Starting phenix.real_space_refine on Fri Feb 6 06:42:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pxf_71966/02_2026/9pxf_71966_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pxf_71966/02_2026/9pxf_71966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pxf_71966/02_2026/9pxf_71966_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pxf_71966/02_2026/9pxf_71966_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pxf_71966/02_2026/9pxf_71966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pxf_71966/02_2026/9pxf_71966.map" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cu 9 5.60 5 P 3 5.49 5 S 150 5.16 5 C 14616 2.51 5 N 3582 2.21 5 O 4580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22940 Number of models: 1 Model: "" Number of chains: 24 Chain: "G" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2092 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain: "D" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2210 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain: "A" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3007 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 27, 'TRANS': 353} Chain: "E" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2210 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain: "F" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2210 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain: "B" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3007 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 27, 'TRANS': 353} Chain: "C" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3007 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 27, 'TRANS': 353} Chain: "H" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2092 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain: "I" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2092 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain: "G" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' CU': 2, '6PL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' CU': 2, '6PL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' CU': 2, '6PL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 183 Classifications: {'water': 183} Link IDs: {None: 182} Chain: "E" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 177 Classifications: {'water': 177} Link IDs: {None: 176} Chain: "C" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 172 Classifications: {'water': 172} Link IDs: {None: 171} Chain: "H" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Time building chain proxies: 5.57, per 1000 atoms: 0.24 Number of scatterers: 22940 At special positions: 0 Unit cell: (114.838, 110.616, 127.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 9 28.99 S 150 16.00 P 3 15.00 O 4580 8.00 N 3582 7.00 C 14616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 1.0 seconds 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 27 sheets defined 57.5% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'G' and resid 19 through 23 removed outlier: 3.714A pdb=" N GLU G 22 " --> pdb=" O ASP G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 55 removed outlier: 6.002A pdb=" N TYR G 52 " --> pdb=" O ARG G 48 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N SER G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 92 removed outlier: 3.868A pdb=" N GLY G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) Proline residue: G 79 - end of helix Processing helix chain 'G' and resid 96 through 100 removed outlier: 3.652A pdb=" N ASN G 99 " --> pdb=" O ASN G 96 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU G 100 " --> pdb=" O LEU G 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 96 through 100' Processing helix chain 'G' and resid 101 through 128 Processing helix chain 'G' and resid 128 through 138 removed outlier: 3.937A pdb=" N ALA G 135 " --> pdb=" O THR G 131 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 155 removed outlier: 4.108A pdb=" N VAL G 153 " --> pdb=" O PRO G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 177 Processing helix chain 'G' and resid 177 through 183 Processing helix chain 'G' and resid 186 through 193 Processing helix chain 'G' and resid 193 through 198 removed outlier: 3.730A pdb=" N MET G 197 " --> pdb=" O ALA G 193 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE G 198 " --> pdb=" O GLY G 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 193 through 198' Processing helix chain 'G' and resid 198 through 212 Processing helix chain 'G' and resid 220 through 225 removed outlier: 4.599A pdb=" N GLY G 225 " --> pdb=" O LEU G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 234 removed outlier: 4.096A pdb=" N GLY G 230 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY G 233 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 234 " --> pdb=" O GLY G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 255 removed outlier: 3.528A pdb=" N THR G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR G 251 " --> pdb=" O TYR G 247 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP G 252 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 264 removed outlier: 3.711A pdb=" N ILE G 262 " --> pdb=" O SER G 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 14 through 54 removed outlier: 3.623A pdb=" N LYS D 19 " --> pdb=" O PRO D 15 " (cutoff:3.500A) Proline residue: D 30 - end of helix removed outlier: 3.590A pdb=" N HIS D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TRP D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TRP D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 58 Processing helix chain 'D' and resid 62 through 87 removed outlier: 3.544A pdb=" N THR D 67 " --> pdb=" O TRP D 63 " (cutoff:3.500A) Proline residue: D 68 - end of helix removed outlier: 4.223A pdb=" N THR D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N CYS D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 110 Processing helix chain 'D' and resid 127 through 142 Processing helix chain 'D' and resid 143 through 158 Processing helix chain 'D' and resid 158 through 168 removed outlier: 4.396A pdb=" N THR D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 183 through 191 Processing helix chain 'D' and resid 197 through 201 removed outlier: 3.620A pdb=" N VAL D 200 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 removed outlier: 4.653A pdb=" N PHE D 211 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 212 " --> pdb=" O ARG D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 212' Processing helix chain 'D' and resid 214 through 241 removed outlier: 3.746A pdb=" N ILE D 218 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D 229 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS D 239 " --> pdb=" O TRP D 235 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 266 Processing helix chain 'D' and resid 268 through 274 removed outlier: 3.575A pdb=" N GLY D 272 " --> pdb=" O GLY D 268 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 273 " --> pdb=" O PHE D 269 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 268 through 274' Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 186 through 209 removed outlier: 4.041A pdb=" N TYR A 207 " --> pdb=" O TRP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.790A pdb=" N ILE A 229 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 Processing helix chain 'A' and resid 326 through 332 removed outlier: 3.721A pdb=" N HIS A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 14 through 54 removed outlier: 3.625A pdb=" N LYS E 19 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Proline residue: E 30 - end of helix removed outlier: 3.603A pdb=" N HIS E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP E 50 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TRP E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TRP E 54 " --> pdb=" O ASP E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 58 Processing helix chain 'E' and resid 62 through 87 removed outlier: 3.552A pdb=" N THR E 67 " --> pdb=" O TRP E 63 " (cutoff:3.500A) Proline residue: E 68 - end of helix removed outlier: 4.217A pdb=" N THR E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR E 74 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS E 75 " --> pdb=" O GLY E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 110 Processing helix chain 'E' and resid 127 through 142 Processing helix chain 'E' and resid 143 through 158 Processing helix chain 'E' and resid 158 through 168 removed outlier: 4.402A pdb=" N THR E 165 " --> pdb=" O PRO E 161 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ILE E 166 " --> pdb=" O GLY E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'E' and resid 183 through 191 Processing helix chain 'E' and resid 197 through 201 removed outlier: 3.588A pdb=" N VAL E 200 " --> pdb=" O PRO E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 241 removed outlier: 3.810A pdb=" N ILE E 218 " --> pdb=" O HIS E 214 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS E 239 " --> pdb=" O TRP E 235 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 266 Processing helix chain 'E' and resid 268 through 274 removed outlier: 3.572A pdb=" N GLY E 272 " --> pdb=" O GLY E 268 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE E 273 " --> pdb=" O PHE E 269 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS E 274 " --> pdb=" O PRO E 