Starting phenix.real_space_refine (version: dev) on Tue Feb 21 12:44:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/02_2023/6mrt_9212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/02_2023/6mrt_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_9212/02_2023/6mrt_9212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/02_2023/6mrt_9212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/02_2023/6mrt_9212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/02_2023/6mrt_9212.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A ARG 49": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26868 Number of models: 1 Model: "" Number of chains: 12 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} Chain: "B" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "C" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "D" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "E" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "F" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "G" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "H" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "I" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "J" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "K" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "L" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Time building chain proxies: 11.03, per 1000 atoms: 0.41 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 - 3.50 Amino acid : False - 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: 8.09 Conformation dependent library (CDL) restraints added in 3.1 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: 0.44 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: 6.27 Time building geometry restraints manager: 8.82 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: 100.18 - 106.94: 276 106.94 - 113.71: 15800 113.71 - 120.48: 11886 120.48 - 127.25: 8710 127.25 - 134.02: 108 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 2.440 nonbonded pdb=" OH TYR I 54 " pdb=" OD2 ASP I 158 " model vdw 2.260 2.440 nonbonded pdb=" OH TYR L 54 " pdb=" OD2 ASP L 158 " model vdw 2.260 2.440 nonbonded pdb=" OH TYR J 54 " pdb=" OD2 ASP J 158 " model vdw 2.261 2.440 nonbonded pdb=" OH TYR K 54 " pdb=" OD2 ASP K 158 " model vdw 2.261 2.440 ... (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 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 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. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.340 Construct map_model_manager: 0.020 Extract box with map and model: 6.920 Check model and map are aligned: 0.300 Process input model: 49.980 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:9.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 % 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 *********************** 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 : 2.527 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 550 average time/residue: 1.3360 time to fit residues: 830.5987 Evaluate side-chains 249 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 2.468 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 86 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 263 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 305 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 52 GLN A 112 GLN A 169 GLN B 15 ASN B 52 GLN B 112 GLN C 28 ASN C 52 GLN C 112 GLN D 15 ASN D 28 ASN D 52 GLN D 112 GLN E 15 ASN E 28 ASN E 52 GLN E 112 GLN F 28 ASN F 52 GLN F 112 GLN G 52 GLN G 112 GLN H 15 ASN H 52 GLN H 56 GLN H 112 GLN I 52 GLN I 112 GLN I 128 ASN J 28 ASN J 52 GLN J 112 GLN K 15 ASN K 52 GLN K 112 GLN L 15 ASN L 28 ASN L 52 GLN L 112 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 27240 Z= 0.161 Angle : 0.464 5.627 36780 Z= 0.246 Chirality : 0.032 0.133 4332 Planarity : 0.003 0.030 4632 Dihedral : 3.466 16.031 3612 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.03 % 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: 2.60 (0.14), residues: 3396 helix: 2.08 (0.09), residues: 3084 sheet: None (None), residues: 0 loop : -1.95 (0.22), residues: 312 *********************** 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 436 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 347 time to evaluate : 2.513 Fit side-chains outliers start: 89 outliers final: 8 residues processed: 387 average time/residue: 1.3167 time to fit residues: 577.9419 Evaluate side-chains 250 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 242 time to evaluate : 2.475 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.9041 time to fit residues: 8.6860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 253 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 0.8980 chunk 330 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 303 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 169 GLN B 52 GLN D 52 GLN E 28 ASN G 52 GLN J 15 ASN J 52 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2519 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= 0.155 Angle : 0.426 5.560 36780 Z= 0.229 Chirality : 0.032 0.132 4332 Planarity : 0.003 0.035 4632 Dihedral : 3.181 14.468 3612 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.17 (0.14), residues: 3396 helix: 3.06 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -1.34 (0.26), residues: 288 *********************** 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 301 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 255 time to evaluate : 2.540 Fit side-chains outliers start: 46 outliers final: 22 residues processed: 288 average time/residue: 1.4119 time to fit residues: 459.0306 Evaluate side-chains 242 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 2.477 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.7960 time to fit residues: 7.2172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 1.9990 chunk 229 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 306 optimal weight: 0.5980 chunk 324 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 27240 Z= 0.160 Angle : 0.418 5.507 36780 Z= 0.225 Chirality : 0.032 0.127 4332 Planarity : 0.002 0.031 4632 Dihedral : 3.109 14.254 3612 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer Outliers : 1.53 % 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: 4.77 (0.14), residues: 3396 helix: 3.45 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -1.12 (0.28), residues: 288 *********************** 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 276 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 231 time to evaluate : 2.513 Fit side-chains outliers start: 45 outliers final: 23 residues processed: 265 average time/residue: 1.4355 time to fit residues: 429.0964 Evaluate side-chains 240 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 2.492 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 2 average time/residue: 0.2446 time to fit residues: 4.2832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 291 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN C 128 ASN F 128 ASN I 28 ASN I 56 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 27240 Z= 0.203 Angle : 0.452 6.131 36780 Z= 0.242 Chirality : 0.033 0.131 4332 Planarity : 0.002 0.031 4632 Dihedral : 3.146 14.339 3612 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer Outliers : 1.60 % 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: 