Starting phenix.real_space_refine on Tue Nov 14 12:42:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mru_9213/11_2023/6mru_9213.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mru_9213/11_2023/6mru_9213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mru_9213/11_2023/6mru_9213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mru_9213/11_2023/6mru_9213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mru_9213/11_2023/6mru_9213.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mru_9213/11_2023/6mru_9213.pdb" } resolution = 3.2 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= 0.007 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 29068 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 65 5.16 5 C 18577 2.51 5 N 4680 2.21 5 O 5785 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" Residue "M ARG 49": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 29107 Number of models: 1 Model: "" Number of chains: 13 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} Chain: "M" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Time building chain proxies: 11.28, per 1000 atoms: 0.39 Number of scatterers: 29107 At special positions: 0 Unit cell: (139.1, 139.1, 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 65 16.00 O 5785 8.00 N 4680 7.00 C 18577 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: 8.86 Conformation dependent library (CDL) restraints added in 3.9 seconds 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7098 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 0 sheets defined 94.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 8 through 35 removed outlier: 3.602A pdb=" N GLU A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 101 removed outlier: 3.758A pdb=" N PHE A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 140 removed outlier: 3.879A pdb=" N LYS A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 3.851A 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 189 through 206 removed outlier: 3.924A pdb=" N SER A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 265 removed outlier: 3.632A pdb=" N GLU A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 removed outlier: 3.528A pdb=" N ASN A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 35 removed outlier: 3.602A pdb=" N GLU B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 101 removed outlier: 3.758A pdb=" N PHE B 40 " --> pdb=" O PRO B 36 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 140 removed outlier: 3.879A pdb=" N LYS B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 3.852A 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 189 through 206 removed outlier: 3.922A pdb=" N SER B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 265 removed outlier: 3.632A pdb=" N GLU B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 292 removed outlier: 3.528A pdb=" N ASN B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 35 removed outlier: 3.602A pdb=" N GLU C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 101 removed outlier: 3.758A pdb=" N PHE C 40 " --> pdb=" O PRO C 36 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 140 removed outlier: 3.879A pdb=" N LYS C 113 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER C 160 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP C 171 " --> pdb=" O GLN C 167 " (cutoff:3.500A) removed outlier: 3.851A 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 189 through 206 removed outlier: 3.924A pdb=" N SER C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 265 removed outlier: 3.632A pdb=" N GLU C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 234 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 292 removed outlier: 3.528A pdb=" N ASN C 283 " --> pdb=" O LYS C 279 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 35 removed outlier: 3.601A pdb=" N GLU D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 101 removed outlier: 3.757A pdb=" N PHE D 40 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 140 removed outlier: 3.878A pdb=" N LYS D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR D 165 " --> pdb=" O GLU D 161 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP D 171 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 3.852A 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 189 through 206 removed outlier: 3.923A pdb=" N SER D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 265 removed outlier: 3.631A pdb=" N GLU D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 234 " --> pdb=" O LYS D 230 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 292 removed outlier: 3.529A pdb=" N ASN D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 35 removed outlier: 3.602A pdb=" N GLU E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 101 removed outlier: 3.758A pdb=" N PHE E 40 " --> pdb=" O PRO E 36 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA E 95 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 140 removed outlier: 3.879A pdb=" N LYS E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER E 160 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR E 165 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.852A 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 189 through 206 removed outlier: 3.924A pdb=" N SER E 195 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 265 removed outlier: 3.632A pdb=" N GLU E 210 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 