Starting phenix.real_space_refine on Fri Apr 5 13:27:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/04_2024/6mrt_9212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/04_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_9212/04_2024/6mrt_9212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/04_2024/6mrt_9212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/04_2024/6mrt_9212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrt_9212/04_2024/6mrt_9212.pdb" } 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 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-5288/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: 10.73, per 1000 atoms: 0.40 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: 8.16 Conformation dependent library (CDL) restraints added in 3.8 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: 1.41 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: 6.38 Time building geometry restraints manager: 9.02 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.020 Extract box with map and model: 5.880 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 52.240 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.140 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:12.120 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.550 ------------------------------------------------------------------------------- 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 : 2.335 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: 1.3159 time to fit residues: 816.6493 Evaluate side-chains 274 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 271 time to evaluate : 2.381 ------------------------------------------------------------------------------- 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: 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: 5.9990 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 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 28 ASN E 52 GLN E 112 GLN F 28 ASN F 52 GLN F 112 GLN G 52 GLN G 112 GLN H 52 GLN H 56 GLN H 112 GLN I 52 GLN I 112 GLN J 28 ASN J 52 GLN J 112 GLN K 52 GLN K 112 GLN L 28 ASN L 52 GLN L 112 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 27240 Z= 0.163 Angle : 0.460 5.333 36780 Z= 0.244 Chirality : 0.032 0.133 4332 Planarity : 0.003 0.030 4632 Dihedral : 3.619 34.550 3618 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.96 % Allowed : 7.93 % Favored : 89.12 % 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: 2.55 (0.14), residues: 3396 helix: 1.93 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.30 (0.25), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 86 HIS 0.002 0.001 HIS C 292 PHE 0.008 0.001 PHE D 50 TYR 0.017 0.001 TYR H 54 ARG 0.002 0.000 ARG J 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 454 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 367 time to evaluate : 2.456 Fit side-chains REVERT: A 18 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6715 (mt-10) REVERT: A 42 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: A 45 LYS cc_start: 0.7914 (mttm) cc_final: 0.7554 (mtpt) REVERT: A 210 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: A 216 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7383 (tmtm) REVERT: A 234 LYS cc_start: 0.8006 (mttp) cc_final: 0.7770 (mtmt) REVERT: A 267 ASP cc_start: 0.8052 (t0) cc_final: 0.7709 (t0) REVERT: B 15 ASN cc_start: 0.7613 (m-40) cc_final: 0.7211 (m110) REVERT: B 18 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6823 (mt-10) REVERT: B 102 ASP cc_start: 0.7988 (t0) cc_final: 0.7681 (m-30) REVERT: B 267 ASP cc_start: 0.8116 (t0) cc_final: 0.7772 (t0) REVERT: C 45 LYS cc_start: 0.8077 (mttm) cc_final: 0.7639 (mtpt) REVERT: C 56 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7627 (mm-40) REVERT: C 129 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7081 (mm-30) REVERT: C 210 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6899 (mm-30) REVERT: C 216 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7654 (tmtm) REVERT: C 267 ASP cc_start: 0.7822 (t0) cc_final: 0.7522 (t0) REVERT: D 267 ASP cc_start: 0.7909 (t0) cc_final: 0.7559 (t70) REVERT: E 15 ASN cc_start: 0.7362 (m-40) cc_final: 0.7072 (m110) REVERT: E 114 ASP cc_start: 0.7671 (m-30) cc_final: 0.7450 (m-30) REVERT: E 118 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7950 (mtmm) REVERT: E 267 ASP cc_start: 0.7946 (t0) cc_final: 0.7652 (t0) REVERT: F 56 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: F 129 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6942 (mm-30) REVERT: F 132 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8388 (mttp) REVERT: F 267 ASP cc_start: 0.7771 (t0) cc_final: 0.7473 (t0) REVERT: G 18 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6659 (mt-10) REVERT: G 129 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6835 (mm-30) REVERT: G 216 LYS cc_start: 0.7800 (tptt) cc_final: 0.7487 (ttmm) REVERT: G 267 ASP cc_start: 0.7991 (t0) cc_final: 0.7607 (t0) REVERT: H 15 ASN cc_start: 0.7624 (m-40) cc_final: 0.7301 (m110) REVERT: H 267 ASP cc_start: 0.8043 (t0) cc_final: 0.7744 (t0) REVERT: I 45 LYS cc_start: 0.8086 (mttm) cc_final: 0.7654 (mtpt) REVERT: I 129 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6872 (mm-30) REVERT: I 210 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6835 (mm-30) REVERT: I 216 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7648 (tmtm) REVERT: I 267 ASP cc_start: 0.7695 (t0) cc_final: 0.7401 (t0) REVERT: I 287 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7585 (mm-30) REVERT: J 18 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6639 (mt-10) REVERT: J 45 LYS cc_start: 0.8022 (mttm) cc_final: 0.7634 (mtpt) REVERT: J 210 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6776 (mm-30) REVERT: J 216 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7582 (ttmm) REVERT: J 267 ASP cc_start: 0.7820 (t0) cc_final: 0.7531 (t70) REVERT: K 15 ASN cc_start: 0.7632 (m-40) cc_final: 0.7223 (m110) REVERT: K 102 ASP cc_start: 0.8081 (t0) cc_final: 0.7673 (m-30) REVERT: K 107 LYS cc_start: 0.8644 (tttp) cc_final: 0.8392 (mtmt) REVERT: K 114 ASP cc_start: 0.7706 (m-30) cc_final: 0.7491 (m-30) REVERT: K 118 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7966 (mtmm) REVERT: K 267 ASP cc_start: 0.7724 (t0) cc_final: 0.7399 (t0) REVERT: L 15 ASN cc_start: 0.7657 (m-40) cc_final: 0.7301 (m110) REVERT: L 42 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7006 (mm-30) REVERT: L 267 ASP cc_start: 0.7765 (t0) cc_final: 0.7489 (t0) outliers start: 87 outliers final: 9 residues processed: 409 average time/residue: 1.2366 time to fit residues: 576.2942 Evaluate side-chains 290 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 267 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU 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 A residue 252 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 107 LYS 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 132 LYS Chi-restraints excluded: chain H 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 253 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 305 optimal weight: 0.8980 chunk 330 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 chunk 303 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7961 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 27240 Z= 0.152 Angle : 0.422 5.399 36780 Z= 0.227 Chirality : 0.031 0.129 4332 Planarity : 0.002 0.026 4632 Dihedral : 3.211 15.010 3612 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.70 % Allowed : 10.95 % Favored : 87.35 % 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: 4.13 (0.14), residues: 3396 helix: 3.06 (0.09), residues: 3096 sheet: None (None), residues: 0 loop : -1.50 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 86 HIS 0.002 0.001 HIS I 292 PHE 0.010 0.001 PHE D 50 TYR 0.014 0.001 TYR K 54 ARG 0.001 0.000 ARG L 49 *********************** 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 326 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 276 time to evaluate : 2.377 Fit side-chains REVERT: A 18 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6689 (mt-10) REVERT: A 45 LYS cc_start: 0.7925 (mttm) cc_final: 0.7564 (mtpt) REVERT: A 99 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8317 (tp) REVERT: A 129 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6940 (mm-30) REVERT: A 210 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6623 (mm-30) REVERT: A 216 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7369 (tmtm) REVERT: A 267 ASP cc_start: 0.8066 (t0) cc_final: 0.7720 (t0) REVERT: B 15 ASN cc_start: 0.7593 (m-40) cc_final: 0.7202 (m110) REVERT: B 18 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6823 (mt-10) REVERT: B 102 ASP cc_start: 0.7922 (t0) cc_final: 0.7567 (m-30) REVERT: B 129 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: B 267 ASP cc_start: 0.8134 (t0) cc_final: 0.7799 (t0) REVERT: C 45 LYS cc_start: 0.7998 (mttm) cc_final: 0.7675 (mtpt) REVERT: C 118 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7464 (tttt) REVERT: C 129 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6966 (mm-30) REVERT: C 132 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8434 (mttp) REVERT: C 267 ASP cc_start: 0.7806 (t0) cc_final: 0.7491 (t0) REVERT: D 216 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7583 (ttmm) REVERT: D 267 ASP cc_start: 0.8036 (t0) cc_final: 0.7671 (t0) REVERT: E 15 ASN cc_start: 0.7364 (m-40) cc_final: 0.7070 (m110) REVERT: E 114 ASP cc_start: 0.7596 (m-30) cc_final: 0.7381 (m-30) REVERT: E 118 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7922 (mtmm) REVERT: E 234 LYS cc_start: 0.7863 (mttm) cc_final: 0.7658 (mtmt) REVERT: E 267 ASP cc_start: 0.8047 (t0) cc_final: 0.7700 (t0) REVERT: F 129 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6974 (mm-30) REVERT: F 267 ASP cc_start: 0.7786 (t0) cc_final: 0.7480 (t0) REVERT: G 18 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6644 (mt-10) REVERT: G 129 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6924 (mm-30) REVERT: G 216 LYS cc_start: 0.7813 (tptt) cc_final: 0.7537 (ttmt) REVERT: G 267 ASP cc_start: 0.8073 (t0) cc_final: 0.7657 (t0) REVERT: H 15 ASN cc_start: 0.7579 (m-40) cc_final: 0.7255 (m110) REVERT: H 18 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6837 (mt-10) REVERT: H 107 LYS cc_start: 0.8563 (tttm) cc_final: 0.8306 (tttt) REVERT: H 267 ASP cc_start: 0.8061 (t0) cc_final: 0.7748 (t0) REVERT: I 45 LYS cc_start: 0.8089 (mttm) cc_final: 0.7689 (mtpt) REVERT: I 129 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6856 (mm-30) REVERT: I 216 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7607 (tmtm) REVERT: I 267 ASP cc_start: 0.7788 (t0) cc_final: 0.7480 (t0) REVERT: J 18 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6698 (mt-10) REVERT: J 45 LYS cc_start: 0.7934 (mttm) cc_final: 0.7575 (mtpt) REVERT: J 210 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6816 (mm-30) REVERT: J 216 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7568 (ttmt) REVERT: J 258 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7310 (mt-10) REVERT: J 267 ASP cc_start: 0.7947 (t0) cc_final: 0.7540 (t0) REVERT: K 15 ASN cc_start: 0.7605 (m-40) cc_final: 0.7219 (m110) REVERT: K 102 ASP cc_start: 0.8028 (t0) cc_final: 0.7603 (m-30) REVERT: K 114 ASP cc_start: 0.7608 (m-30) cc_final: 0.7393 (m-30) REVERT: K 118 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7934 (mtmm) REVERT: K 234 LYS cc_start: 0.7860 (mttm) cc_final: 0.7654 (mtmt) REVERT: K 267 ASP cc_start: 0.8007 (t0) cc_final: 0.7662 (t0) REVERT: L 15 ASN cc_start: 0.7645 (m-40) cc_final: 0.7297 (m110) REVERT: L 129 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6956 (mm-30) REVERT: L 267 ASP cc_start: 0.7833 (t0) cc_final: 0.7544 (t0) outliers start: 50 outliers final: 12 residues processed: 305 average time/residue: 1.3634 time to fit residues: 469.2145 Evaluate side-chains 271 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 143 ASN 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 B residue 129 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 197 SER Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain J residue 18 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 L residue 164 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.9990 chunk 229 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 205 optimal weight: 0.0370 chunk 306 optimal weight: 0.7980 chunk 324 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 290 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 27240 Z= 0.131 Angle : 0.382 5.168 36780 Z= 0.207 Chirality : 0.031 0.126 4332 Planarity : 0.002 0.025 4632 Dihedral : 3.044 14.091 3612 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.87 % Allowed : 11.39 % Favored : 86.73 % 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: 4.98 (0.14), residues: 3396 helix: 3.63 (0.09), residues: 3096 sheet: None (None), residues: 0 loop : -1.38 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 86 HIS 0.001 0.001 HIS I 292 PHE 0.010 0.001 PHE A 50 TYR 0.014 0.001 TYR E 54 ARG 0.001 0.000 ARG I 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 355 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 300 time to evaluate : 2.379 Fit side-chains REVERT: A 18 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6651 (mt-10) REVERT: A 42 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: A 210 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6492 (mm-30) REVERT: A 216 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7481 (ttmm) REVERT: A 267 ASP cc_start: 0.8083 (t0) cc_final: 0.7711 (t0) REVERT: B 15 ASN cc_start: 0.7582 (m-40) cc_final: 0.7208 (m110) REVERT: B 18 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6624 (mt-10) REVERT: B 102 ASP cc_start: 0.7904 (t0) cc_final: 0.7495 (m-30) REVERT: C 18 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6573 (mt-10) REVERT: C 45 LYS cc_start: 0.7995 (mttm) cc_final: 0.7635 (mtpt) REVERT: C 118 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7475 (tttt) REVERT: C 129 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6998 (mm-30) REVERT: C 132 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8329 (mttp) REVERT: C 267 ASP cc_start: 0.7880 (t0) cc_final: 0.7561 (t0) REVERT: D 267 ASP cc_start: 0.8050 (t0) cc_final: 0.7687 (t0) REVERT: E 15 ASN cc_start: 0.7339 (m-40) cc_final: 0.7043 (m110) REVERT: E 118 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7782 (mtmm) REVERT: E 267 ASP cc_start: 0.8037 (t0) cc_final: 0.7738 (t0) REVERT: F 45 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7612 (mtpt) REVERT: F 129 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7036 (mm-30) REVERT: F 132 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8387 (mttp) REVERT: F 219 GLN cc_start: 0.7708 (mt0) cc_final: 0.7414 (mt0) REVERT: F 267 ASP cc_start: 0.7850 (t0) cc_final: 0.7534 (t0) REVERT: G 18 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6689 (mt-10) REVERT: G 267 ASP cc_start: 0.8073 (t0) cc_final: 0.7714 (t0) REVERT: H 15 ASN cc_start: 0.7616 (m-40) cc_final: 0.7299 (m110) REVERT: H 18 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6854 (mt-10) REVERT: I 18 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6642 (mt-10) REVERT: I 45 LYS cc_start: 0.8046 (mttm) cc_final: 0.7683 (mtpt) REVERT: I 103 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7247 (mp0) REVERT: I 129 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6984 (mm-30) REVERT: I 216 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7487 (tmtm) REVERT: I 267 ASP cc_start: 0.7817 (t0) cc_final: 0.7487 (t0) REVERT: J 18 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6612 (mt-10) REVERT: J 42 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: J 210 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6695 (mm-30) REVERT: J 216 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7563 (ttmt) REVERT: J 258 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7208 (mt-10) REVERT: J 267 ASP cc_start: 0.7992 (t0) cc_final: 0.7645 (t0) REVERT: K 15 ASN cc_start: 0.7561 (m-40) cc_final: 0.7213 (m110) REVERT: K 102 ASP cc_start: 0.7992 (t0) cc_final: 0.7551 (m-30) REVERT: K 114 ASP cc_start: 0.7603 (m-30) cc_final: 0.7385 (m-30) REVERT: K 118 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7783 (mtmm) REVERT: K 132 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8381 (mtmm) REVERT: K 267 ASP cc_start: 0.8096 (t0) cc_final: 0.7779 (t0) REVERT: L 15 ASN cc_start: 0.7613 (m-40) cc_final: 0.7246 (m110) REVERT: L 118 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7300 (tttt) REVERT: L 129 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7013 (mm-30) REVERT: L 267 ASP cc_start: 0.7902 (t0) cc_final: 0.7612 (t0) outliers start: 55 outliers final: 11 residues processed: 341 average time/residue: 1.2575 time to fit residues: 488.1030 Evaluate side-chains 271 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 244 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU 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 B residue 197 SER Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 164 SER 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 132 LYS Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 164 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 129 GLU Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 164 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 241 optimal weight: 0.0980 chunk 134 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN F 52 GLN J 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2658 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= 0.173 Angle : 0.423 5.710 36780 Z= 0.228 Chirality : 0.032 0.126 4332 Planarity : 0.002 0.026 4632 Dihedral : 3.056 14.297 3612 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.77 % Allowed : 13.57 % Favored : 84.66 % 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: 5.07 (0.14), residues: 3396 helix: 3.64 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.96 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 86 HIS 0.002 0.001 HIS L 292 PHE 0.012 0.001 PHE A 50 TYR 0.014 0.001 TYR L 54 ARG 0.001 0.000 ARG C 174 *********************** 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 309 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 257 time to evaluate : 2.416 Fit side-chains REVERT: A 18 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: A 42 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: A 99 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8315 (tp) REVERT: A 216 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7383 (tmtm) REVERT: A 267 ASP cc_start: 0.8093 (t0) cc_final: 0.7721 (t0) REVERT: B 15 ASN cc_start: 0.7617 (m-40) cc_final: 0.7237 (m110) REVERT: B 18 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6816 (mt-10) REVERT: B 102 ASP cc_start: 0.7933 (t0) cc_final: 0.7522 (m-30) REVERT: C 18 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6644 (mt-10) REVERT: C 45 LYS cc_start: 0.7985 (mttm) cc_final: 0.7626 (mtpt) REVERT: C 118 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7464 (tttt) REVERT: C 129 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6965 (mm-30) REVERT: C 132 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8393 (mttp) REVERT: C 267 ASP cc_start: 0.7985 (t0) cc_final: 0.7675 (t0) REVERT: D 216 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7589 (ttmm) REVERT: D 267 ASP cc_start: 0.8079 (t0) cc_final: 0.7703 (t0) REVERT: E 15 ASN cc_start: 0.7423 (m-40) cc_final: 0.7114 (m110) REVERT: E 118 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7952 (mtmm) REVERT: E 267 ASP cc_start: 0.8094 (t0) cc_final: 0.7767 (t0) REVERT: F 92 GLN cc_start: 0.8369 (mt0) cc_final: 0.8164 (mt0) REVERT: F 129 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7041 (mm-30) REVERT: F 219 GLN cc_start: 0.7644 (mt0) cc_final: 0.7360 (mt0) REVERT: F 267 ASP cc_start: 0.7977 (t0) cc_final: 0.7682 (t0) REVERT: G 18 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: G 216 LYS cc_start: 0.7830 (tptt) cc_final: 0.7568 (ttmm) REVERT: G 267 ASP cc_start: 0.8097 (t0) cc_final: 0.7715 (t0) REVERT: H 15 ASN cc_start: 0.7642 (m-40) cc_final: 0.7318 (m110) REVERT: H 18 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6865 (mt-10) REVERT: I 45 LYS cc_start: 0.8043 (mttm) cc_final: 0.7690 (mtpt) REVERT: I 99 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8533 (tp) REVERT: I 129 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6881 (mm-30) REVERT: J 18 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6642 (mt-10) REVERT: J 42 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: J 45 LYS cc_start: 0.8015 (mttm) cc_final: 0.7518 (mtpt) REVERT: J 216 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7370 (tmtm) REVERT: J 267 ASP cc_start: 0.8056 (t0) cc_final: 0.7702 (t0) REVERT: K 15 ASN cc_start: 0.7613 (m-40) cc_final: 0.7243 (m110) REVERT: K 102 ASP cc_start: 0.7918 (t0) cc_final: 0.7534 (m-30) REVERT: K 118 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7956 (mtmm) REVERT: K 267 ASP cc_start: 0.8088 (t0) cc_final: 0.7768 (t0) REVERT: L 15 ASN cc_start: 0.7649 (m-40) cc_final: 0.7286 (m110) REVERT: L 118 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7373 (tttt) REVERT: L 129 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7000 (mm-30) REVERT: L 267 ASP cc_start: 0.7951 (t0) cc_final: 0.7675 (t70) outliers start: 52 outliers final: 22 residues processed: 291 average time/residue: 1.3628 time to fit residues: 447.6797 Evaluate side-chains 281 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 245 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 164 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 164 SER Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 164 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.9990 