASP cc_start: 0.7990 (t0) cc_final: 0.7707 (t0) REVERT: G 18 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6717 (mt-10) REVERT: G 129 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6778 (pt0) REVERT: G 267 ASP cc_start: 0.8099 (t0) cc_final: 0.7759 (t0) REVERT: H 15 ASN cc_start: 0.7569 (m-40) cc_final: 0.7256 (m110) REVERT: H 106 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7064 (pm20) REVERT: I 45 LYS cc_start: 0.7988 (mttm) cc_final: 0.7598 (mtpt) REVERT: I 118 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7451 (tttt) REVERT: I 129 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6999 (mm-30) REVERT: I 219 GLN cc_start: 0.7646 (mt0) cc_final: 0.7347 (mt0) REVERT: I 267 ASP cc_start: 0.7994 (t0) cc_final: 0.7709 (t0) REVERT: J 216 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7547 (ttmt) REVERT: J 258 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7192 (mt-10) REVERT: J 267 ASP cc_start: 0.8057 (t0) cc_final: 0.7722 (t0) REVERT: K 15 ASN cc_start: 0.7560 (m-40) cc_final: 0.7232 (m110) REVERT: K 102 ASP cc_start: 0.7907 (t0) cc_final: 0.7509 (m-30) REVERT: L 18 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6623 (mt-10) REVERT: L 56 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7547 (mm-40) REVERT: L 118 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7390 (tttt) REVERT: L 129 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7061 (mm-30) REVERT: L 267 ASP cc_start: 0.7999 (t0) cc_final: 0.7713 (t0) outliers start: 45 outliers final: 22 residues processed: 297 average time/residue: 1.3711 time to fit residues: 461.5574 Evaluate side-chains 282 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 252 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 56 GLN Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 205 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 254 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 GLN F 52 GLN I 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 27240 Z= 0.141 Angle : 0.389 4.901 36780 Z= 0.213 Chirality : 0.031 0.144 4332 Planarity : 0.002 0.025 4632 Dihedral : 2.964 13.719 3612 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.56 % Allowed : 13.06 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.63 (0.14), residues: 3396 helix: 4.01 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.92 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 86 HIS 0.001 0.001 HIS A 292 PHE 0.013 0.001 PHE G 50 TYR 0.014 0.001 TYR L 54 ARG 0.000 0.000 ARG K 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 256 time to evaluate : 2.281 Fit side-chains REVERT: A 45 LYS cc_start: 0.7938 (mttm) cc_final: 0.7560 (mtpt) REVERT: A 107 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8115 (tttt) REVERT: A 129 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6759 (pt0) REVERT: A 210 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6765 (mm-30) REVERT: A 216 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7318 (tmtm) REVERT: A 267 ASP cc_start: 0.8094 (t0) cc_final: 0.7754 (t0) REVERT: B 15 ASN cc_start: 0.7558 (m-40) cc_final: 0.7232 (m110) REVERT: B 18 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6660 (mt-10) REVERT: B 102 ASP cc_start: 0.7871 (t0) cc_final: 0.7516 (t0) REVERT: C 18 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6623 (mt-10) REVERT: C 45 LYS cc_start: 0.8026 (mttm) cc_final: 0.7657 (mtpt) REVERT: C 118 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7456 (tttt) REVERT: C 129 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6971 (mm-30) REVERT: C 132 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8326 (mttp) REVERT: C 267 ASP cc_start: 0.8001 (t0) cc_final: 0.7717 (t0) REVERT: D 129 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6745 (pt0) REVERT: D 267 ASP cc_start: 0.8107 (t0) cc_final: 0.7757 (t0) REVERT: E 15 ASN cc_start: 0.7496 (m-40) cc_final: 0.7186 (m110) REVERT: F 118 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7454 (tttt) REVERT: F 129 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6961 (mm-30) REVERT: F 132 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8352 (mttp) REVERT: F 267 ASP cc_start: 0.8009 (t0) cc_final: 0.7743 (t70) REVERT: G 18 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6719 (mt-10) REVERT: G 129 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6768 (pt0) REVERT: G 267 ASP cc_start: 0.8103 (t0) cc_final: 0.7761 (t0) REVERT: H 15 ASN cc_start: 0.7568 (m-40) cc_final: 0.7256 (m110) REVERT: H 106 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: I 45 LYS cc_start: 0.8023 (mttm) cc_final: 0.7656 (mtpt) REVERT: I 56 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7627 (mm-40) REVERT: I 118 LYS cc_start: 0.8003 (ttmt) cc_final: 0.7448 (tttt) REVERT: I 129 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7000 (mm-30) REVERT: I 219 GLN cc_start: 0.7635 (mt0) cc_final: 