234 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP E 265 " --> pdb=" O ARG E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 292 removed outlier: 3.529A pdb=" N ASN E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 35 removed outlier: 3.602A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 101 removed outlier: 3.758A pdb=" N PHE F 40 " --> pdb=" O PRO F 36 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 140 removed outlier: 3.879A pdb=" N LYS F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR F 125 " --> pdb=" O ASP F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR F 165 " --> pdb=" O GLU F 161 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP F 171 " --> pdb=" O GLN F 167 " (cutoff:3.500A) removed outlier: 3.850A 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 189 through 206 removed outlier: 3.923A pdb=" N SER F 195 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 265 removed outlier: 3.631A pdb=" N GLU F 210 " --> pdb=" O LYS F 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 234 " --> pdb=" O LYS F 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP F 265 " --> pdb=" O ARG F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 292 removed outlier: 3.529A pdb=" N ASN F 283 " --> pdb=" O LYS F 279 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 35 removed outlier: 3.602A pdb=" N GLU G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 101 removed outlier: 3.757A pdb=" N PHE G 40 " --> pdb=" O PRO G 36 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN G 73 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA G 95 " --> pdb=" O THR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 140 removed outlier: 3.878A pdb=" N LYS G 113 " --> pdb=" O ALA G 109 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR G 125 " --> pdb=" O ASP G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP G 171 " --> pdb=" O GLN G 167 " (cutoff:3.500A) removed outlier: 3.851A 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 189 through 206 removed outlier: 3.923A pdb=" N SER G 195 " --> pdb=" O GLY G 191 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 265 removed outlier: 3.631A pdb=" N GLU G 210 " --> pdb=" O LYS G 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS G 234 " --> pdb=" O LYS G 230 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU G 256 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP G 265 " --> pdb=" O ARG G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 292 removed outlier: 3.527A pdb=" N ASN G 283 " --> pdb=" O LYS G 279 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG G 291 " --> pdb=" O GLU G 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 35 removed outlier: 3.602A pdb=" N GLU H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 101 removed outlier: 3.759A pdb=" N PHE H 40 " --> pdb=" O PRO H 36 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL H 60 " --> pdb=" O GLN H 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN H 73 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 140 removed outlier: 3.879A pdb=" N LYS H 113 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR H 125 " --> pdb=" O ASP H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN H 154 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER H 160 " --> pdb=" O THR H 156 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR H 165 " --> pdb=" O GLU H 161 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP H 171 " --> pdb=" O GLN H 167 " (cutoff:3.500A) removed outlier: 3.850A 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 189 through 206 removed outlier: 3.923A pdb=" N SER H 195 " --> pdb=" O GLY H 191 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE H 198 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 265 removed outlier: 3.632A pdb=" N GLU H 210 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS H 234 " --> pdb=" O LYS H 230 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE H 253 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 292 removed outlier: 3.528A pdb=" N ASN H 283 " --> pdb=" O LYS H 279 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG H 291 " --> pdb=" O GLU H 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 35 removed outlier: 3.602A pdb=" N GLU I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN I 33 " --> pdb=" O LYS I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 101 removed outlier: 3.758A pdb=" N PHE I 40 " --> pdb=" O PRO I 36 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL I 60 " --> pdb=" O GLN I 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN I 73 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA I 95 " --> pdb=" O THR I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 140 removed outlier: 3.879A pdb=" N LYS I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR I 125 " --> pdb=" O ASP I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN I 154 " --> pdb=" O ALA I 150 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER I 160 " --> pdb=" O THR I 156 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR I 165 " --> pdb=" O GLU I 161 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN I 167 " --> pdb=" O SER I 163 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP I 171 " --> pdb=" O GLN I 167 " (cutoff:3.500A) removed outlier: 3.851A 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 189 through 206 removed outlier: 3.923A