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 268 through 274' Processing helix chain 'F' and resid 3 through 12 Processing helix chain 'F' and resid 14 through 54 removed outlier: 3.660A pdb=" N LYS F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) Proline residue: F 30 - end of helix removed outlier: 3.603A pdb=" N HIS F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP F 50 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N TRP F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 58 Processing helix chain 'F' and resid 62 through 87 removed outlier: 3.547A pdb=" N THR F 67 " --> pdb=" O TRP F 63 " (cutoff:3.500A) Proline residue: F 68 - end of helix removed outlier: 4.200A pdb=" N THR F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 110 Processing helix chain 'F' and resid 127 through 142 Processing helix chain 'F' and resid 143 through 158 Processing helix chain 'F' and resid 158 through 168 removed outlier: 4.373A pdb=" N THR F 165 " --> pdb=" O PRO F 161 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE F 166 " --> pdb=" O GLY F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 171 No H-bonds generated for 'chain 'F' and resid 169 through 171' Processing helix chain 'F' and resid 183 through 191 Processing helix chain 'F' and resid 197 through 201 removed outlier: 3.606A pdb=" N VAL F 200 " --> pdb=" O PRO F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 241 removed outlier: 3.848A pdb=" N ILE F 218 " --> pdb=" O HIS F 214 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS F 239 " --> pdb=" O TRP F 235 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU F 240 " --> pdb=" O TYR F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 268 through 274 removed outlier: 3.575A pdb=" N GLY F 272 " --> pdb=" O GLY F 268 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE F 273 " --> pdb=" O PHE F 269 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS F 274 " --> pdb=" O PRO F 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 268 through 274' Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 186 through 209 removed outlier: 4.030A pdb=" N TYR B 207 " --> pdb=" O TRP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.795A pdb=" N ILE B 229 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 Processing helix chain 'B' and resid 326 through 332 removed outlier: 3.702A pdb=" N HIS B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 186 through 209 removed outlier: 4.028A pdb=" N TYR C 207 " --> pdb=" O TRP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.836A pdb=" N ILE C 229 " --> pdb=" O GLU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 259 Processing helix chain 'C' and resid 326 through 332 removed outlier: 3.700A pdb=" N HIS C 332 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.714A pdb=" N GLU H 22 " --> pdb=" O ASP H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 55 removed outlier: 6.002A pdb=" N TYR H 52 " --> pdb=" O ARG H 48 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N SER H 53 " --> pdb=" O THR H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 92 removed outlier: 3.868A pdb=" N GLY H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Proline residue: H 79 - end of helix Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.652A pdb=" N ASN H 99 " --> pdb=" O ASN H 96 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU H 100 " --> pdb=" O LEU H 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 96 through 100' Processing helix chain 'H' and resid 101 through 128 Processing helix chain 'H' and resid 128 through 138 removed outlier: 3.938A pdb=" N ALA H 135 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER H 136 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 155 removed outlier: 4.108A pdb=" N VAL H 153 " --> pdb=" O PRO H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 177 Processing helix chain 'H' and resid 177 through 183 Processing helix chain 'H' and resid 186 through 193 Processing helix chain 'H' and resid 193 through 198 removed outlier: 3.731A pdb=" N MET H 197 " --> pdb=" O ALA H 193 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE H 198 " --> pdb=" O GLY H 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 193 through 198' Processing helix chain 'H' and resid 198 through 212 Processing helix chain 'H' and resid 220 through 225 removed outlier: 4.599A pdb=" N GLY H 225 " --> pdb=" O LEU H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 234 removed outlier: 4.096A pdb=" N GLY H 230 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU H 234 " --> pdb=" O GLY H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 255 removed outlier: 3.527A pdb=" N THR H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR H 251 " --> pdb=" O TYR H 247 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP H 252 " --> pdb=" O SER H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 264 removed outlier: 3.711A pdb=" N ILE H 262 " --> pdb=" O SER H 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 23 removed outlier: 3.714A pdb=" N GLU I 22 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 55 removed outlier: 6.003A pdb=" N TYR I 52 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N SER I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 92 removed outlier: 3.868A pdb=" N GLY I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU I 70 " --> pdb=" O VAL I 66 " (cutoff:3.500A) Proline residue: I 79 - end of helix Processing helix chain 'I' and resid 96 through 100 removed outlier: 3.652A pdb=" N ASN I 99 " --> pdb=" O ASN I 96 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU I 100 " --> pdb=" O LEU I 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 96 through 100' Processing helix chain 'I' and resid 101 through 128 Processing helix chain 'I' and resid 128 through 138 removed outlier: 3.937A pdb=" N ALA I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 155 removed outlier: 4.108A pdb=" N VAL I 153 " --> pdb=" O PRO I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 177 Processing helix chain 'I' and resid 177 through 183 Processing helix chain 'I' and resid 186 through 193 Processing helix chain 'I' and resid 193 through 198 removed outlier: 3.731A pdb=" N MET I 197 " --> pdb=" O ALA I 193 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE I 198 " --> pdb=" O GLY I 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 193 through 198' Processing helix chain 'I' and resid 198 through 212 Processing helix chain 'I' and resid 220 through 225 removed outlier: 4.600A pdb=" N GLY I 225 " --> pdb=" O LEU I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 234 removed outlier: 4.095A pdb=" N GLY I 230 " --> pdb=" O PHE I 226 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY I 233 " --> pdb=" O LEU I 229 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU I 234 " --> pdb=" O GLY I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 255 removed outlier: 3.528A pdb=" N THR I 245 " --> pdb=" O ALA I 241 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR I 251 " --> pdb=" O TYR I 247 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP I 252 " --> pdb=" O SER I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 264 removed outlier: 3.710A pdb=" N ILE I 262 " --> pdb=" O SER I 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 184 through 185 Processing sheet with id=AA2, first strand: chain 'D' and resid 173 through 176 Processing sheet with id=AA3, first strand: chain 'D' and resid 255 through 258 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.693A pdb=" N SER A 103 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS A 130 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG A 101 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.497A pdb=" N ILE A 145 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ALA A 152 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 143 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 141 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA8, first strand: chain 'A' and resid 282 through 286 Processing sheet with id=AA9, first strand: chain 'A' and resid 282 through 286 removed outlier: 3.906A pdb=" N ALA A 297 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 291 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 412 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 342 through 343 removed outlier: 6.248A pdb=" N ARG A 323 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE A 314 " --> pdb=" O TRP A 394 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP A 394 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 316 " --> pdb=" O MET A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 173 through 176 Processing sheet with id=AB3, first strand: chain 'F' and resid 173 through 176 Processing sheet with id=AB4, first strand: chain 'F' and resid 255 through 258 Processing sheet with id=AB5, first strand: chain 'B' and resid 48 through 50 Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.703A pdb=" N SER B 103 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS B 130 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG B 101 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 59 through 61 removed outlier: 6.519A pdb=" N ILE B 145 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ALA B 152 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 143 