4.81 (0.14), residues: 3396 helix: 3.47 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.94 (0.30), residues: 288 *********************** 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 285 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 238 time to evaluate : 2.478 Fit side-chains outliers start: 47 outliers final: 30 residues processed: 273 average time/residue: 1.5060 time to fit residues: 460.6330 Evaluate side-chains 258 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 228 time to evaluate : 2.487 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 3 average time/residue: 0.9614 time to fit residues: 6.7145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 325 optimal weight: 0.6980 chunk 269 optimal weight: 0.0370 chunk 150 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3004 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= 0.129 Angle : 0.378 4.890 36780 Z= 0.207 Chirality : 0.031 0.122 4332 Planarity : 0.002 0.030 4632 Dihedral : 3.007 14.057 3612 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.44 (0.14), residues: 3396 helix: 3.89 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -1.02 (0.29), residues: 288 *********************** 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 319 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 269 time to evaluate : 2.464 Fit side-chains outliers start: 50 outliers final: 28 residues processed: 317 average time/residue: 1.3528 time to fit residues: 487.1656 Evaluate side-chains 259 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 231 time to evaluate : 2.461 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 0.1860 time to fit residues: 3.6969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 273 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 323 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 chunk 197 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 27240 Z= 0.173 Angle : 0.420 5.392 36780 Z= 0.227 Chirality : 0.032 0.124 4332 Planarity : 0.002 0.030 4632 Dihedral : 3.031 14.181 3612 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer Outliers : 1.43 % 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: 5.34 (0.14), residues: 3396 helix: 3.82 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 288 *********************** 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 278 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 236 time to evaluate : 2.501 Fit side-chains outliers start: 42 outliers final: 30 residues processed: 271 average time/residue: 1.4778 time to fit residues: 450.2342 Evaluate side-chains 260 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 230 time to evaluate : 2.497 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 3 average time/residue: 0.9739 time to fit residues: 6.7870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.9980 chunk 129 optimal weight: 0.0570 chunk 193 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 205 optimal weight: 6.9990 chunk 220 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3033 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= 0.136 Angle : 0.387 5.066 36780 Z= 0.210 Chirality : 0.031 0.121 4332 Planarity : 0.002 0.030 4632 Dihedral : 2.975 14.115 3612 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer Outliers : 1.43 % 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: 4.02 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -1.00 (0.30), residues: 288 *********************** 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 276 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 2.509 Fit side-chains outliers start: 42 outliers final: 29 residues processed: 272 average time/residue: 1.4335 time to fit residues: 441.7702 Evaluate side-chains 258 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 2.475 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 3.3400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 301 optimal weight: 0.8980 chunk 181 optimal weight: 0.0670 chunk 131 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 272 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 0.9980 overall best weight: 0.7918 ------------------------------------------------------------------------------- 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: 0.8310 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 27240 Z= 0.140 Angle : 0.391 5.056 36780 Z= 0.212 Chirality : 0.031 0.120 4332 Planarity : 0.002 0.030 4632 Dihedral : 2.953 14.205 3612 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer Outliers : 1.33 % 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 : -0.98 (0.30), residues: 288 *********************** 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 274 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 235 time to evaluate : 2.450 Fit side-chains outliers start: 39 outliers final: 31 residues processed: 269 average time/residue: 1.4319 time to fit residues: 434.4006 Evaluate side-chains 258 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 227 time to evaluate : 2.467 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 29 residues processed: 2 average time/residue: 0.2029 time to fit residues: 4.0815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 194 optimal weight: 0.1980 chunk 151 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 334 optimal weight: 0.9990 chunk 308 optimal weight: 0.0020 chunk 266 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN K 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3198 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= 0.128 Angle : 0.375 5.200 36780 Z= 0.204 Chirality : 0.030 0.118 4332 Planarity : 0.002 0.029 4632 Dihedral : 2.918 14.299 3612 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer Outliers : 1.09 % 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: 5.83 (0.14), residues: 3396 helix: 4.16 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -1.03 (0.29), residues: 288 ********************** 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 272 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 240 time to evaluate : 2.706 Fit side-chains outliers start: 32 outliers final: 29 residues processed: 272 average time/residue: 1.3808 time to fit residues: 425.7116 Evaluate side-chains 261 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 232 time to evaluate : 2.646 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 3.3663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 7.9990 chunk 283 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 274 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN K 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.091193 restraints weight = 28769.242| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.31 r_work: 0.2818 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 27240 Z= 0.204 Angle : 0.448 5.742 36780 Z= 0.240 Chirality : 0.033 0.126 4332 Planarity : 0.002 0.030 4632 Dihedral : 3.024 14.043 3612 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 1.33 % 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: 5.41 (0.14), residues: 3396 helix: 3.86 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.87 (0.31), residues: 288 =============================================================================== Job complete usr+sys time: 7483.82 seconds wall clock time: 131 minutes 44.21 seconds (7904.21 seconds total)