pdb=" N SER I 195 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE I 198 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU I 204 " --> pdb=" O ALA I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 265 removed outlier: 3.632A pdb=" N GLU I 210 " --> pdb=" O LYS I 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS I 234 " --> pdb=" O LYS I 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU I 246 " --> pdb=" O LYS I 242 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE I 253 " --> pdb=" O ALA I 249 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU I 256 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP I 265 " --> pdb=" O ARG I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 292 removed outlier: 3.528A pdb=" N ASN I 283 " --> pdb=" O LYS I 279 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG I 291 " --> pdb=" O GLU I 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 35 removed outlier: 3.601A pdb=" N GLU J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN J 33 " --> pdb=" O LYS J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 101 removed outlier: 3.758A pdb=" N PHE J 40 " --> pdb=" O PRO J 36 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL J 60 " --> pdb=" O GLN J 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN J 73 " --> pdb=" O LEU J 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN J 92 " --> pdb=" O GLY J 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA J 95 " --> pdb=" O THR J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 140 removed outlier: 3.880A pdb=" N LYS J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP J 114 " --> pdb=" O SER J 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR J 125 " --> pdb=" O ASP J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN J 154 " --> pdb=" O ALA J 150 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER J 160 " --> pdb=" O THR J 156 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR J 165 " --> pdb=" O GLU J 161 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP J 171 " --> pdb=" O GLN J 167 " (cutoff:3.500A) removed outlier: 3.851A 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 189 through 206 removed outlier: 3.923A pdb=" N SER J 195 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE J 198 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU J 204 " --> pdb=" O ALA J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 265 removed outlier: 3.632A pdb=" N GLU J 210 " --> pdb=" O LYS J 206 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS J 234 " --> pdb=" O LYS J 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU J 246 " --> pdb=" O LYS J 242 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE J 253 " --> pdb=" O ALA J 249 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU J 256 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP J 265 " --> pdb=" O ARG J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 292 removed outlier: 3.528A pdb=" N ASN J 283 " --> pdb=" O LYS J 279 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG J 291 " --> pdb=" O GLU J 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 35 removed outlier: 3.602A pdb=" N GLU K 18 " --> pdb=" O LYS K 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN K 33 " --> pdb=" O LYS K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 101 removed outlier: 3.757A pdb=" N PHE K 40 " --> pdb=" O PRO K 36 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL K 60 " --> pdb=" O GLN K 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU K 61 " --> pdb=" O ALA K 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN K 73 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN K 92 " --> pdb=" O GLY K 88 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA K 95 " --> pdb=" O THR K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 140 removed outlier: 3.879A pdb=" N LYS K 113 " --> pdb=" O ALA K 109 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR K 125 " --> pdb=" O ASP K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU K 149 " --> pdb=" O SER K 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN K 154 " --> pdb=" O ALA K 150 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER K 160 " --> pdb=" O THR K 156 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR K 165 " --> pdb=" O GLU K 161 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN K 167 " --> pdb=" O SER K 163 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP K 171 " --> pdb=" O GLN K 167 " (cutoff:3.500A) removed outlier: 3.851A 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 189 through 206 removed outlier: 3.924A pdb=" N SER K 195 " --> pdb=" O GLY K 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE K 198 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU K 204 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 265 removed outlier: 3.631A pdb=" N GLU K 210 " --> pdb=" O LYS K 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS K 234 " --> pdb=" O LYS K 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU K 246 " --> pdb=" O LYS K 242 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE K 253 " --> pdb=" O ALA K 249 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU K 256 " --> pdb=" O GLU K 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP K 265 " --> pdb=" O ARG K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 292 removed outlier: 3.528A pdb=" N ASN K 283 " --> pdb=" O