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 141 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AB9, first strand: chain 'B' and resid 282 through 286 Processing sheet with id=AC1, first strand: chain 'B' and resid 282 through 286 removed outlier: 3.937A pdb=" N ALA B 297 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR B 291 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 412 " --> pdb=" O TYR B 291 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 342 through 343 removed outlier: 6.248A pdb=" N ARG B 323 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE B 314 " --> pdb=" O TRP B 394 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP B 394 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 316 " --> pdb=" O MET B 392 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 48 through 50 Processing sheet with id=AC4, first strand: chain 'C' and resid 48 through 50 removed outlier: 3.735A pdb=" N SER C 103 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS C 130 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG C 101 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 59 through 61 removed outlier: 6.497A pdb=" N ILE C 145 " --> pdb=" O PRO C 150 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA C 152 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 143 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 141 " --> pdb=" O PRO C 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AC7, first strand: chain 'C' and resid 282 through 286 Processing sheet with id=AC8, first strand: chain 'C' and resid 282 through 286 removed outlier: 3.952A pdb=" N ALA C 297 " --> pdb=" O ASP C 292 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TYR C 291 " --> pdb=" O VAL C 412 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 342 through 343 removed outlier: 6.221A pdb=" N ARG C 323 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE C 314 " --> pdb=" O TRP C 394 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP C 394 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 316 " --> pdb=" O MET C 392 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3444 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: 4.46 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3300 1.31 - 1.43: 6995 1.43 - 1.56: 12265 1.56 - 1.68: 6 1.68 - 1.81: 279 Bond restraints: 22845 Sorted by residual: bond pdb=" C39 6PL G 303 " pdb=" C40 6PL G 303 " ideal model delta sigma weight residual 1.524 1.312 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C39 6PL H 303 " pdb=" C40 6PL H 303 " ideal model delta sigma weight residual 1.524 1.312 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C39 6PL I 303 " pdb=" C40 6PL I 303 " ideal model delta sigma weight residual 1.524 1.312 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C11 6PL G 303 " pdb=" O3 6PL G 303 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C11 6PL I 303 " pdb=" O3 6PL I 303 " ideal model delta sigma weight residual 1.327 1.396 -0.069 2.00e-02 2.50e+03 1.21e+01 ... (remaining 22840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 30896 3.71 - 7.42: 212 7.42 - 11.13: 5 11.13 - 14.84: 0 14.84 - 18.55: 6 Bond angle restraints: 31119 Sorted by residual: angle pdb=" O1P 6PL I 303 " pdb=" P 6PL I 303 " pdb=" O2P 6PL I 303 " ideal model delta sigma weight residual 119.71 101.16 18.55 3.00e+00 1.11e-01 3.82e+01 angle pdb=" O1P 6PL G 303 " pdb=" P 6PL G 303 " pdb=" O2P 6PL G 303 " ideal model delta sigma weight residual 119.71 101.17 18.54 3.00e+00 1.11e-01 3.82e+01 angle pdb=" O1P 6PL H 303 " pdb=" P 6PL H 303 " pdb=" O2P 6PL H 303 " ideal model delta sigma weight residual 119.71 101.17 18.54 3.00e+00 1.11e-01 3.82e+01 angle pdb=" O3P 6PL I 303 " pdb=" P 6PL I 303 " pdb=" O4P 6PL I 303 " ideal model delta sigma weight residual 93.65 110.07 -16.42 3.00e+00 1.11e-01 3.00e+01 angle pdb=" O3P 6PL G 303 " pdb=" P 6PL G 303 " pdb=" O4P 6PL G 303 " ideal model delta sigma weight residual 93.65 110.06 -16.41 3.00e+00 1.11e-01 2.99e+01 ... (remaining 31114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11108 17.93 - 35.86: 1418 35.86 - 53.79: 372 53.79 - 71.73: 77 71.73 - 89.66: 15 Dihedral angle restraints: 12990 sinusoidal: 5211 harmonic: 7779 Sorted by residual: dihedral pdb=" CA MET B 212 " pdb=" C MET B 212 " pdb=" N PHE B 213 " pdb=" CA PHE B 213 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA MET C 212 " pdb=" C MET C 212 " pdb=" N PHE C 213 " pdb=" CA PHE C 213 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA MET A 212 " pdb=" C MET A 212 " pdb=" N PHE A 213 " pdb=" CA PHE A 213 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 12987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2191 0.041 - 0.083: 805 0.083 - 0.124: 246 0.124 - 0.165: 28 0.165 - 0.207: 6 Chirality restraints: 3276 Sorted by residual: chirality pdb=" CA TYR C 51 " pdb=" N TYR C 51 " pdb=" C TYR C 51 " pdb=" CB TYR C 51 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA TYR A 51 " pdb=" N TYR A 51 " pdb=" C TYR A 51 " pdb=" CB TYR A 51 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA TYR B 51 " pdb=" N TYR B 51 " pdb=" C TYR B 51 " pdb=" CB TYR B 51 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.96e-01 ... (remaining 3273 not shown) Planarity restraints: 3831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 194 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO I 195 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO I 195 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 195 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 194 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO H 195 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO H 195 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 195 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 194 " -0.038 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO G 195 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO G 195 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 195 " -0.033 5.00e-02 4.00e+02 ... (remaining 3828 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 348 2.59 - 3.16: 17751 3.16 - 3.74: 35908 3.74 - 4.32: 55704 4.32 - 4.90: 89374 Nonbonded interactions: 199085 Sorted by model distance: nonbonded pdb=" OE2 GLU H 64 " pdb=" O HOH H 401 " model vdw 2.006 3.040 nonbonded pdb=" O HOH D 354 " pdb=" O HOH D 360 " model vdw 2.010 3.040 nonbonded pdb=" OE2 GLU B 109 " pdb=" O HOH B 601 " model vdw 2.012 3.040 nonbonded pdb=" O ARG E 201 " pdb=" O HOH E 301 " model vdw 2.021 3.040 nonbonded pdb=" CE MET G 59 " pdb=" O HOH G 419 " model vdw 2.024 3.460 ... (remaining 199080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 24.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.860 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.860 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:9.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 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 0.212 22845 Z= 0.229 Angle : 0.747 18.550 31119 Z= 0.372 Chirality : 0.046 0.207 3276 Planarity : 0.005 0.059 3831 Dihedral : 17.042 89.657 8040 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.92 % Allowed : 19.31 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2697 helix: 1.13 (0.15), residues: 1275 sheet: 0.71 (0.24), residues: 459 loop : -0.88 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.026 0.002 TYR H 162 PHE 0.015 0.002 PHE A 90 TRP 0.018 0.001 TRP I 88 HIS 0.010 0.002 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00492 (22845) covalent geometry : angle 0.74667 (31119) hydrogen bonds : bond 0.15610 ( 1187) hydrogen bonds : angle 6.74447 ( 3444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 367 time to evaluate : 0.887 Fit side-chains REVERT: G 59 MET cc_start: 0.8695 (mtm) cc_final: 0.8442 (mtt) REVERT: G 62 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7328 (pt0) REVERT: A 61 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8179 (ttpp) REVERT: A 111 THR cc_start: 0.8363 (m) cc_final: 0.8078 (p) REVERT: A 172 LYS cc_start: 0.8809 (tttt) cc_final: 0.8379 (tttm) REVERT: A 234 LYS cc_start: 0.7907 (mttt) cc_final: 0.7280 (mtpt) REVERT: A 339 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8110 (mmpt) REVERT: A 363 LYS cc_start: 0.8817 (mttt) cc_final: 0.7752 (tptt) REVERT: B 61 LYS cc_start: 0.8403 (mtmm) cc_final: 0.8167 (ttpp) REVERT: B 111 THR cc_start: 0.8461 (m) cc_final: 0.8166 (p) REVERT: B 172 LYS cc_start: 0.8845 (tttt) cc_final: 0.8533 (tttm) REVERT: B 234 LYS cc_start: 0.7974 (mttt) cc_final: 0.7358 (mtpt) REVERT: B 323 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8020 (mtm-85) REVERT: B 327 LYS cc_start: 0.8324 (mmmt) cc_final: 0.7824 (mppt) REVERT: B 333 MET cc_start: 0.7682 (tpp) cc_final: 0.6269 (ttm) REVERT: B 339 LYS cc_start: 0.8345 (mmtt) cc_final: 0.8107 (mmpt) REVERT: C 111 THR cc_start: 0.8355 (m) cc_final: 0.7954 (p) REVERT: C 234 LYS cc_start: 0.7922 (mttt) cc_final: 0.7273 (mtpt) REVERT: C 323 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7959 (mtm-85) REVERT: C 327 LYS cc_start: 0.8455 (mmmt) cc_final: 0.7888 (mppt) REVERT: C 339 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8131 (mmpt) REVERT: H 59 MET cc_start: 0.8227 (mtm) cc_final: 0.7906 (mtt) REVERT: H 62 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7340 (pt0) REVERT: H 265 ASN cc_start: 0.8376 (m110) cc_final: 0.7932 (m110) REVERT: I 62 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7395 (pt0) outliers start: 44 outliers final: 31 residues processed: 397 average time/residue: 0.6213 time to fit residues: 282.5123 Evaluate side-chains 383 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 350 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 205 ASN Chi-restraints excluded: chain G residue 212 TRP Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 212 TRP Chi-restraints excluded: chain I residue 205 ASN Chi-restraints excluded: chain I residue 212 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 201 ASN D 171 HIS H 201 ASN I 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109924 restraints weight = 22270.609| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.19 r_work: 0.3086 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22845 Z= 0.157 Angle : 0.615 6.915 31119 Z= 0.325 Chirality : 0.045 0.180 3276 Planarity : 0.005 0.059 3831 Dihedral : 8.836 70.321 3162 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.41 % Allowed : 16.60 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.16), residues: 2697 helix: 1.39 (0.15), residues: 1266 sheet: 0.68 (0.24), residues: 462 loop : -0.93 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 299 TYR 0.026 0.002 TYR H 162 PHE 0.016 0.002 PHE A 99 TRP 0.013 0.001 TRP D 234 HIS 0.008 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00363 (22845) covalent geometry : angle 0.61506 (31119) hydrogen bonds : bond 0.06061 ( 1187) hydrogen bonds : angle 5.22843 ( 3444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 373 time to evaluate : 0.886 Fit side-chains REVERT: G 59 MET cc_start: 0.8407 (mtm) cc_final: 0.8046 (mtt) REVERT: G 62 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: G 228 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7443 (pp) REVERT: D 142 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8179 (mtm180) REVERT: A 49 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8231 (mt0) REVERT: A 61 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8154 (ttpp) REVERT: A 111 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8070 (p) REVERT: A 112 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7855 (mpt) REVERT: A 128 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8659 (mtpp) REVERT: A 172 LYS cc_start: 0.8732 (tttt) cc_final: 0.8361 (tttm) REVERT: A 234 LYS cc_start: 0.7867 (mttt) cc_final: 0.7216 (mtpt) REVERT: A 339 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7986 (mmpt) REVERT: A 363 LYS cc_start: 0.8817 (mttt) cc_final: 0.7794 (tmtm) REVERT: A 375 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7614 (mtt-85) REVERT: B 111 THR cc_start: 0.8456 (m) cc_final: 0.8127 (p) REVERT: B 172 LYS cc_start: 0.8811 (tttt) cc_final: 0.8413 (tttm) REVERT: B 234 LYS cc_start: 0.7827 (mttt) cc_final: 0.7198 (mtpt) REVERT: B 327 LYS cc_start: 0.8361 (mmmt) cc_final: 0.7785 (mppt) REVERT: B 339 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7969 (mmpt) REVERT: B 363 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8646 (mtmt) REVERT: B 375 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.6933 (mtt-85) REVERT: C 49 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8228 (mt0) REVERT: C 111 THR cc_start: 0.8299 (m) cc_final: 0.7963 (p) REVERT: C 112 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7892 (mpt) REVERT: C 234 LYS cc_start: 0.7827 (mttt) cc_final: 0.7179 (mtpt) REVERT: C 323 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7710 (mtm-85) REVERT: C 327 LYS cc_start: 0.8389 (mmmt) cc_final: 0.7823 (mppt) REVERT: C 339 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8005 (mmpt) REVERT: C 375 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7100 (mtt-85) REVERT: H 59 MET cc_start: 0.8182 (mtm) cc_final: 0.7287 (mtt) REVERT: H 62 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7328 (pt0) REVERT: H 228 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7450 (pt) REVERT: I 59 MET cc_start: 0.8245 (mtm) cc_final: 0.7600 (mtt) REVERT: I 62 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7390 (pt0) REVERT: I 64 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6503 (mp0) REVERT: I 65 LYS cc_start: 0.7894 (tttt) cc_final: 0.7664 (tttm) REVERT: I 228 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7388 (pp) REVERT: I 265 ASN cc_start: 0.8360 (m110) cc_final: 0.8093 (m110) outliers start: 101 outliers final: 42 residues processed: 429 average time/residue: 0.6386 time to fit residues: 313.9725 Evaluate side-chains 426 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 366 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 212 TRP Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 212 TRP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 212 TRP Chi-restraints excluded: chain I residue 228 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 211 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 HIS A 39 GLN A 355 GLN E 43 HIS F 43 HIS B 355 GLN C 355 GLN H 133 GLN H 201 ASN I 133 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107802 restraints weight = 22179.906| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.21 r_work: 0.3042 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 22845 Z= 0.232 Angle : 0.695 8.358 31119 Z= 0.370 Chirality : 0.049 0.225 3276 Planarity : 0.006 0.061 3831 Dihedral : 8.410 58.962 3131 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.16 % Allowed : 16.25 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.16), residues: 2697 helix: 1.20 (0.15), residues: 1275 sheet: 0.40 (0.24), residues: 426 loop : -0.96 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 193 TYR 0.026 0.003 TYR C 51 PHE 0.020 0.003 PHE C 90 TRP 0.013 0.002 TRP D 234 HIS 0.009 0.002 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00569 (22845) covalent geometry : angle 0.69492 (31119) hydrogen bonds : bond 0.07203 ( 1187) hydrogen bonds : angle 5.38773 ( 3444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 397 time to evaluate : 1.009 Fit side-chains REVERT: G 59 MET cc_start: 0.8481 (mtm) cc_final: 0.8163 (mtt) REVERT: G 62 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: G 65 LYS cc_start: 0.7941 (tttt) cc_final: 0.7685 (tttt) REVERT: G 228 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7614 (mp) REVERT: D 142 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8223 (mtm180) REVERT: A 49 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: A 61 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8208 (ttpp) REVERT: A 111 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8160 (p) REVERT: A 165 ASP cc_start: 0.7865 (m-30) cc_final: 0.7662 (m-30) REVERT: A 172 LYS cc_start: 0.8792 (tttt) cc_final: 0.8486 (tttm) REVERT: A 234 LYS cc_start: 0.7989 (mttt) cc_final: 0.7338 (mtpt) REVERT: A 323 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.7425 (mtm180) REVERT: A 327 LYS cc_start: 0.8349 (mmmt) cc_final: 0.7823 (mppt) REVERT: A 339 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8067 (mmpt) REVERT: A 363 LYS cc_start: 0.8849 (mttt) cc_final: 0.7849 (tmtm) REVERT: A 375 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7502 (mtt-85) REVERT: E 142 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8191 (mtm180) REVERT: B 103 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8412 (p) REVERT: B 111 THR cc_start: 0.8515 (m) cc_final: 0.8218 (p) REVERT: B 165 ASP cc_start: 0.7817 (m-30) cc_final: 0.7609 (m-30) REVERT: B 172 LYS cc_start: 0.8830 (tttt) cc_final: 0.8434 (tttm) REVERT: B 234 LYS cc_start: 0.7964 (mttt) cc_final: 0.7292 (mtpt) REVERT: B 323 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.7289 (mtt180) REVERT: B 327 LYS cc_start: 0.8419 (mmmt) cc_final: 0.7843 (mppt) REVERT: B 339 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8040 (mmpt) REVERT: B 375 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7504 (mtt-85) REVERT: C 49 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: C 111 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8089 (p) REVERT: C 234 LYS cc_start: 0.7938 (mttt) cc_final: 0.7309 (mtpt) REVERT: C 323 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.7741 (mtm-85) REVERT: C 327 LYS cc_start: 0.8383 (mmmt) cc_final: 0.7866 (mppt) REVERT: C 333 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.6450 (ttt) REVERT: C 339 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8100 (mmpt) REVERT: C 375 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7876 (mtt-85) REVERT: H 59 MET cc_start: 0.8266 (mtm) cc_final: 0.7877 (mtt) REVERT: H 62 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7368 (pt0) REVERT: H 228 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7611 (mp) REVERT: H 265 ASN cc_start: 0.8401 (m110) cc_final: 0.7947 (m110) REVERT: I 62 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: I 64 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6573 (mp0) REVERT: I 65 LYS cc_start: 0.8011 (tttt) cc_final: 0.7811 (tttm) REVERT: I 228 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7569 (mp) REVERT: I 265 ASN cc_start: 0.8366 (m110) cc_final: 0.8086 (m110) outliers start: 118 outliers final: 61 residues processed: 467 average time/residue: 0.6240 time to fit residues: 335.1268 Evaluate side-chains 462 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 381 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 205 ASN Chi-restraints excluded: chain G residue 212 TRP Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 