Starting phenix.real_space_refine on Sat Aug 23 13:53:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gf0_51308/08_2025/9gf0_51308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gf0_51308/08_2025/9gf0_51308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gf0_51308/08_2025/9gf0_51308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gf0_51308/08_2025/9gf0_51308.map" model { file = "/net/cci-nas-00/data/ceres_data/9gf0_51308/08_2025/9gf0_51308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gf0_51308/08_2025/9gf0_51308.cif" } resolution = 2.85 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= 0.001 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 7869 2.51 5 N 2105 2.21 5 O 2600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12619 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Chain: "B" Number of atoms: 2521 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 331, 2509 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 bond proxies already assigned to first conformer: 2543 Chain: "C" Number of atoms: 2536 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 333, 2524 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 325} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 333, 2524 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 325} Chain breaks: 1 bond proxies already assigned to first conformer: 2559 Chain: "D" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2516 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 324} Chain breaks: 1 Chain: "E" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2504 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR B 127 " occ=0.70 ... (22 atoms not shown) pdb=" OH BTYR B 127 " occ=0.30 residue: pdb=" N ATYR C 127 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 127 " occ=0.50 Time building chain proxies: 3.99, per 1000 atoms: 0.32 Number of scatterers: 12619 At special positions: 0 Unit cell: (75.985, 111.89, 116.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2600 8.00 N 2105 7.00 C 7869 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: 1.01 Conformation dependent library (CDL) restraints added in 785.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 9.0% alpha, 45.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.740A pdb=" N MET A 28 " --> pdb=" O TYR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.728A pdb=" N GLN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 23 through 29 removed outlier: 3.679A pdb=" N MET B 28 " --> pdb=" O TYR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 82 removed outlier: 3.534A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 23 through 29 removed outlier: 3.639A pdb=" N PHE C 27 " --> pdb=" O PRO C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 removed outlier: 3.661A pdb=" N SER C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.644A pdb=" N MET D 28 " --> pdb=" O TYR D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 25 through 30 removed outlier: 3.791A pdb=" N ALA E 29 " --> pdb=" O TYR E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 removed outlier: 3.764A pdb=" N SER E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.546A pdb=" N ALA A 64 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 114 " --> pdb=" O TRP A 121 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 141 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA A 144 " --> pdb=" O PHE A 163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 155 through 164 current: chain 'A' and resid 175 through 178 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 175 through 178 current: chain 'A' and resid 197 through 211 removed outlier: 6.953A pdb=" N PHE A 239 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN A 238 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 266 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU A 285 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A 261 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 283 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N MET A 263 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLN A 281 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N VAL A 265 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL A 279 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS A 267 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ALA A 277 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 288 " --> pdb=" O THR A 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 296 through 298 current: chain 'A' and resid 315 through 321 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 321 current: chain 'B' and resid 49 through 55 removed outlier: 3.509A pdb=" N TRP B 119 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS B 140 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B 167 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 142 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY B 165 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 144 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP B 155 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR B 190 " --> pdb=" O TRP B 155 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE B 157 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL B 188 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 159 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 186 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN B 161 