LYS K 279 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG K 291 " --> pdb=" O GLU K 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 35 removed outlier: 3.602A pdb=" N GLU L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN L 33 " --> pdb=" O LYS L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 101 removed outlier: 3.758A pdb=" N PHE L 40 " --> pdb=" O PRO L 36 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL L 60 " --> pdb=" O GLN L 56 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN L 92 " --> pdb=" O GLY L 88 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 140 removed outlier: 3.880A pdb=" N LYS L 113 " --> pdb=" O ALA L 109 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR L 125 " --> pdb=" O ASP L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU L 149 " --> pdb=" O SER L 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN L 154 " --> pdb=" O ALA L 150 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER L 160 " --> pdb=" O THR L 156 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR L 165 " --> pdb=" O GLU L 161 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN L 167 " --> pdb=" O SER L 163 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP L 171 " --> pdb=" O GLN L 167 " (cutoff:3.500A) removed outlier: 3.851A 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 189 through 206 removed outlier: 3.923A pdb=" N SER L 195 " --> pdb=" O GLY L 191 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE L 198 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU L 204 " --> pdb=" O ALA L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 265 removed outlier: 3.632A pdb=" N GLU L 210 " --> pdb=" O LYS L 206 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS L 234 " --> pdb=" O LYS L 230 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU L 246 " --> pdb=" O LYS L 242 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE L 253 " --> pdb=" O ALA L 249 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU L 256 " --> pdb=" O GLU L 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP L 265 " --> pdb=" O ARG L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 292 removed outlier: 3.528A pdb=" N ASN L 283 " --> pdb=" O LYS L 279 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG L 291 " --> pdb=" O GLU L 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 35 removed outlier: 3.602A pdb=" N GLU M 18 " --> pdb=" O LYS M 14 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN M 33 " --> pdb=" O LYS M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 101 removed outlier: 3.758A pdb=" N PHE M 40 " --> pdb=" O PRO M 36 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS M 51 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL M 60 " --> pdb=" O GLN M 56 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU M 61 " --> pdb=" O ALA M 57 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN M 73 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL M 89 " --> pdb=" O GLU M 85 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN M 92 " --> pdb=" O GLY M 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 140 removed outlier: 3.879A pdb=" N LYS M 113 " --> pdb=" O ALA M 109 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR M 125 " --> pdb=" O ASP M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 181 removed outlier: 4.203A pdb=" N LEU M 149 " --> pdb=" O SER M 145 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN M 154 " --> pdb=" O ALA M 150 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER M 160 " --> pdb=" O THR M 156 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR M 165 " --> pdb=" O GLU M 161 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN M 167 " --> pdb=" O SER M 163 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP M 171 " --> pdb=" O GLN M 167 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS M 172 " --> pdb=" O SER M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 184 No H-bonds generated for 'chain 'M' and resid 182 through 184' Processing helix chain 'M' and resid 189 through 206 removed outlier: 3.924A pdb=" N SER M 195 " --> pdb=" O GLY M 191 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE M 198 " --> pdb=" O ILE M 194 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU M 204 " --> pdb=" O ALA M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 265 removed outlier: 3.632A pdb=" N GLU M 210 " --> pdb=" O LYS M 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS M 234 " --> pdb=" O LYS M 230 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU M 256 " --> pdb=" O GLU M 252 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP M 265 " --> pdb=" O ARG M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 292 removed outlier: 3.528A pdb=" N ASN M 283 " --> pdb=" O LYS M 279 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG M 291 " --> pdb=" O GLU M 287 " (cutoff:3.500A) 2679 hydrogen bonds defined for protein. 8037 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.16 Time building geometry restraints manager: 9.