212 TRP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 205 ASN Chi-restraints excluded: chain I residue 212 TRP Chi-restraints excluded: chain I residue 228 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 105 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 211 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 269 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 201 ASN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN H 201 ASN I 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113919 restraints weight = 22350.390| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.23 r_work: 0.3126 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22845 Z= 0.118 Angle : 0.559 8.347 31119 Z= 0.295 Chirality : 0.043 0.159 3276 Planarity : 0.005 0.059 3831 Dihedral : 7.956 58.986 3127 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.76 % Allowed : 16.95 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 2697 helix: 1.60 (0.15), residues: 1272 sheet: 0.91 (0.24), residues: 444 loop : -0.99 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 176 TYR 0.021 0.001 TYR I 162 PHE 0.014 0.001 PHE A 186 TRP 0.014 0.001 TRP D 234 HIS 0.005 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00254 (22845) covalent geometry : angle 0.55887 (31119) hydrogen bonds : bond 0.04931 ( 1187) hydrogen bonds : angle 4.88205 ( 3444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 389 time to evaluate : 0.965 Fit side-chains REVERT: G 59 MET cc_start: 0.8313 (mtm) cc_final: 0.7809 (mtt) REVERT: G 62 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7298 (pt0) REVERT: G 65 LYS cc_start: 0.7849 (tttt) cc_final: 0.7648 (tttm) REVERT: A 61 LYS cc_start: 0.8411 (mtmm) cc_final: 0.8162 (ttpp) REVERT: A 111 THR cc_start: 0.8312 (m) cc_final: 0.8042 (p) REVERT: A 172 LYS cc_start: 0.8703 (tttt) cc_final: 0.8405 (tttm) REVERT: A 234 LYS cc_start: 0.7819 (mttt) cc_final: 0.7176 (mtpt) REVERT: A 327 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7762 (mppt) REVERT: A 339 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7937 (mmpt) REVERT: A 363 LYS cc_start: 0.8778 (mttt) cc_final: 0.7820 (tmtm) REVERT: A 392 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8620 (mtt) REVERT: F 202 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8522 (tp) REVERT: B 103 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8573 (t) REVERT: B 111 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8099 (p) REVERT: B 172 LYS cc_start: 0.8759 (tttt) cc_final: 0.8382 (tttm) REVERT: B 234 LYS cc_start: 0.7741 (mttt) cc_final: 0.7071 (mtpt) REVERT: B 323 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7332 (mtm180) REVERT: B 327 LYS cc_start: 0.8388 (mmmt) cc_final: 0.7804 (mppt) REVERT: B 339 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7932 (mmpt) REVERT: B 361 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: B 363 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8638 (mtmt) REVERT: B 375 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.6969 (mtt-85) REVERT: C 111 THR cc_start: 0.8306 (m) cc_final: 0.7956 (p) REVERT: C 323 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7380 (mtm-85) REVERT: C 327 LYS cc_start: 0.8329 (mmmt) cc_final: 0.7818 (mppt) REVERT: C 339 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7946 (mmpt) REVERT: C 361 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: C 363 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8620 (mtmt) REVERT: C 392 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8751 (mtt) REVERT: H 59 MET cc_start: 0.8187 (mtm) cc_final: 0.7371 (mtt) REVERT: H 62 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7363 (pt0) REVERT: H 65 LYS cc_start: 0.7868 (tttt) cc_final: 0.7655 (tttm) REVERT: H 265 ASN cc_start: 0.8411 (m110) cc_final: 0.8043 (m110) REVERT: I 59 MET cc_start: 0.8216 (mtm) cc_final: 0.7749 (mtt) REVERT: I 62 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: I 64 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6444 (mp0) REVERT: I 65 LYS cc_start: 0.7882 (tttt) cc_final: 0.7652 (tttm) REVERT: I 114 MET cc_start: 0.8682 (mtt) cc_final: 0.8452 (mtt) REVERT: I 265 ASN cc_start: 0.8385 (m110) cc_final: 0.8101 (m110) outliers start: 86 outliers final: 44 residues processed: 441 average time/residue: 0.6515 time to fit residues: 328.8523 Evaluate side-chains 435 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 376 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 205 ASN Chi-restraints excluded: chain G residue 212 TRP Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 212 TRP Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 205 ASN Chi-restraints excluded: chain I residue 212 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 90 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 178 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 0.0370 chunk 72 optimal weight: 0.8980 chunk 266 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 201 ASN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN H 201 ASN I 133 GLN I 201 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115342 restraints weight = 22156.053| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.21 r_work: 0.3147 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22845 Z= 0.111 Angle : 0.539 8.312 31119 Z= 0.283 Chirality : 0.042 0.145 3276 Planarity : 0.005 0.057 3831 Dihedral : 7.622 58.892 3124 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.02 % Allowed : 17.04 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.16), residues: 2697 helix: 1.78 (0.15), residues: 1269 sheet: 1.00 (0.24), residues: 444 loop : -0.90 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 299 TYR 0.020 0.001 TYR I 162 PHE 0.013 0.001 PHE A 186 TRP 0.013 0.001 TRP B 50 HIS 0.005 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00234 (22845) covalent geometry : angle 0.53947 (31119) hydrogen bonds : bond 0.04642 ( 1187) hydrogen bonds : angle 4.70781 ( 3444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 395 time to evaluate : 0.967 Fit side-chains REVERT: G 59 MET cc_start: 0.8251 (mtm) cc_final: 0.7779 (mtt) REVERT: G 62 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7290 (pt0) REVERT: G 65 LYS cc_start: 0.7762 (tttt) cc_final: 0.7530 (tttt) REVERT: G 212 TRP cc_start: 0.6725 (OUTLIER) cc_final: 0.6487 (p90) REVERT: G 265 ASN cc_start: 0.8312 (m110) cc_final: 0.7996 (m110) REVERT: A 61 LYS cc_start: 0.8393 (mtmm) cc_final: 0.8177 (ttpp) REVERT: A 111 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8082 (p) REVERT: A 172 LYS cc_start: 0.8698 (tttt) cc_final: 0.8371 (tttm) REVERT: A 234 LYS cc_start: 0.7735 (mttt) cc_final: 0.7092 (mtpt) REVERT: A 323 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7457 (mtm180) REVERT: A 327 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7720 (mppt) REVERT: A 339 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7865 (mmpt) REVERT: A 361 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7881 (tp30) REVERT: A 363 LYS cc_start: 0.8774 (mttt) cc_final: 0.7760 (tmtm) REVERT: A 392 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8624 (mtt) REVERT: F 202 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8504 (tp) REVERT: B 61 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8049 (ttpp) REVERT: B 103 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8575 (t) REVERT: B 111 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8101 (p) REVERT: B 172 LYS cc_start: 0.8731 (tttt) cc_final: 0.8341 (tttm) REVERT: B 234 LYS cc_start: 0.7659 (mttt) cc_final: 0.6970 (mtpt) REVERT: B 323 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7220 (mtm180) REVERT: B 327 LYS cc_start: 0.8376 (mmmt) cc_final: 0.7763 (mppt) REVERT: B 339 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7859 (mmpt) REVERT: B 361 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: B 363 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8614 (mtmt) REVERT: C 61 LYS cc_start: 0.8360 (mtmm) cc_final: 0.8062 (ttpp) REVERT: C 111 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8011 (p) REVERT: C 323 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7192 (mtm-85) REVERT: C 327 LYS cc_start: 0.8332 (mmmt) cc_final: 0.7808 (mppt) REVERT: C 339 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7887 (mmpt) REVERT: C 361 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: C 363 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8640 (mttm) REVERT: C 392 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8695 (mtt) REVERT: H 59 MET cc_start: 0.8121 (mtm) cc_final: 0.7625 (mtt) REVERT: H 62 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7259 (pt0) REVERT: H 65 LYS cc_start: 0.7784 (tttt) cc_final: 0.7579 (tttm) REVERT: H 212 TRP cc_start: 0.6727 (OUTLIER) cc_final: 0.6523 (p90) REVERT: H 265 ASN cc_start: 0.8414 (m110) cc_final: 0.8022 (m110) REVERT: I 59 MET cc_start: 0.8167 (mtm) cc_final: 0.7769 (mtt) REVERT: I 62 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: I 64 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6356 (mp0) REVERT: I 212 TRP cc_start: 0.6782 (OUTLIER) cc_final: 0.6575 (p90) REVERT: I 228 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7438 (mp) REVERT: I 265 ASN cc_start: 0.8371 (m110) cc_final: 0.8081 (m110) outliers start: 92 outliers final: 43 residues processed: 450 average time/residue: 0.6448 time to fit residues: 