0.7359 (mt0) REVERT: I 267 ASP cc_start: 0.7998 (t0) cc_final: 0.7711 (t0) REVERT: J 216 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7551 (ttmt) REVERT: J 258 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7197 (mt-10) REVERT: J 267 ASP cc_start: 0.8095 (t0) cc_final: 0.7762 (t0) REVERT: K 15 ASN cc_start: 0.7562 (m-40) cc_final: 0.7232 (m110) REVERT: K 102 ASP cc_start: 0.7914 (t0) cc_final: 0.7522 (m-30) REVERT: L 18 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6630 (mt-10) REVERT: L 118 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7423 (tttt) REVERT: L 129 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7031 (mm-30) REVERT: L 267 ASP cc_start: 0.7997 (t0) cc_final: 0.7716 (t0) outliers start: 46 outliers final: 23 residues processed: 289 average time/residue: 1.4096 time to fit residues: 461.4225 Evaluate side-chains 276 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 245 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain I residue 56 GLN Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 0.6980 chunk 310 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 301 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 272 optimal weight: 0.7980 chunk 285 optimal weight: 4.9990 chunk 300 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27240 Z= 0.150 Angle : 0.401 5.087 36780 Z= 0.218 Chirality : 0.031 0.149 4332 Planarity : 0.002 0.025 4632 Dihedral : 2.971 13.835 3612 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.22 % Allowed : 13.37 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.60 (0.14), residues: 3396 helix: 4.00 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.90 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 86 HIS 0.001 0.001 HIS A 292 PHE 0.013 0.001 PHE B 50 TYR 0.015 0.001 TYR I 54 ARG 0.001 0.000 ARG K 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 255 time to evaluate : 2.319 Fit side-chains REVERT: A 45 LYS cc_start: 0.7944 (mttm) cc_final: 0.7566 (mtpt) REVERT: A 129 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6754 (pt0) REVERT: A 216 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7363 (tmtm) REVERT: A 267 ASP cc_start: 0.8100 (t0) cc_final: 0.7758 (t0) REVERT: B 15 ASN cc_start: 0.7567 (m-40) cc_final: 0.7240 (m110) REVERT: B 18 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6667 (mt-10) REVERT: B 102 ASP cc_start: 0.7877 (t0) cc_final: 0.7524 (t0) REVERT: C 18 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6629 (mt-10) REVERT: C 45 LYS cc_start: 0.8015 (mttm) cc_final: 0.7647 (mtpt) REVERT: C 118 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7460 (tttt) REVERT: C 129 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6966 (mm-30) REVERT: C 132 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8364 (mttp) REVERT: C 267 ASP cc_start: 0.8008 (t0) cc_final: 0.7719 (t0) REVERT: D 129 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6739 (pt0) REVERT: D 267 ASP cc_start: 0.8104 (t0) cc_final: 0.7754 (t0) REVERT: E 15 ASN cc_start: 0.7506 (m-40) cc_final: 0.7196 (m110) REVERT: F 118 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7456 (tttt) REVERT: F 129 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6970 (mm-30) REVERT: F 132 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8365 (mttp) REVERT: F 267 ASP cc_start: 0.8017 (t0) cc_final: 0.7730 (t0) REVERT: G 18 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6671 (mt-10) REVERT: G 129 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6769 (pt0) REVERT: G 267 ASP cc_start: 0.8100 (t0) cc_final: 0.7761 (t0) REVERT: H 15 ASN cc_start: 0.7570 (m-40) cc_final: 0.7259 (m110) REVERT: I 45 LYS cc_start: 0.8010 (mttm) cc_final: 0.7637 (mtpt) REVERT: I 118 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7456 (tttt) REVERT: I 129 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6962 (mm-30) REVERT: I 267 ASP cc_start: 0.8016 (t0) cc_final: 0.7727 (t0) REVERT: J 216 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7517 (ttmt) REVERT: J 258 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7218 (mt-10) REVERT: J 267 ASP cc_start: 0.8103 (t0) cc_final: 0.7764 (t0) REVERT: K 15 ASN cc_start: 0.7567 (m-40) cc_final: 0.7241 (m110) REVERT: K 102 ASP cc_start: 0.7889 (t0) cc_final: 0.7544 (t0) REVERT: L 18 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6631 (mt-10) REVERT: L 118 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7426 (tttt) REVERT: L 129 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7020 (mm-30) REVERT: L 267 ASP cc_start: 0.8003 (t0) cc_final: 0.7718 (t0) outliers start: 36 outliers final: 23 residues processed: 283 average time/residue: 1.3874 time to fit residues: 444.1088 Evaluate side-chains 276 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.8980 chunk 319 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 221 optimal weight: 0.6980 