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9328 1.34 - 1.46: 3835 1.46 - 1.57: 16243 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 29510 Sorted by residual: bond pdb=" C ILE A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.336 1.355 -0.020 1.23e-02 6.61e+03 2.57e+00 bond pdb=" C ILE I 208 " pdb=" N PRO I 209 " ideal model delta sigma weight residual 1.336 1.355 -0.020 1.23e-02 6.61e+03 2.57e+00 bond pdb=" C ILE G 208 " pdb=" N PRO G 209 " ideal model delta sigma weight residual 1.336 1.355 -0.020 1.23e-02 6.61e+03 2.52e+00 bond pdb=" C ILE J 208 " pdb=" N PRO J 209 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.51e+00 bond pdb=" C ILE H 208 " pdb=" N PRO H 209 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.50e+00 ... (remaining 29505 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.18: 285 107.18 - 113.87: 17148 113.87 - 120.57: 13208 120.57 - 127.26: 9113 127.26 - 133.95: 91 Bond angle restraints: 39845 Sorted by residual: angle pdb=" CA ILE K 208 " pdb=" C ILE K 208 " pdb=" N PRO K 209 " ideal model delta sigma weight residual 118.88 122.55 -3.67 1.54e+00 4.22e-01 5.69e+00 angle pdb=" CA ILE D 208 " pdb=" C ILE D 208 " pdb=" N PRO D 209 " ideal model delta sigma weight residual 118.88 122.54 -3.66 1.54e+00 4.22e-01 5.66e+00 angle pdb=" CA ILE E 208 " pdb=" C ILE E 208 " pdb=" N PRO E 209 " ideal model delta sigma weight residual 118.88 122.54 -3.66 1.54e+00 4.22e-01 5.65e+00 angle pdb=" CA ILE M 208 " pdb=" C ILE M 208 " pdb=" N PRO M 209 " ideal model delta sigma weight residual 118.88 122.53 -3.65 1.54e+00 4.22e-01 5.63e+00 angle pdb=" CA ILE H 208 " pdb=" C ILE H 208 " pdb=" N PRO H 209 " ideal model delta sigma weight residual 118.88 122.53 -3.65 1.54e+00 4.22e-01 5.62e+00 ... (remaining 39840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 17134 15.63 - 31.26: 637 31.26 - 46.90: 221 46.90 - 62.53: 0 62.53 - 78.16: 26 Dihedral angle restraints: 18018 sinusoidal: 7059 harmonic: 10959 Sorted by residual: dihedral pdb=" CA PHE F 141 " pdb=" C PHE F 141 " pdb=" N ASN F 142 " pdb=" CA ASN F 142 " ideal model delta harmonic sigma weight residual -180.00 -161.55 -18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA PHE D 141 " pdb=" C PHE D 141 " pdb=" N ASN D 142 " pdb=" CA ASN D 142 " ideal model delta harmonic sigma weight residual 180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA PHE C 141 " pdb=" C PHE C 141 " pdb=" N ASN C 142 " pdb=" CA ASN C 142 " ideal model delta harmonic sigma weight residual 180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 18015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3064 0.036 - 0.071: 1236 0.071 - 0.107: 341 0.107 - 0.143: 39 0.143 - 0.179: 13 Chirality restraints: 4693 Sorted by residual: chirality pdb=" CA TYR H 54 " pdb=" N TYR H 54 " pdb=" C TYR H 54 " pdb=" CB TYR H 54 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA TYR G 54 " pdb=" N TYR G 54 " pdb=" C TYR G 54 " pdb=" CB TYR G 54 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA TYR F 54 " pdb=" N TYR F 54 " pdb=" C TYR F 54 " pdb=" CB TYR F 54 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.74e-01 ... (remaining 4690 not shown) Planarity restraints: 5018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 86 " 0.016 2.00e-02 2.50e+03 1.06e-02 2.79e+00 pdb=" CG TRP I 86 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP I 86 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP I 86 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP I 86 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 86 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP I 86 " 0.000 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 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 86 " 0.016 2.00e-02 2.50e+03 1.05e-02 2.78e+00 pdb=" CG TRP G 86 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP G 86 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP G 86 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 86 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 86 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 86 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 86 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 86 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 86 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 86 " 0.016 2.00e-02 2.50e+03 1.05e-02 2.78e+00 pdb=" CG TRP J 86 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP J 86 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP J 86 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 86 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP J 86 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP J 86 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 86 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 86 " 0.001 2.00e-02 2.50e+03 ... (remaining 5015 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 8018 2.82 - 3.34: 28400 3.34 - 3.86: 47460 3.86 - 4.38: 51462 4.38 - 4.90: 92470 Nonbonded interactions: 227810 Sorted by model distance: nonbonded pdb=" OD1 ASP A 71 " pdb=" ND2 ASN B 142 " model vdw 2.297 2.520 nonbonded pdb=" OH TYR M 54 " pdb=" OD2 ASP M 158 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR D 54 " pdb=" OD2 ASP D 158 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR G 54 " pdb=" OD2 ASP G 158 " model vdw 2.300 2.440 nonbonded pdb=" OH TYR K 54 " pdb=" OD2 ASP K 158 " model vdw 2.300 2.440 ... (remaining 227805 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' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.020 Extract box with map and model: 5.640 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 56.540 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.005 0.045 29510 Z= 0.286 Angle : 0.729 7.540 39845 Z= 0.389 Chirality : 0.041 0.179 4693 Planarity : 0.005 0.037 5018 Dihedral : 10.165 