332.6484 Evaluate side-chains 446 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 380 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 205 ASN Chi-restraints excluded: chain G residue 212 TRP Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 212 TRP Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 205 ASN Chi-restraints excluded: chain I residue 212 TRP Chi-restraints excluded: chain I residue 228 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 143 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 205 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 263 optimal weight: 0.5980 chunk 166 optimal weight: 6.9990 chunk 265 optimal weight: 0.2980 chunk 227 optimal weight: 0.0570 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 133 GLN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS E 143 ASN H 133 GLN H 201 ASN I 201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110490 restraints weight = 22169.963| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.22 r_work: 0.3080 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22845 Z= 0.163 Angle : 0.609 8.965 31119 Z= 0.324 Chirality : 0.045 0.187 3276 Planarity : 0.005 0.057 3831 Dihedral : 7.946 59.980 3124 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.50 % Allowed : 16.56 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.16), residues: 2697 helix: 1.59 (0.15), residues: 1272 sheet: 0.67 (0.24), residues: 462 loop : -0.93 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 48 TYR 0.025 0.002 TYR B 51 PHE 0.015 0.002 PHE A 99 TRP 0.014 0.001 TRP B 50 HIS 0.008 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00381 (22845) covalent geometry : angle 0.60949 (31119) hydrogen bonds : bond 0.05933 ( 1187) hydrogen bonds : angle 4.99861 ( 3444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 390 time to evaluate : 1.000 Fit side-chains REVERT: G 59 MET cc_start: 0.8358 (mtm) cc_final: 0.7726 (mtt) REVERT: G 62 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7302 (pt0) REVERT: G 65 LYS cc_start: 0.7796 (tttt) cc_final: 0.7524 (tttt) REVERT: G 212 TRP cc_start: 0.6856 (OUTLIER) cc_final: 0.6613 (p90) REVERT: G 228 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7533 (mp) REVERT: G 265 ASN cc_start: 0.8326 (m110) cc_final: 0.7983 (m110) REVERT: A 61 LYS cc_start: 0.8408 (mtmm) cc_final: 0.8141 (ttpp) REVERT: A 103 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8575 (t) REVERT: A 111 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8109 (p) REVERT: A 172 LYS cc_start: 0.8763 (tttt) cc_final: 0.8438 (tttm) REVERT: A 234 LYS cc_start: 0.7839 (mttt) cc_final: 0.7184 (mtpt) REVERT: A 296 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6956 (mpp80) REVERT: A 323 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7380 (mtm180) REVERT: A 327 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7748 (mppt) REVERT: A 339 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7923 (mmpt) REVERT: A 363 LYS cc_start: 0.8806 (mttt) cc_final: 0.7763 (tmtm) REVERT: A 375 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7696 (mtt-85) REVERT: E 142 ARG cc_start: 0.8384 (mtm110) cc_final: 0.7537 (mtp85) REVERT: B 61 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8047 (ttmm) REVERT: B 103 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8546 (t) REVERT: B 111 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8159 (p) REVERT: B 172 LYS cc_start: 0.8801 (tttt) cc_final: 0.8383 (tttm) REVERT: B 234 LYS cc_start: 0.7779 (mttt) cc_final: 0.7089 (mtpt) REVERT: B 323 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7397 (mtm180) REVERT: B 327 LYS cc_start: 0.8392 (mmmt) cc_final: 0.7776 (mppt) REVERT: B 339 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7934 (mmpt) REVERT: B 361 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7801 (tp30) REVERT: B 375 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.6934 (mtt-85) REVERT: C 49 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: C 111 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8045 (p) REVERT: C 234 LYS cc_start: 0.7768 (mttt) cc_final: 0.7106 (mtpt) REVERT: C 323 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7551 (mtm-85) REVERT: C 327 LYS cc_start: 0.8364 (mmmt) cc_final: 0.7811 (mppt) REVERT: C 333 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.6468 (ttt) REVERT: C 339 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7971 (mmpt) REVERT: C 361 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: C 363 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8668 (mttm) REVERT: C 375 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7571 (mtt-85) REVERT: H 59 MET cc_start: 0.8209 (mtm) cc_final: 0.7471 (mtt) REVERT: H 62 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7363 (pt0) REVERT: H 65 LYS cc_start: 0.7823 (tttt) cc_final: 0.7615 (tttm) REVERT: H 212 TRP cc_start: 0.6837 (OUTLIER) cc_final: 0.6619 (p90) REVERT: H 228 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7511 (mp) REVERT: H 265 ASN cc_start: 0.8429 (m110) cc_final: 0.7999 (m110) REVERT: I 59 MET cc_start: 0.8236 (mtm) cc_final: 0.7696 (mtt) REVERT: I 62 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: I 64 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6428 (mp0) REVERT: I 212 TRP cc_start: 0.6912 (OUTLIER) cc_final: 0.6703 (p90) REVERT: I 228 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7441 (mp) REVERT: I 265 ASN cc_start: 0.8393 (m110) cc_final: 0.8099 (m110) outliers start: 103 outliers final: 48 residues processed: 452 average time/residue: 0.6526 time to fit residues: 338.3765 Evaluate side-chains 457 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 383 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 205 ASN Chi-restraints excluded: chain G residue 212 TRP Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 212 TRP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 205 ASN Chi-restraints excluded: chain I residue 212 TRP Chi-restraints excluded: chain I residue 228 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 95 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 133 GLN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS E 143 ASN H 133 GLN H 201 ASN I 133 GLN I 201 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111330 restraints weight = 22132.919| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.21 r_work: 0.3090 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22845 Z= 0.147 Angle : 0.592 11.181 31119 Z= 0.313 Chirality : 0.044 0.176 3276 Planarity : 0.005 0.057 3831 Dihedral : 7.932 59.981 3124 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.15 % Allowed : 16.69 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 2697 helix: 1.60 (0.15), residues: 1272 sheet: 0.72 (0.24), residues: 447 loop : -0.89 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 48 TYR 0.023 0.002 TYR G 162 PHE 0.014 0.002 PHE B 99 TRP 0.014 0.001 TRP B 50 HIS 0.006 0.001 HIS C 288 Details of bonding type rmsd covalent geometry : bond 0.00341 (22845) covalent geometry : angle 0.59209 (31119) hydrogen bonds : bond 0.05615 ( 1187) hydrogen bonds : angle 4.93860 ( 3444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 390 time to evaluate : 0.954 Fit side-chains REVERT: G 59 MET cc_start: 0.8345 (mtm) cc_final: 0.7846 (mtt) REVERT: G 62 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7292 (pt0) REVERT: G 65 LYS cc_start: 0.7802 (tttt) cc_final: 0.7524 (tttt) REVERT: G 212 TRP cc_start: 0.6838 (OUTLIER) cc_final: 0.6594 (p90) REVERT: G 228 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7519 (mp) REVERT: A 61 LYS cc_start: 0.8389 (mtmm) cc_final: 0.8138 (ttpp) REVERT: A 103 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8576 (t) REVERT: A 111 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 172 LYS cc_start: 0.8764 (tttt) cc_final: 0.8440 (tttm) REVERT: A 234 LYS cc_start: 0.7829 (mttt) cc_final: 0.7170 (mtpt) REVERT: A 296 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6949 (mpp80) REVERT: A 323 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7324 (mtm180) REVERT: A 327 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7736 (mppt) REVERT: A 339 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7949 (mmpt) REVERT: A 363 LYS cc_start: 0.8798 (mttt) cc_final: 0.7772 (tmtm) REVERT: A 375 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7659 (mtt-85) REVERT: E 142 ARG cc_start: 0.8375 (mtm110) cc_final: 0.7527 (mtp85) REVERT: F 202 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8532 (tp) REVERT: B 46 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6682 (mtt180) REVERT: B 103 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8561 (t) REVERT: B 111 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8146 (p) REVERT: B 172 LYS cc_start: 0.8797 (tttt) cc_final: 0.8387 (tttm) REVERT: B 234 LYS cc_start: 0.7769 (mttt) cc_final: 0.7070 (mtpt) REVERT: B 323 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.7383 (mtm180) REVERT: B 327 LYS cc_start: 0.8393 (mmmt) cc_final: 0.7775 (mppt) REVERT: B 339 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7916 (mmpt) REVERT: B 361 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7729 (tp30) REVERT: B 375 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.6936 (mtt-85) REVERT: B 392 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8565 (mtt) REVERT: C 49 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8216 (mt0) REVERT: C 103 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8586 (t) REVERT: C 111 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8033 (p) REVERT: C 112 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7987 (mpt) REVERT: C 234 LYS cc_start: 0.7748 (mttt) cc_final: 0.7081 (mtpt) REVERT: C 323 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7495 (mtm-85) REVERT: C 327 LYS cc_start: 0.8358 (mmmt) cc_final: 0.7808 (mppt) REVERT: C 333 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.6390 (ttt) REVERT: C 339 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7961 (mmpt) REVERT: C 361 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: C 363 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8673 (mttm) REVERT: H 59 MET cc_start: 0.8185 (mtm) cc_final: 0.7447 (mtt) REVERT: H 62 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: H 65 LYS cc_start: 0.7880 (tttt) cc_final: 0.7669 (tttm) REVERT: H 212 TRP cc_start: 0.6824 (OUTLIER) cc_final: 0.6604 (p90) REVERT: H 228 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7482 (mp) REVERT: H 265 ASN cc_start: 0.8434 (m110) cc_final: 0.8022 (m110) REVERT: I 59 MET cc_start: 0.8206 (mtm) cc_final: 0.7670 (mtt) REVERT: I 62 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7439 (pt0) REVERT: I 64 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6425 (mp0) REVERT: I 114 MET cc_start: 0.8675 (mtt) cc_final: 0.8449 (mtt) REVERT: I 212 TRP cc_start: 0.6887 (OUTLIER) cc_final: 0.6678 (p90) REVERT: I 228 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7405 (mp) REVERT: I 265 ASN cc_start: 0.8387 (m110) cc_final: 0.8100 (m110) outliers start: 95 outliers final: 52 residues processed: 450 average time/residue: 0.5961 time to fit residues: 306.9214 Evaluate side-chains 462 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 381 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain G residue 205 ASN Chi-restraints excluded: chain G residue 212 TRP Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain H residue 212 TRP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 205 ASN Chi-restraints excluded: chain I residue 212 TRP Chi-restraints excluded: chain I residue 228 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 13 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 133 GLN G 201 ASN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS A 49 GLN E 143 ASN H 201 ASN I 133 GLN I 201 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.114155 restraints weight = 22044.929| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.14 r_work: 0.3121 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22845 Z= 0.119 Angle : 0.553 11.530 31119 Z= 0.291 Chirality : 0.043 0.154 3276 Planarity : 0.005 0.056 3831 Dihedral : 7.761 59.948 3124 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.15 % Allowed : 16.51 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.17), residues: 2697 helix: 1.72 (0.15), residues: 1272 sheet: 1.02 (0.25), residues: 429 loop : -0.86 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 48 TYR 0.020 0.001 TYR I 162 PHE 0.013 0.001 PHE A 186 TRP 0.013 0.001 TRP B 50 HIS 0.005 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00257 (22845) covalent geometry : angle 0.55334 (31119) hydrogen bonds : bond 0.04927 ( 1187) hydrogen bonds : angle 4.77319 ( 3444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 389 time to evaluate : 0.947 Fit side-chains REVERT: G 59 MET cc_start: 0.8292 (mtm) cc_final: 0.8073 (mtt) REVERT: G 62 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7370 (pt0) REVERT: G 65 LYS cc_start: 0.7858 (tttt) cc_final: 0.7611 (tttt) REVERT: G 212 TRP cc_start: 0.6807 (OUTLIER) cc_final: 0.6585 (p90) REVERT: G 228 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7547 (mp) REVERT: A 61 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8192 (ttpp) REVERT: A 103 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8589 (t) REVERT: A 111 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8092 (p) REVERT: A 172 LYS cc_start: 0.8750 (tttt) cc_final: 0.8443 (tttm) REVERT: A 234 LYS cc_start: 0.7858 (mttt) cc_final: 0.7222 (mtpt) REVERT: A 323 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7323 (mtm180) REVERT: A 327 LYS cc_start: 0.8321 (mmmt) cc_final: 0.7778 (mppt) REVERT: A 339 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7958 (mmpt) REVERT: A 363 LYS cc_start: 0.8781 (mttt) cc_final: 0.7845 (tmtm) REVERT: A 392 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8672 (mtt) REVERT: E 142 ARG cc_start: 0.8386 (mtm110) cc_final: 0.7583 (mtp85) REVERT: B 103 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8553 (t) REVERT: B 111 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8125 (p) REVERT: B 172 LYS cc_start: 0.8775 (tttt) cc_final: 0.8406 (tttm) REVERT: B 234 LYS cc_start: 0.7753 (mttt) cc_final: 0.7080 (mtpt) REVERT: B 323 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7342 (mtm180) REVERT: B 327 LYS cc_start: 0.8414 (mmmt) cc_final: 0.7826 (mppt) REVERT: B 339 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7927 (mmpt) REVERT: B 361 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7681 (tp30) REVERT: B 363 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8650 (mtmt) REVERT: C 61 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8042 (ttmm) REVERT: C 103 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8573 (t) REVERT: C 111 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8016 (p) REVERT: C 225 ASP cc_start: 0.7612 (t0) cc_final: 0.7348 (t0) REVERT: C 323 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7280 (mtm-85) REVERT: C 327 LYS cc_start: 0.8363 (mmmt) cc_final: 0.7862 (mppt) REVERT: C 339 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7953 (mmpt) REVERT: C 361 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: C 363 LYS cc_start: 0.8960 (mmmt) cc_final: 0.8698 (mttm) REVERT: H 59 MET cc_start: 0.8147 (mtm) cc_final: 0.7665 (mtt) REVERT: H 62 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: H 228 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7519 (mp) REVERT: H 265 ASN cc_start: 0.8455 (m110) cc_final: 0.8067 (m110) REVERT: I 62 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7558 (pt0) REVERT: I 64 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6472 (mp0) REVERT: I 114 MET cc_start: 0.8698 (mtt) cc_final: 0.8497 (mtt) REVERT: I 228 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7428 (mp) REVERT: I 265 ASN cc_start: 0.8386 (m110) cc_final: 0.8120 (m110) outliers start: 95 outliers final: 45 residues processed: 448 average time/residue: 0.6212 time to fit residues: 319.3070 Evaluate side-chains 445 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 379 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 205 ASN Chi-restraints excluded: chain G residue 212 TRP Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain F residue 9 LYS Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 205 ASN Chi-restraints excluded: chain I residue 228 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 91 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 252 optimal weight: 0.3980 chunk 89 optimal weight: 8.9990 chunk 157 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 198 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 133 GLN G 201 ASN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS H 133 GLN H 201 ASN I 201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114661 restraints weight = 22185.169| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.24 r_work: 0.3135 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22845 Z= 0.115 Angle : 0.546 11.231 31119 Z= 0.287 Chirality : 0.043 0.151 3276 Planarity : 0.005 0.056 3831 Dihedral : 7.602 59.975 3120 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.19 % Allowed : 17.52 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2697 helix: 1.78 (0.15), residues: 1269 sheet: 1.06 (0.25), residues: 429 loop : -0.83 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 87 TYR 0.021 0.001 TYR I 162 PHE 0.013 0.001 PHE A 186 TRP 0.013 0.001 TRP B 50 HIS 0.005 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00248 (22845) covalent geometry : angle 0.54613 (31119) hydrogen bonds : bond 0.04795 ( 1187) hydrogen bonds : angle 4.71736 ( 3444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 386 time to evaluate : 0.737 Fit side-chains REVERT: G 59 MET cc_start: 0.8247 (mtm) cc_final: 0.7769 (mtt) REVERT: G 62 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7333 (pt0) REVERT: G 65 LYS cc_start: 0.7783 (tttt) cc_final: 0.7543 (tttt) REVERT: G 228 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7469 (mp) REVERT: D 202 LEU cc_start: 0.8816 (tp) cc_final: 0.8592 (tp) REVERT: A 61 LYS cc_start: 0.8372 (mtmm) cc_final: 0.8157 (ttpp) REVERT: A 103 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8582 (t) REVERT: A 111 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8090 (p) REVERT: A 172 LYS cc_start: 0.8731 (tttt) cc_final: 0.8385 (tttm) REVERT: A 296 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6944 (mpp80) REVERT: A 323 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7328 (mtm180) REVERT: A 327 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7723 (mppt) REVERT: A 339 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7873 (mmpt) REVERT: A 361 