chunk 334 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 205 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 27240 Z= 0.141 Angle : 0.396 5.265 36780 Z= 0.216 Chirality : 0.031 0.148 4332 Planarity : 0.002 0.025 4632 Dihedral : 2.956 13.499 3612 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.05 % Allowed : 13.47 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.68 (0.14), residues: 3396 helix: 4.05 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.93 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 86 HIS 0.001 0.001 HIS E 292 PHE 0.013 0.001 PHE J 50 TYR 0.015 0.001 TYR F 54 ARG 0.001 0.000 ARG H 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 250 time to evaluate : 2.302 Fit side-chains REVERT: A 45 LYS cc_start: 0.7943 (mttm) cc_final: 0.7565 (mtpt) REVERT: A 129 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6751 (pt0) REVERT: A 210 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6767 (mm-30) REVERT: A 216 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7324 (tmtm) REVERT: A 267 ASP cc_start: 0.8092 (t0) cc_final: 0.7749 (t0) REVERT: B 15 ASN cc_start: 0.7556 (m-40) cc_final: 0.7233 (m110) REVERT: B 18 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6662 (mt-10) REVERT: B 102 ASP cc_start: 0.7870 (t0) cc_final: 0.7522 (t0) REVERT: C 18 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6622 (mt-10) REVERT: C 45 LYS cc_start: 0.8023 (mttm) cc_final: 0.7651 (mtpt) REVERT: C 118 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7453 (tttt) REVERT: C 129 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6986 (mm-30) REVERT: C 132 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8290 (mttp) REVERT: C 267 ASP cc_start: 0.8000 (t0) cc_final: 0.7709 (t0) REVERT: D 129 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6737 (pt0) REVERT: D 267 ASP cc_start: 0.8125 (t0) cc_final: 0.7756 (t0) REVERT: E 15 ASN cc_start: 0.7497 (m-40) cc_final: 0.7186 (m110) REVERT: F 118 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7448 (tttt) REVERT: F 129 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6957 (mm-30) REVERT: F 132 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8365 (mttp) REVERT: F 267 ASP cc_start: 0.8001 (t0) cc_final: 0.7725 (t0) REVERT: G 18 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6708 (mt-10) REVERT: G 129 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6770 (pt0) REVERT: G 267 ASP cc_start: 0.8091 (t0) cc_final: 0.7753 (t0) REVERT: H 15 ASN cc_start: 0.7563 (m-40) cc_final: 0.7250 (m110) REVERT: I 45 LYS cc_start: 0.8018 (mttm) cc_final: 0.7646 (mtpt) REVERT: I 118 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7448 (tttt) REVERT: I 129 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6994 (mm-30) REVERT: I 219 GLN cc_start: 0.7627 (mt0) cc_final: 0.7340 (mt0) REVERT: I 267 ASP cc_start: 0.8004 (t0) cc_final: 0.7715 (t0) REVERT: J 210 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6771 (mm-30) REVERT: J 216 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7561 (ttmt) REVERT: J 258 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7199 (mt-10) REVERT: J 267 ASP cc_start: 0.8094 (t0) cc_final: 0.7755 (t0) REVERT: K 15 ASN cc_start: 0.7554 (m-40) cc_final: 0.7230 (m110) REVERT: K 102 ASP cc_start: 0.7890 (t0) cc_final: 0.7636 (t0) REVERT: L 18 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6627 (mt-10) REVERT: L 118 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7416 (tttt) REVERT: L 129 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7053 (mm-30) REVERT: L 267 ASP cc_start: 0.8002 (t0) cc_final: 0.7706 (t0) outliers start: 31 outliers final: 22 residues processed: 275 average time/residue: 1.3952 time to fit residues: 433.4580 Evaluate side-chains 275 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 210 GLU Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 168 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.5980 chunk 283 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 274 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095628 restraints weight = 28835.360| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.30 r_work: 0.2881 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27240 Z= 0.148 Angle : 0.406 5.478 36780 Z= 0.221 Chirality : 0.031 0.147 4332 Planarity : 0.002 0.025 4632 Dihedral : 2.959 13.567 3612 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.36 % Allowed : 13.27 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.66 (0.14), residues: 3396 helix: 4.03 (0.08), residues: 3108 sheet: None (None), residues: 0 loop : -0.90 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 86 HIS 0.001 0.001 HIS A 292 PHE 0.013 0.001 PHE J 50 TYR 0.015 0.001 TYR I 54 ARG 0.001 0.000 ARG K 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7836.87 seconds wall clock time: 136 minutes 34.99 seconds (8194.99 seconds total)