78.162 10920 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.82 % Allowed : 2.92 % Favored : 96.26 % 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: -1.59 (0.11), residues: 3679 helix: -0.69 (0.07), residues: 3328 sheet: None (None), residues: 0 loop : -2.93 (0.20), residues: 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 499 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 2 residues processed: 525 average time/residue: 0.3677 time to fit residues: 292.0706 Evaluate side-chains 202 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 200 time to evaluate : 2.587 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1982 time to fit residues: 4.2686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 0.9980 chunk 275 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 285 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 330 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN B 52 GLN B 289 GLN C 52 GLN C 289 GLN D 52 GLN D 289 GLN E 52 GLN E 289 GLN F 289 GLN G 289 GLN H 289 GLN I 169 GLN I 289 GLN J 52 GLN J 289 GLN K 52 GLN K 289 GLN L 289 GLN M 52 GLN M 289 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 29510 Z= 0.165 Angle : 0.451 6.001 39845 Z= 0.240 Chirality : 0.032 0.136 4693 Planarity : 0.003 0.026 5018 Dihedral : 3.551 17.336 3913 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.48 % Allowed : 6.53 % Favored : 91.99 % 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: 2.08 (0.14), residues: 3679 helix: 1.65 (0.09), residues: 3393 sheet: None (None), residues: 0 loop : -1.59 (0.25), residues: 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 203 time to evaluate : 2.609 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 16 residues processed: 243 average time/residue: 0.2783 time to fit residues: 116.0390 Evaluate side-chains 170 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 2.563 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2043 time to fit residues: 9.6027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 331 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 328 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 265 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 112 GLN C 112 GLN D 52 GLN D 112 GLN E 52 GLN E 112 GLN F 112 GLN G 112 GLN G 292 HIS H 112 GLN I 112 GLN J 52 GLN J 112 GLN K 52 GLN L 112 GLN M 112 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 29510 Z= 0.169 Angle : 0.432 5.955 39845 Z= 0.227 Chirality : 0.032 0.138 4693 Planarity : 0.002 0.022 5018 Dihedral : 3.312 15.713 3913 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.41 % Allowed : 6.72 % Favored : 91.87 % 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: 3.59 (0.14), residues: 3679 helix: 2.62 (0.09), residues: 3406 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 150 time to evaluate : 2.581 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 17 residues processed: 191 average time/residue: 0.2695 time to fit residues: 90.4221 Evaluate side-chains 150 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 2.582 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1977 time to fit residues: 10.1328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 chunk 332 optimal weight: 0.8980 chunk 351 optimal weight: 0.5980 chunk 173 optimal weight: 4.9990 chunk 314 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN C 52 GLN K 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 29510 Z= 0.136 Angle : 0.397 5.424 39845 Z= 0.210 Chirality : 0.031 0.128 4693 Planarity : 0.002 0.020 5018 Dihedral : 3.173 15.084 3913 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 0.47 % Allowed : 6.69 % Favored : 92.84 % 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: 4.55 (0.14), residues: 3679 helix: 3.40 (0.09), residues: 3328 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 351 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 2.596 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 183 average time/residue: 0.2831 time to fit residues: 90.8094 Evaluate side-chains 144 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 2.578 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2032 time to fit residues: 6.2185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 300 optimal weight: 0.2980 chunk 243 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 315 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7944 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 29510 Z= 0.164 Angle : 0.408 5.692 39845 Z= 0.216 Chirality : 0.032 0.136 4693 Planarity : 0.002 0.021 5018 Dihedral : 3.134 14.932 3913 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.38 % Allowed : 6.94 % Favored : 92.68 % 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: 4.82 (0.14), residues: 3679 helix: 3.46 (0.09), residues: 3393 sheet: None (None), residues: 0 loop : -1.33 (0.27), residues: 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 2.614 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 151 average time/residue: 0.2782 time to fit residues: 73.6129 Evaluate side-chains 130 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2716 time to fit residues: 5.2881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 0.7980 chunk 316 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 352 optimal weight: 2.9990 chunk 292 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 184 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 29510 Z= 0.150 Angle : 0.393 