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: A 363 LYS cc_start: 0.8784 (mttt) cc_final: 0.7753 (tmtm) REVERT: A 392 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8646 (mtt) REVERT: E 142 ARG cc_start: 0.8337 (mtm110) cc_final: 0.7477 (mtp85) REVERT: B 103 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8568 (t) REVERT: B 111 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8122 (p) REVERT: B 172 LYS cc_start: 0.8760 (tttt) cc_final: 0.8352 (tttm) REVERT: B 234 LYS cc_start: 0.7673 (mttt) cc_final: 0.6961 (mtpt) REVERT: B 323 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.7210 (mtm180) REVERT: B 327 LYS cc_start: 0.8386 (mmmt) cc_final: 0.7763 (mppt) REVERT: B 339 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7854 (mmpt) REVERT: B 361 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7613 (tp30) REVERT: B 363 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8615 (mtmt) REVERT: C 61 LYS cc_start: 0.8356 (mtmm) cc_final: 0.8058 (ttpp) REVERT: C 103 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8601 (t) REVERT: C 111 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8034 (p) REVERT: C 225 ASP cc_start: 0.7576 (t0) cc_final: 0.7259 (t0) REVERT: C 323 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7269 (mtm-85) REVERT: C 327 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7811 (mppt) REVERT: C 339 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7876 (mmpt) REVERT: C 361 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: C 363 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8651 (mttm) REVERT: H 20 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.5991 (tpt) REVERT: H 59 MET cc_start: 0.8069 (mtm) cc_final: 0.7586 (mtt) REVERT: H 62 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: H 228 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7423 (mp) REVERT: H 265 ASN cc_start: 0.8453 (m110) cc_final: 0.8048 (m110) REVERT: I 59 MET cc_start: 0.8103 (mtm) cc_final: 0.7662 (mtt) REVERT: I 62 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: I 64 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6374 (mp0) REVERT: I 114 MET cc_start: 0.8653 (mtt) cc_final: 0.8437 (mtt) REVERT: I 228 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7349 (mp) REVERT: I 246 ARG cc_start: 0.8471 (tpt170) cc_final: 0.8265 (tpt170) REVERT: I 265 ASN cc_start: 0.8390 (m110) cc_final: 0.8105 (m110) outliers start: 73 outliers final: 43 residues processed: 437 average time/residue: 0.6099 time to fit residues: 305.3609 Evaluate side-chains 443 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 378 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 205 ASN Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 212 TRP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 212 TRP Chi-restraints excluded: chain I residue 228 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 129 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 245 optimal weight: 0.0970 chunk 67 optimal weight: 0.6980 chunk 256 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 133 GLN G 201 ASN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS H 201 ASN I 133 GLN I 201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.141842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.114850 restraints weight = 22257.799| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.13 r_work: 0.3149 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22845 Z= 0.111 Angle : 0.537 10.997 31119 Z= 0.281 Chirality : 0.042 0.149 3276 Planarity : 0.005 0.056 3831 Dihedral : 7.459 59.968 3117 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.32 % Allowed : 17.43 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.17), residues: 2697 helix: 1.80 (0.15), residues: 1272 sheet: 1.07 (0.25), residues: 429 loop : -0.80 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 87 TYR 0.020 0.001 TYR G 162 PHE 0.011 0.001 PHE A 99 TRP 0.013 0.001 TRP C 50 HIS 0.005 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00237 (22845) covalent geometry : angle 0.53708 (31119) hydrogen bonds : bond 0.04616 ( 1187) hydrogen bonds : angle 4.66896 ( 3444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5394 Ramachandran restraints generated. 2697 Oldfield, 0 Emsley, 2697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 385 time to evaluate : 0.945 Fit side-chains REVERT: G 59 MET cc_start: 0.8203 (mtm) cc_final: 0.7787 (mtt) REVERT: G 62 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: G 65 LYS cc_start: 0.7822 (tttt) cc_final: 0.7594 (tttt) REVERT: G 228 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7509 (mp) REVERT: D 202 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8578 (tp) REVERT: A 61 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8167 (ttpp) REVERT: A 103 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8566 (t) REVERT: A 111 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8089 (p) REVERT: A 172 LYS cc_start: 0.8726 (tttt) cc_final: 0.8426 (tttm) REVERT: A 323 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7445 (mtm180) REVERT: A 327 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7772 (mppt) REVERT: A 339 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7908 (mmpt) REVERT: A 361 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7914 (tp30) REVERT: A 363 LYS cc_start: 0.8774 (mttt) cc_final: 0.7817 (tmtm) REVERT: E 142 ARG cc_start: 0.8344 (mtm110) cc_final: 0.7567 (mtp85) REVERT: B 103 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8557 (t) REVERT: B 111 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8126 (p) REVERT: B 172 LYS cc_start: 0.8756 (tttt) cc_final: 0.8389 (tttm) REVERT: B 234 LYS cc_start: 0.7708 (mttt) cc_final: 0.7025 (mtpt) REVERT: B 323 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7221 (mtm180) REVERT: B 327 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7816 (mppt) REVERT: B 339 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7882 (mmpt) REVERT: B 361 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: B 363 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8611 (mtmt) REVERT: C 61 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8114 (ttpp) REVERT: C 103 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8608 (t) REVERT: C 111 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.8024 (p) REVERT: C 225 ASP cc_start: 0.7534 (t0) cc_final: 0.7262 (t0) REVERT: C 323 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7178 (mtm-85) REVERT: C 327 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7874 (mppt) REVERT: C 339 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7919 (mmpt) REVERT: C 361 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: C 363 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8685 (mttm) REVERT: H 59 MET cc_start: 0.8059 (mtm) cc_final: 0.7598 (mtt) REVERT: H 62 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: H 114 MET cc_start: 0.8696 (mtt) cc_final: 0.8426 (mtt) REVERT: H 228 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7449 (mp) REVERT: H 265 ASN cc_start: 0.8465 (m110) cc_final: 0.8087 (m110) REVERT: I 62 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7571 (pt0) REVERT: I 64 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6439 (mp0) REVERT: I 114 MET cc_start: 0.8671 (mtt) cc_final: 0.8459 (mtt) REVERT: I 228 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7414 (mp) REVERT: I 265 ASN cc_start: 0.8387 (m110) cc_final: 0.8121 (m110) outliers start: 76 outliers final: 44 residues processed: 434 average time/residue: 0.6576 time to fit residues: 327.4956 Evaluate side-chains 441 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 376 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 205 ASN Chi-restraints excluded: chain G residue 212 TRP Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain A residue 50 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 212 TRP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 212 TRP Chi-restraints excluded: chain I residue 228 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 211 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 263 optimal weight: 0.0050 chunk 85 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 133 GLN G 201 ASN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS B 355 GLN H 201 ASN I 133 GLN I 201 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.141033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.114088 restraints weight = 22097.988| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.17 r_work: 0.3124 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22845 Z= 0.123 Angle : 0.557 10.904 31119 Z= 0.293 Chirality : 0.043 0.155 3276 Planarity : 0.005 0.056 3831 Dihedral : 7.508 60.000 3117 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.10 % Allowed : 17.78 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2697 helix: 1.74 (0.15), residues: 1275 sheet: 1.03 (0.25), residues: 429 loop : -0.81 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 87 TYR 0.022 0.001 TYR I 162 PHE 0.012 0.001 PHE A 99 TRP 0.014 0.001 TRP B 50 HIS 0.005 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00273 (22845) covalent geometry : angle 0.55659 (31119) hydrogen bonds : bond 0.04972 ( 1187) hydrogen bonds : angle 4.74668 ( 3444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9498.68 seconds wall clock time: 162 minutes 11.04 seconds (9731.04 seconds total)