chunk 292 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 325 optimal weight: 0.0770 chunk 269 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 56 GLN L 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 27240 Z= 0.133 Angle : 0.381 4.907 36780 Z= 0.208 Chirality : 0.031 0.122 4332 Planarity : 0.002 0.025 4632 Dihedral : 2.985 14.216 3612 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 1.90 % Allowed : 13.54 % Favored : 84.56 % 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: 5.47 (0.14), residues: 3396 helix: 3.91 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.98 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 86 HIS 0.001 0.001 HIS F 292 PHE 0.011 0.001 PHE E 50 TYR 0.013 0.001 TYR F 54 ARG 0.001 0.000 ARG B 291 *********************** 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 305 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 249 time to evaluate : 2.348 Fit side-chains REVERT: A 18 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6663 (mt-10) REVERT: A 42 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: A 216 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7548 (ttmt) REVERT: A 267 ASP cc_start: 0.8077 (t0) cc_final: 0.7711 (t0) REVERT: B 15 ASN cc_start: 0.7447 (m-40) cc_final: 0.7096 (m110) REVERT: B 18 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6677 (mt-10) REVERT: C 18 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6639 (mt-10) REVERT: C 45 LYS cc_start: 0.8011 (mttm) cc_final: 0.7644 (mtpt) REVERT: C 118 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7475 (tttt) REVERT: C 129 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6978 (mm-30) REVERT: C 132 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8305 (mttp) REVERT: C 267 ASP cc_start: 0.7951 (t0) cc_final: 0.7657 (t0) REVERT: D 267 ASP cc_start: 0.8074 (t0) cc_final: 0.7714 (t0) REVERT: E 15 ASN cc_start: 0.7449 (m-40) cc_final: 0.7162 (m110) REVERT: E 118 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7948 (mtmm) REVERT: E 267 ASP cc_start: 0.8069 (t0) cc_final: 0.7747 (t0) REVERT: F 129 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6980 (mm-30) REVERT: F 132 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8268 (mttp) REVERT: F 267 ASP cc_start: 0.7947 (t0) cc_final: 0.7674 (t0) REVERT: G 18 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6687 (mt-10) REVERT: G 267 ASP cc_start: 0.8083 (t0) cc_final: 0.7708 (t0) REVERT: H 15 ASN cc_start: 0.7613 (m-40) cc_final: 0.7301 (m110) REVERT: H 18 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6841 (mt-10) REVERT: I 45 LYS cc_start: 0.7922 (mttm) cc_final: 0.7576 (mtpt) REVERT: I 99 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8427 (tp) REVERT: I 129 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6992 (mm-30) REVERT: J 18 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6619 (mt-10) REVERT: J 42 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: J 45 LYS cc_start: 0.8042 (mttm) cc_final: 0.7543 (mtpt) REVERT: J 216 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7526 (ttmm) REVERT: J 267 ASP cc_start: 0.8061 (t0) cc_final: 0.7694 (t0) REVERT: K 15 ASN cc_start: 0.7443 (m-40) cc_final: 0.7094 (m110) REVERT: K 102 ASP cc_start: 0.7895 (t0) cc_final: 0.7498 (m-30) REVERT: K 118 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7946 (mtmm) REVERT: L 118 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7325 (tttt) REVERT: L 129 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7015 (mm-30) REVERT: L 267 ASP cc_start: 0.7947 (t0) cc_final: 0.7696 (t70) outliers start: 56 outliers final: 17 residues processed: 293 average time/residue: 1.3472 time to fit residues: 446.0654 Evaluate side-chains 269 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 164 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 143 ASN Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 118 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 185 optimal weight: 0.2980 chunk 237 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 273 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 323 optimal weight: 0.9990 chunk 202 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 27240 Z= 0.128 Angle : 0.374 4.918 36780 Z= 0.203 Chirality : 0.030 0.118 4332 Planarity : 0.002 0.025 4632 Dihedral : 2.922 14.143 3612 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.77 % Allowed : 13.98 % Favored : 84.25 % 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: 5.70 (0.14), residues: 3396 helix: 4.07 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.99 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 86 HIS 0.001 0.000 HIS L 292 PHE 0.012 0.001 PHE E 50 TYR 0.012 0.001 TYR F 54 ARG 0.001 0.000 ARG J 261 *********************** 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 311 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 259 time to evaluate : 2.426 Fit side-chains REVERT: A 18 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6653 (mt-10) REVERT: A 42 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: A 99 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8193 (tp) REVERT: A 210 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6712 (mm-30) REVERT: A 216 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7450 (ttmm) REVERT: A 267 ASP cc_start: 0.8080 (t0) cc_final: 0.7732 (t0) REVERT: B 15 ASN cc_start: 0.7489 (m-40) cc_final: 0.7150 (m110) REVERT: B 18 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6671 (mt-10) REVERT: B 102 ASP cc_start: 0.7831 (t0) cc_final: 0.7508 (t0) REVERT: C 18 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6649 (mt-10) REVERT: C 45 LYS cc_start: 0.7993 (mttm) cc_final: 0.7626 (mtpt) REVERT: C 56 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7566 (mm-40) REVERT: C 118 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7440 (tttt) REVERT: C 129 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6906 (mm-30) REVERT: C 132 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8318 (mttp) REVERT: C 267 ASP cc_start: 0.7972 (t0) cc_final: 0.7719 (t70) REVERT: D 267 ASP cc_start: 0.8070 (t0) cc_final: 0.7696 (t0) REVERT: E 15 ASN cc_start: 0.7510 (m-40) cc_final: 0.7221 (m110) REVERT: F 118 LYS cc_start: 0.8025 (ttmt) cc_final: 0.7452 (tttt) REVERT: F 129 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7015 (mm-30) REVERT: F 132 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8329 (mttp) REVERT: G 18 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6701 (mt-10) REVERT: G 267 ASP cc_start: 0.8059 (t0) cc_final: 0.7700 (t0) REVERT: H 15 ASN cc_start: 0.7615 (m-40) cc_final: 0.7299 (m110) REVERT: I 45 LYS cc_start: 0.7937 (mttm) cc_final: 0.7586 (mtpt) REVERT: I 99 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8433 (tp) REVERT: I 129 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6998 (mm-30) REVERT: J 18 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6630 (mt-10) REVERT: J 42 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: J 45 LYS cc_start: 0.8001 (mttm) cc_final: 0.7502 (mtpt) REVERT: J 210 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6743 (mm-30) REVERT: J 216 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7505 (ttmm) REVERT: J 267 ASP cc_start: 0.8120 (t0) cc_final: 0.7765 (t0) REVERT: K 15 ASN cc_start: 0.7484 (m-40) cc_final: 0.7143 (m110) REVERT: K 56 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7724 (tm-30) REVERT: K 102 ASP cc_start: 0.7862 (t0) cc_final: 0.7541 (t0) REVERT: L 118 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7292 (tttt) REVERT: L 129 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7054 (mm-30) REVERT: L 267 ASP cc_start: 0.7943 (t0) cc_final: 0.7705 (t70) outliers start: 52 outliers final: 25 residues processed: 300 average time/residue: 1.3792 time to fit residues: 466.7373 Evaluate side-chains 283 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 244 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 197 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 99 LEU Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 164 SER 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 143 ASN Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 164 SER 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: 0.8980 chunk 193 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.2869 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= 0.159 Angle : 0.405 5.055 36780 Z= 0.219 Chirality : 0.031 0.121 4332 Planarity : 0.002 0.025 4632 Dihedral : 2.967 14.036 3612 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.80 % Allowed : 13.71 % Favored : 84.49 % 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: 5.56 (0.14), residues: 3396 helix: 3.97 (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 0.017 0.002 TRP I 86 HIS 0.002 0.001 HIS C 292 PHE 0.012 0.001 PHE E 50 TYR 0.014 0.001 TYR K 54 ARG 0.001 0.000 ARG I 174 *********************** 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 305 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 252 time to evaluate : 2.370 Fit side-chains REVERT: A 18 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6692 (mt-10) REVERT: A 42 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6944 (tt0) REVERT: A 99 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8282 (tp) REVERT: A 216 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7514 (ttmt) REVERT: A 267 ASP cc_start: 0.8142 (t0) cc_final: 0.7785 (t0) REVERT: B 15 ASN cc_start: 0.7557 (m-40) cc_final: 0.7221 (m110) REVERT: B 18 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6701 (mt-10) REVERT: B 102 ASP cc_start: 0.7879 (t0) cc_final: 0.7530 (t0) REVERT: C 45 LYS cc_start: 0.7984 (mttm) cc_final: 0.7627 (mtpt) REVERT: C 118 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7480 (tttt) REVERT: C 129 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6982 (mm-30) REVERT: C 132 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8378 (mttp) REVERT: C 267 ASP cc_start: 0.7995 (t0) cc_final: 0.7744 (t70) REVERT: D 102 ASP cc_start: 0.8125 (t0) cc_final: 0.7910 (t0) REVERT: D 216 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7587 (ttmm) REVERT: D 267 ASP cc_start: 0.8121 (t0) cc_final: 0.7744 (t0) REVERT: E 15 ASN cc_start: 0.7493 (m-40) cc_final: 0.7189 (m110) REVERT: E 42 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7196 (tt0) REVERT: F 92 GLN cc_start: 0.8379 (mt0) cc_final: 0.8139 (mt0) REVERT: F 129 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6993 (mm-30) REVERT: F 132 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8243 (mttp) REVERT: F 267 ASP cc_start: 0.7973 (t0) cc_final: 0.7728 (t70) REVERT: G 18 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6685 (mt-10) REVERT: G 99 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8279 (tp) REVERT: G 267 ASP cc_start: 0.8085 (t0) cc_final: 0.7721 (t0) REVERT: H 15 ASN cc_start: 0.7553 (m-40) cc_final: 0.7238 (m110) REVERT: I 