5.031 39845 Z= 0.209 Chirality : 0.032 0.132 4693 Planarity : 0.002 0.021 5018 Dihedral : 3.099 14.760 3913 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.35 % Allowed : 6.97 % Favored : 92.68 % 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: 5.19 (0.14), residues: 3679 helix: 3.82 (0.09), residues: 3328 sheet: None (None), residues: 0 loop : -1.59 (0.25), residues: 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 2.540 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 143 average time/residue: 0.2936 time to fit residues: 73.7607 Evaluate side-chains 132 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 2.594 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2125 time to fit residues: 5.6430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 196 optimal weight: 10.0000 chunk 350 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN D 28 ASN E 28 ASN F 28 ASN H 28 ASN I 28 ASN I 169 GLN J 28 ASN L 28 ASN M 28 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 29510 Z= 0.211 Angle : 0.437 6.882 39845 Z= 0.230 Chirality : 0.033 0.141 4693 Planarity : 0.002 0.021 5018 Dihedral : 3.179 15.530 3913 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.38 % Allowed : 6.84 % Favored : 92.78 % 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: 5.06 (0.14), residues: 3679 helix: 3.66 (0.09), residues: 3354 sheet: None (None), residues: 0 loop : -1.20 (0.27), residues: 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 2.653 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 139 average time/residue: 0.2855 time to fit residues: 69.4696 Evaluate side-chains 129 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 2.543 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1987 time to fit residues: 6.0674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 275 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29510 Z= 0.138 Angle : 0.386 6.156 39845 Z= 0.207 Chirality : 0.031 0.131 4693 Planarity : 0.002 0.022 5018 Dihedral : 3.101 14.921 3913 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.41 (0.14), residues: 3679 helix: 3.96 (0.09), residues: 3328 sheet: None (None), residues: 0 loop : -1.35 (0.27), residues: 351 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 2.569 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 137 average time/residue: 0.2832 time to fit residues: 68.3180 Evaluate side-chains 126 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 2.568 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2038 time to fit residues: 4.3121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 0.9980 chunk 336 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 326 optimal weight: 0.0670 chunk 196 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 309 optimal weight: 1.9990 chunk 325 optimal weight: 0.0670 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29510 Z= 0.137 Angle : 0.384 6.443 39845 Z= 0.205 Chirality : 0.031 0.130 4693 Planarity : 0.002 0.021 5018 Dihedral : 3.044 14.551 3913 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.06 % Allowed : 7.28 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.59 (0.13), residues: 3679 helix: 4.07 (0.09), residues: 3328 sheet: None (None), residues: 0 loop : -1.29 (0.27), residues: 351 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 2.603 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 135 average time/residue: 0.2849 time to fit residues: 67.8204 Evaluate side-chains 126 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 2.595 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2008 time to fit residues: 3.8760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 362 optimal weight: 0.9990 chunk 333 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7963 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29510 Z= 0.177 Angle : 0.412 6.474 39845 Z= 0.218 Chirality : 0.032 0.136 4693 Planarity : 0.002 0.021 5018 Dihedral : 3.094 14.842 3913 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.03 % Allowed : 7.63 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.36 (0.14), residues: 3679 helix: 3.74 (0.09), residues: 3419 sheet: None (None), residues: 0 loop : -0.51 (0.32), residues: 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7358 Ramachandran restraints generated. 3679 Oldfield, 0 Emsley, 3679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 2.576 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.3010 time to fit residues: 69.0321 Evaluate side-chains 126 residues out of total 3185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 2.576 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2472 time to fit residues: 4.1986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 296 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100608 restraints weight = 35168.384| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.27 r_work: 0.3100 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29510 Z= 0.136 Angle : 0.383 6.723 39845 Z= 0.205 Chirality : 0.031 0.131 4693 Planarity : 0.002 0.021 5018 Dihedral : 3.053 14.539 3913 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % 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: 5.67 (0.13), residues: 3679 helix: 4.12 (0.08), residues: 3328 sheet: None (None), residues: 0 loop : -1.22 (0.28), residues: 351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3657.04 seconds wall clock time: 67 minutes 9.56 seconds (4029.56 seconds total)