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 184 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE B 163 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY B 182 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLY B 165 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 178 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASP B 210 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER B 180 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU B 208 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 182 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 231 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE B 239 " --> pdb=" O LEU B 231 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 254 through 258 current: chain 'B' and resid 273 through 282 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 282 current: chain 'B' and resid 315 through 321 removed outlier: 6.835A pdb=" N VAL B 316 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR B 340 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP B 318 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL B 338 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 297 through 298 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 297 through 298 current: chain 'C' and resid 49 through 55 removed outlier: 3.553A pdb=" N ALA C 64 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY C 138 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU C 169 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS C 140 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER C 167 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 142 " --> pdb=" O GLY C 165 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY C 165 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA C 144 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 183 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N THR C 164 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS C 181 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS C 166 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU C 179 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU C 168 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU C 177 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS C 206 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU C 183 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET C 204 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN C 185 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL C 202 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 187 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY C 200 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY C 189 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 198 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE C 239 " --> pdb=" O LEU C 231 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 254 through 258 current: chain 'C' and resid 275 through 282 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 275 through 282 current: chain 'C' and resid 296 through 298 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 296 through 298 current: chain 'C' and resid 315 through 321 removed outlier: 6.786A pdb=" N VAL C 316 " --> pdb=" O TYR C 340 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR C 340 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP C 318 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C 338 " --> pdb=" O ASP C 318 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 335 through 343 current: chain 'D' and resid 49 through 53 removed outlier: 3.650A pdb=" N ALA D 64 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS D 140 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER D 167 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR D 142 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY D 165 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA D 144 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU D 183 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N THR D 164 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LYS D 181 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS D 166 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU D 179 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU D 168 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU D 177 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP D 170 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR D 175 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS D 206 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU D 183 " --> pdb=" O MET D 204 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET D 204 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN D 185 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 202 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR D 187 " --> pdb=" O GLY D 200 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY D 200 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY D 189 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL D 198 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N HIS D 191 " --> pdb=" O MET D 196 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N MET D 196 " --> pdb=" O HIS D 191 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER D 254 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU D 255 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU D 287 " --> pdb=" O