45 LYS cc_start: 0.7994 (mttm) cc_final: 0.7645 (mtpt) REVERT: I 99 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8482 (tp) REVERT: I 129 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6939 (mm-30) REVERT: J 18 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6717 (mt-10) REVERT: J 42 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: J 45 LYS cc_start: 0.8044 (mttm) cc_final: 0.7490 (mtpt) REVERT: J 216 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7461 (ttmm) REVERT: J 267 ASP cc_start: 0.8140 (t0) cc_final: 0.7786 (t0) REVERT: K 15 ASN cc_start: 0.7554 (m-40) cc_final: 0.7219 (m110) REVERT: L 15 ASN cc_start: 0.7632 (m-40) cc_final: 0.7168 (m110) REVERT: L 118 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7362 (tttt) REVERT: L 129 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7032 (mm-30) REVERT: L 267 ASP cc_start: 0.7965 (t0) cc_final: 0.7729 (t70) outliers start: 53 outliers final: 26 residues processed: 291 average time/residue: 1.3433 time to fit residues: 441.7854 Evaluate side-chains 292 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 253 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 164 SER 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 D residue 98 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 164 SER 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 G residue 18 GLU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 197 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 99 LEU Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 164 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 0.7980 chunk 310 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 chunk 301 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7949 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 27240 Z= 0.143 Angle : 0.390 4.907 36780 Z= 0.211 Chirality : 0.031 0.120 4332 Planarity : 0.002 0.025 4632 Dihedral : 2.943 14.011 3612 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.53 % Allowed : 13.88 % Favored : 84.59 % 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 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.91 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 86 HIS 0.001 0.001 HIS F 292 PHE 0.012 0.001 PHE E 50 TYR 0.013 0.001 TYR K 54 ARG 0.001 0.000 ARG C 174 *********************** 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 299 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 254 time to evaluate : 2.448 Fit side-chains REVERT: A 18 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6684 (mt-10) REVERT: A 42 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7009 (tt0) REVERT: A 45 LYS cc_start: 0.8041 (mttm) cc_final: 0.7525 (mtpt) REVERT: A 99 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8240 (tp) REVERT: A 216 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7549 (ttmt) REVERT: A 267 ASP cc_start: 0.8094 (t0) cc_final: 0.7738 (t0) REVERT: B 15 ASN cc_start: 0.7539 (m-40) cc_final: 0.7204 (m110) REVERT: B 18 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6687 (mt-10) REVERT: B 102 ASP cc_start: 0.7875 (t0) cc_final: 0.7560 (t0) REVERT: C 18 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6661 (mt-10) REVERT: C 45 LYS cc_start: 0.7985 (mttm) cc_final: 0.7626 (mtpt) REVERT: C 118 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7445 (tttt) REVERT: C 129 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6977 (mm-30) REVERT: C 132 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8267 (mttp) REVERT: C 267 ASP cc_start: 0.7980 (t0) cc_final: 0.7739 (t70) REVERT: D 102 ASP cc_start: 0.8104 (t0) cc_final: 0.7901 (t0) REVERT: D 267 ASP cc_start: 0.8083 (t0) cc_final: 0.7722 (t0) REVERT: E 15 ASN cc_start: 0.7446 (m-40) cc_final: 0.7142 (m110) REVERT: F 129 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6978 (mm-30) REVERT: F 132 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8245 (mttp) REVERT: F 267 ASP cc_start: 0.7970 (t0) cc_final: 0.7737 (t70) REVERT: G 18 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: G 267 ASP cc_start: 0.8081 (t0) cc_final: 0.7712 (t0) REVERT: H 15 ASN cc_start: 0.7541 (m-40) cc_final: 0.7239 (m110) REVERT: I 45 LYS cc_start: 0.7968 (mttm) cc_final: 0.7637 (mtpt) REVERT: I 99 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8432 (tp) REVERT: I 129 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6938 (mm-30) REVERT: J 18 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6689 (mt-10) REVERT: J 42 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6952 (tt0) REVERT: J 45 LYS cc_start: 0.8054 (mttm) cc_final: 0.7503 (mtpt) REVERT: J 216 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7543 (ttmm) REVERT: J 267 ASP cc_start: 0.8127 (t0) cc_final: 0.7768 (t0) REVERT: K 15 ASN cc_start: 0.7536 (m-40) cc_final: 0.7217 (m110) REVERT: K 102 ASP cc_start: 0.7860 (t0) cc_final: 0.7517 (t0) REVERT: L 118 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7353 (tttt) REVERT: L 129 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7018 (mm-30) REVERT: L 267 ASP cc_start: 0.7944 (t0) cc_final: 0.7714 (t70) outliers start: 45 outliers final: 26 residues processed: 288 average time/residue: 1.3718 time to fit residues: 447.0400 Evaluate side-chains 287 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 249 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 164 SER 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 G residue 18 GLU Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 197 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 99 LEU Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 164 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.7980 chunk 319 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 334 optimal weight: 0.9990 chunk 308 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 205 optimal weight: 0.4980 chunk 163 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7938 moved from start: 0.3000 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= 0.138 Angle : 0.384 4.902 36780 Z= 0.209 Chirality : 0.031 0.119 4332 Planarity : 0.002 0.025 4632 Dihedral : 2.930 14.128 3612 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 1.43 % Allowed : 13.84 % Favored : 84.73 % 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: 5.74 (0.14), residues: 3396 helix: 4.09 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.94 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 86 HIS 0.001 0.001 HIS I 292 PHE 0.012 0.001 PHE E 50 TYR 0.013 0.001 TYR F 54 ARG 0.000 0.000 ARG C 174 ********************** 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 295 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 253 time to evaluate : 2.317 Fit side-chains REVERT: A 18 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6665 (mt-10) REVERT: A 42 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: A 45 LYS cc_start: 0.8047 (mttm) cc_final: 0.7526 (mtpt) REVERT: A 99 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8199 (tp) REVERT: A 216 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7538 (ttmt) REVERT: A 267 ASP cc_start: 0.8125 (t0) cc_final: 0.7775 (t0) REVERT: B 15 ASN cc_start: 0.7535 (m-40) cc_final: 0.7201 (m110) REVERT: B 18 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6704 (mt-10) REVERT: B 102 ASP cc_start: 0.7867 (t0) cc_final: 0.7564 (t0) REVERT: C 18 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: C 45 LYS cc_start: 0.7993 (mttm) cc_final: 0.7636 (mtpt) REVERT: C 118 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7437 (tttt) REVERT: C 129 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6978 (mm-30) REVERT: C 132 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8332 (mttp) REVERT: C 267 ASP cc_start: 0.7985 (t0) cc_final: 0.7736 (t70) REVERT: D 267 ASP cc_start: 0.8086 (t0) cc_final: 0.7705 (t0) REVERT: E 15 ASN cc_start: 0.7465 (m-40) cc_final: 0.7153 (m110) REVERT: F 92 GLN cc_start: 0.8321 (mt0) cc_final: 0.8071 (mt0) REVERT: F 129 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7058 (mm-30) REVERT: F 132 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8290 (mttp) REVERT: F 267 ASP cc_start: 0.7956 (t0) cc_final: 0.7721 (t70) REVERT: G 18 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6689 (mt-10) REVERT: G 267 ASP cc_start: 0.8081 (t0) cc_final: 0.7714 (t0) REVERT: H 15 ASN cc_start: 0.7535 (m-40) cc_final: 0.7234 (m110) REVERT: I 45 LYS cc_start: 0.7941 (mttm) cc_final: 0.7624 (mtpt) REVERT: I 99 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8407 (tp) REVERT: I 129 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6992 (mm-30) REVERT: J 18 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6710 (mt-10) REVERT: J 42 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6939 (tt0) REVERT: J 45 LYS cc_start: 0.8004 (mttm) cc_final: 0.7458 (mtpt) REVERT: J 216 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7485 (ttmm) REVERT: J 267 ASP cc_start: 0.8123 (t0) cc_final: 0.7771 (t0) REVERT: K 15 ASN cc_start: 0.7533 (m-40) cc_final: 0.7215 (m110) REVERT: K 102 ASP cc_start: 0.7853 (t0) cc_final: 0.7522 (t0) REVERT: L 118 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7380 (tttt) REVERT: L 129 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7015 (mm-30) REVERT: L 267 ASP cc_start: 0.7942 (t0) cc_final: 0.7712 (t70) outliers start: 42 outliers final: 28 residues processed: 285 average time/residue: 1.3275 time to fit residues: 428.1349 Evaluate side-chains 287 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 247 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 164 SER 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 168 SER Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 197 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 99 LEU Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 197 SER Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 164 SER 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: 0.8980 chunk 81 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN I 28 ASN K 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.091576 restraints weight = 28894.224| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.31 r_work: 0.2818 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2774 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 : 0.444 5.720 36780 Z= 0.238 Chirality : 0.033 0.125 4332 Planarity : 0.002 0.026 4632 Dihedral : 3.036 13.860 3612 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.73 % Allowed : 13.57 % Favored : 84.69 % 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: 5.36 (0.14), residues: 3396 helix: 3.83 (0.09), residues: 3108 sheet: None (None), residues: 0 loop : -0.83 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 86 HIS 0.003 0.002 HIS F 292 PHE 0.012 0.002 PHE L 50 TYR 0.015 0.002 TYR H 54 ARG 0.001 0.000 ARG I 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7634.93 seconds wall clock time: 133 minutes 32.46 seconds (8012.46 seconds total)