GLU D 255 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU D 257 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU D 285 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU D 259 " --> pdb=" O VAL D 283 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 296 through 298 current: chain 'D' and resid 315 through 321 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 315 through 321 current: chain 'E' and resid 49 through 55 removed outlier: 3.760A pdb=" N TRP E 119 " --> pdb=" O MET E 116 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY E 138 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 169 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS E 140 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER E 167 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 142 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY E 165 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA E 144 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU E 183 " --> pdb=" O GLY E 162 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N THR E 164 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LYS E 181 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS E 166 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU E 179 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU E 168 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU E 177 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP E 170 " --> pdb=" O THR E 175 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR E 175 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL E 178 " --> pdb=" O ASP E 210 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASP E 210 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER E 180 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU E 208 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY E 182 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS E 206 " --> pdb=" O GLY E 182 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR E 199 " --> pdb=" O GLY E 226 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE E 239 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN E 238 " --> pdb=" O GLU E 266 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU E 266 " --> pdb=" O ASN E 238 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU E 255 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLU E 287 " --> pdb=" O GLU E 255 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU E 257 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU E 285 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU E 259 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA E 306 " --> pdb=" O PHE E 321 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 316 " --> pdb=" O TYR E 340 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR E 340 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP E 318 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL E 338 " --> pdb=" O ASP E 318 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1553 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: 2.15 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2489 1.32 - 1.45: 3287 1.45 - 1.57: 6966 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 12832 Sorted by residual: bond pdb=" C PRO B 194 " pdb=" N GLU B 195 " ideal model delta sigma weight residual 1.333 1.457 -0.124 1.26e-02 6.30e+03 9.68e+01 bond pdb=" C GLU B 195 " pdb=" N MET B 196 " ideal model delta sigma weight residual 1.329 1.242 0.088 1.36e-02 5.41e+03 4.15e+01 bond pdb=" C ARG E 69 " pdb=" N SER E 70 " ideal model delta sigma weight residual 1.330 1.413 -0.082 1.30e-02 5.92e+03 4.01e+01 bond pdb=" C GLY A 226 " pdb=" N MET A 227 " ideal model delta sigma weight residual 1.330 1.418 -0.088 1.41e-02 5.03e+03 3.86e+01 bond pdb=" C VAL E 174 " pdb=" N THR E 175 " ideal model delta sigma weight residual 1.331 1.400 -0.070 1.34e-02 5.57e+03 2.71e+01 ... (remaining 12827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 16523 2.34 - 4.68: 791 4.68 - 7.03: 67 7.03 - 9.37: 11 9.37 - 11.71: 2 Bond angle restraints: 17394 Sorted by residual: angle pdb=" N ASN A 132 " pdb=" CA ASN A 132 " pdb=" C ASN A 132 " ideal model delta sigma weight residual 114.62 106.50 8.12 1.14e+00 7.69e-01 5.07e+01 angle pdb=" N ASN D 152 " pdb=" CA ASN D 152 " pdb=" C ASN D 152 " ideal model delta sigma weight residual 110.46 101.07 9.39 1.48e+00 4.57e-01 4.03e+01 angle pdb=" O PRO B 194 " pdb=" C PRO B 194 " pdb=" N GLU B 195 " ideal model delta sigma weight residual 122.22 130.36 -8.14 1.29e+00 6.01e-01 3.98e+01 angle pdb=" C ARG E 69 " pdb=" N SER E 70 " pdb=" CA SER E 70 " ideal model delta sigma weight residual 121.06 109.35 11.71 1.88e+00 2.83e-01 3.88e+01 angle pdb=" N PHE D 17 " pdb=" CA PHE D 17 " pdb=" C PHE D 17 " ideal model delta sigma weight residual 113.23 105.85 7.38 1.24e+00 6.50e-01 3.54e+01 ... (remaining 17389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6404 17.76 - 35.52: 766 35.52 - 53.28: 227 53.28 - 71.05: 54 71.05 - 88.81: 27 Dihedral angle restraints: 7478 sinusoidal: 2762 harmonic: 4716 Sorted by residual: dihedral pdb=" C PHE A 111 " pdb=" N PHE A 111 " pdb=" CA PHE A 111 " pdb=" CB PHE A 111 " ideal model delta harmonic sigma weight residual -122.60 -111.64 -10.96 0 2.50e+00 1.60e-01 1.92e+01 dihedral pdb=" CA PHE C 66 " pdb=" C PHE C 66 " pdb=" N GLY C 67 " pdb=" CA GLY C 67 " ideal model delta harmonic sigma weight residual 180.00 162.46 17.54 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 16 " pdb=" CB ASP A 16 " pdb=" CG ASP A 16 " pdb=" OD1 ASP A 16 " ideal model delta sinusoidal sigma weight residual -30.00 -89.01 59.01 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 7475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1353 0.054 - 0.107: 345 0.107 - 0.161: 171 0.161 - 0.214: 39 0.214 - 0.268: 11 Chirality restraints: 1919 Sorted by residual: chirality pdb=" CA PHE C 103 " pdb=" N PHE C 103 " pdb=" C PHE C 103 " pdb=" CB PHE C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA TYR B 223 " pdb=" N TYR B 223 " pdb=" C TYR B 223 " pdb=" CB TYR B 223 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LYS E 206 " pdb=" N LYS E 206 " pdb=" C LYS E 206 " pdb=" CB LYS E 206 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1916 not shown) Planarity restraints: 2290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BTYR C 127 " 0.024 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C BTYR C 127 " -0.084 2.00e-02 2.50e+03 pdb=" O BTYR C 127 " 0.031 2.00e-02 2.50e+03 pdb=" N SER C 128 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 343 " -0.023 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C THR D 343 " 0.080 2.00e-02 2.50e+03 pdb=" O THR D 343 " -0.031 2.00e-02 2.50e+03 pdb=" N PHE D 344 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 343 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C THR A 343 " -0.077 2.00e-02 2.50e+03 pdb=" O THR A 343 " 0.030 2.00e-02 2.50e+03 pdb=" N PHE A 344 " 0.026 2.00e-02 2.50e+03 ... (remaining 2287 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 669 2.71 - 3.26: 11116 3.26 - 3.81: 19748 3.81 - 4.35: 26440 4.35 - 4.90: 46901 Nonbonded interactions: 104874 Sorted by model distance: nonbonded pdb=" O ASN B 332 " pdb=" OD1 ASN B 332 " model vdw 2.163 3.040 nonbonded pdb=" O ASN C 152 " pdb=" OD1 ASN C 152 " model vdw 2.181 3.040 nonbonded pdb=" OG SER D 301 " pdb=" ND2 ASN E 106 " model vdw 2.221 3.120 nonbonded pdb=" OD2 ASP A 318 " pdb=" O HOH A 401 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR E 199 " pdb=" OE2 GLU E 244 " model vdw 2.262 3.040 ... (remaining 104869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 83 or resid 98 through 126 or resid 128 through \ 344)) selection = (chain 'B' and (resid 1 through 83 or resid 98 through 126 or resid 128 through \ 344)) selection = (chain 'C' and (resid 1 through 83 or resid 98 through 126 or resid 128 through \ 344)) selection = (chain 'D' and (resid 1 through 83 or resid 98 through 126 or resid 128 through \ 344)) selection = (chain 'E' and (resid 1 through 126 or resid 128 through 344)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.930 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 12832 Z= 0.536 Angle : 1.011 11.709 17394 Z= 0.697 Chirality : 0.063 0.268 1919 Planarity : 0.006 0.115 2290 Dihedral : 18.171 88.806 4470 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.74 % Favored : 94.01 % Rotamer: Outliers : 4.11 % Allowed : 26.39 % Favored : 69.51 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 16.13 % 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 aren not related in a simple way. whole: -1.14 (0.21), residues: 1643 helix: -1.61 (0.40), residues: 143 sheet: 0.09 (0.17), residues: 974 loop : -2.03 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.023 0.002 TYR E 241 PHE 0.023 0.002 PHE A 111 TRP 0.022 0.002 TRP C 121 HIS 0.004 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00789 (12832) covalent geometry : angle 1.01111 (17394) hydrogen bonds : bond 0.21888 ( 557) hydrogen bonds : angle 8.63883 ( 1553) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 0.496 Fit side-chains REVERT: A 111 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: A 140 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7388 (ttpm) REVERT: B 238 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7614 (t0) REVERT: C 330 ASN cc_start: 0.7525 (p0) cc_final: 0.7322 (p0) REVERT: D 134 ASP cc_start: 0.8039 (t70) cc_final: 0.7083 (p0) REVERT: D 234 SER cc_start: 0.5250 (OUTLIER) cc_final: 0.4592 (m) REVERT: D 249 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7671 (tttp) REVERT: E 217 GLU cc_start: 0.6784 (tt0) cc_final: 0.6499 (tt0) outliers start: 52 outliers final: 28 residues processed: 224 average time/residue: 0.5714 time to fit residues: 140.0360 Evaluate side-chains 169 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 132 ASN B 332 ASN C 152 ASN C 333 ASN E 33 GLN E 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.156456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124497 restraints weight = 34272.553| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 4.17 r_work: 0.3180 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12832 Z= 0.132 Angle : 0.550 6.492 17394 Z= 0.312 Chirality : 0.044 0.149 1919 Planarity : 0.004 0.065 2290 Dihedral : 6.388 59.715 1811 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.71 % Allowed : 27.83 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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 aren not related in a simple way. whole: -0.67 (0.21), residues: 1643 helix: -1.32 (0.40), residues: 145 sheet: 0.38 (0.17), residues: 977 loop : -1.68 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.010 0.001 TYR A 223 PHE 0.013 0.001 PHE C 111 TRP 0.018 0.001 TRP C 121 HIS 0.009 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00293 (12832) covalent geometry : angle 0.54999 (17394) hydrogen bonds : bond 0.03810 ( 557) hydrogen bonds : angle 5.75307 ( 1553) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 0.516 Fit side-chains REVERT: A 132 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7626 (t0) REVERT: A 168 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7296 (mp0) REVERT: A 249 LYS cc_start: 0.7457 (ttmp) cc_final: 0.7066 (mtpp) REVERT: A 258 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8075 (mt) REVERT: D 59 ASP cc_start: 0.7476 (p0) cc_final: 0.7115 (p0) REVERT: D 159 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7538 (tp) REVERT: D 227 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8244 (tmm) REVERT: D 249 LYS cc_start: 0.7663 (tttt) cc_final: 0.7175 (tttp) REVERT: D 303 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7452 (ptp-170) REVERT: E 179 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: E 217 GLU cc_start: 0.7022 (tt0) cc_final: 0.6346 (tt0) outliers start: 60 outliers final: 26 residues processed: 197 average time/residue: 0.5957 time to fit residues: 128.1058 Evaluate side-chains 162 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 7 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 84 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.153282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122705 restraints weight = 39086.798| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 4.71 r_work: 0.3115 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12832 Z= 0.177 Angle : 0.561 5.711 17394 Z= 0.318 Chirality : 0.045 0.154 1919 Planarity : 0.004 0.063 2290 Dihedral : 5.312 47.895 1769 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.11 % Allowed : 28.06 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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 aren not related in a simple way. whole: -0.62 (0.21), residues: 1643 helix: -1.24 (0.40), residues: 145 sheet: 0.37 (0.17), residues: 975 loop : -1.56 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.012 0.001 TYR C 241 PHE 0.015 0.002 PHE D 73 TRP 0.015 0.001 TRP C 121 HIS 0.009 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00410 (12832) covalent geometry : angle 0.56137 (17394) hydrogen bonds : bond 0.03830 ( 557) hydrogen bonds : angle 5.43330 ( 1553) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 0.518 Fit side-chains REVERT: A 192 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7544 (mpp) REVERT: A 249 LYS cc_start: 0.7488 (ttmp) cc_final: 0.7148 (mtpp) REVERT: B 219 GLU cc_start: 0.7491 (tt0) cc_final: 0.6595 (tm-30) REVERT: D 159 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7582 (tp) REVERT: D 179 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: D 227 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8240 (tmm) REVERT: D 249 LYS cc_start: 0.7711 (tttt) cc_final: 0.7207 (tttp) REVERT: D 303 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7539 (ptp-170) REVERT: E 116 MET cc_start: 0.5962 (OUTLIER) cc_final: 0.5583 (pp-130) REVERT: E 179 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: E 217 GLU cc_start: 0.7102 (tt0) cc_final: 0.6370 (tt0) outliers start: 52 outliers final: 27 residues processed: 173 average time/residue: 0.5917 time to fit residues: 111.8285 Evaluate side-chains 165 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 55 optimal weight: 0.0670 chunk 108 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 109 ASN B 332 ASN D 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119922 restraints weight = 34294.328| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 4.13 r_work: 0.3096 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 12832 Z= 0.291 Angle : 0.653 6.617 17394 Z= 0.367 Chirality : 0.049 0.167 1919 Planarity : 0.005 0.063 2290 Dihedral : 5.460 46.672 1761 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.10 % Allowed : 27.68 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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 aren not related in a simple way. whole: -0.81 (0.21), residues: 1643 helix: -1.56 (0.39), residues: 145 sheet: 0.21 (0.16), residues: 989 loop : -1.58 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 12 TYR 0.014 0.002 TYR E 25 PHE 0.021 0.002 PHE D 73 TRP 0.014 0.002 TRP C 121 HIS 0.008 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00686 (12832) covalent geometry : angle 0.65298 (17394) hydrogen bonds : bond 0.04460 ( 557) hydrogen bonds : angle 5.54579 ( 1553) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 129 time to evaluate : 0.426 Fit side-chains REVERT: A 111 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7121 (p90) REVERT: A 168 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7574 (mp0) REVERT: A 249 LYS cc_start: 0.7494 (ttmp) cc_final: 0.7150 (mtpp) REVERT: A 258 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8135 (mt) REVERT: A 263 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8325 (ptt) REVERT: B 219 GLU cc_start: 0.7506 (tt0) cc_final: 0.6633 (tm-30) REVERT: B 253 ASP cc_start: 0.6679 (t0) cc_final: 0.6208 (t70) REVERT: C 236 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: D 140 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7749 (tttm) REVERT: D 159 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7630 (tp) REVERT: D 179 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: D 227 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8226 (tmm) REVERT: D 249 LYS cc_start: 0.7799 (tttt) cc_final: 0.7313 (tttp) REVERT: E 116 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5757 (pp-130) REVERT: E 179 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: E 217 GLU cc_start: 0.7078 (tt0) cc_final: 0.6319 (tt0) outliers start: 65 outliers final: 35 residues processed: 177 average time/residue: 0.5470 time to fit residues: 105.7339 Evaluate side-chains 171 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 82 optimal weight: 0.0170 chunk 51 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS C 26 GLN C 152 ASN D 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122784 restraints weight = 35832.658| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.39 r_work: 0.3161 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12832 Z= 0.105 Angle : 0.489 5.140 17394 Z= 0.278 Chirality : 0.043 0.143 1919 Planarity : 0.003 0.062 2290 Dihedral : 4.726 35.131 1761 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.50 % Allowed : 29.05 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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 aren not related in a simple way. whole: -0.40 (0.21), residues: 1643 helix: -0.89 (0.42), residues: 139 sheet: 0.39 (0.17), residues: 982 loop : -1.23 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 12 TYR 0.009 0.001 TYR D 223 PHE 0.013 0.001 PHE C 111 TRP 0.017 0.001 TRP C 121 HIS 0.009 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00231 (12832) covalent geometry : angle 0.48922 (17394) hydrogen bonds : bond 0.02933 ( 557) hydrogen bonds : angle 5.07916 ( 1553) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.497 Fit side-chains REVERT: A 168 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7389 (mp0) REVERT: A 249 LYS cc_start: 0.7309 (ttmp) cc_final: 0.6977 (mtpp) REVERT: B 204 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7568 (mmm) REVERT: B 219 GLU cc_start: 0.7409 (tt0) cc_final: 0.6525 (tm-30) REVERT: B 234 SER cc_start: 0.8060 (t) cc_final: 0.7501 (m) REVERT: C 116 MET cc_start: 0.6379 (ttt) cc_final: 0.6153 (ptp) REVERT: D 159 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7552 (tp) REVERT: D 179 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6866 (tt0) REVERT: D 227 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8022 (tmt) REVERT: D 249 LYS cc_start: 0.7725 (tttt) cc_final: 0.7269 (tttp) REVERT: D 303 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7894 (ptp-170) REVERT: E 116 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5718 (pp-130) REVERT: E 192 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8044 (mtp) REVERT: E 217 GLU cc_start: 0.7112 (tt0) cc_final: 0.6307 (tt0) outliers start: 44 outliers final: 22 residues processed: 169 average time/residue: 0.5245 time to fit residues: 96.9251 Evaluate side-chains 160 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 304 MET Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 73 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 238 ASN E 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122315 restraints weight = 32759.584| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 4.01 r_work: 0.3146 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12832 Z= 0.181 Angle : 0.548 5.274 17394 Z= 0.309 Chirality : 0.045 0.154 1919 Planarity : 0.004 0.085 2290 Dihedral : 4.873 34.669 1759 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.03 % Allowed : 28.21 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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 aren not related in a simple way. whole: -0.50 (0.21), residues: 1643 helix: -1.18 (0.40), residues: 151 sheet: 0.37 (0.17), residues: 976 loop : -1.30 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 12 TYR 0.013 0.001 TYR C 241 PHE 0.015 0.002 PHE D 73 TRP 0.018 0.001 TRP C 121 HIS 0.009 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00422 (12832) covalent geometry : angle 0.54755 (17394) hydrogen bonds : bond 0.03519 ( 557) hydrogen bonds : angle 5.15267 ( 1553) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 0.500 Fit side-chains REVERT: A 249 LYS cc_start: 0.7454 (ttmp) cc_final: 0.7121 (mtpp) REVERT: B 204 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7584 (mmm) REVERT: B 219 GLU cc_start: 0.7454 (tt0) cc_final: 0.6566 (tm-30) REVERT: B 234 SER cc_start: 0.8093 (t) cc_final: 0.7527 (m) REVERT: D 140 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7763 (tttm) REVERT: D 159 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7579 (tp) REVERT: D 179 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.6914 (tt0) REVERT: D 227 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8171 (tmm) REVERT: D 249 LYS cc_start: 0.7800 (tttt) cc_final: 0.7254 (tttp) REVERT: D 303 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7912 (ptp-170) REVERT: E 116 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5867 (pp-130) REVERT: E 217 GLU cc_start: 0.7079 (tt0) cc_final: 0.6243 (tt0) outliers start: 51 outliers final: 32 residues processed: 166 average time/residue: 0.5362 time to fit residues: 97.4174 Evaluate side-chains 163 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 73 optimal weight: 0.4980 chunk 161 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS C 26 GLN D 238 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.152313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120235 restraints weight = 23359.798| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.56 r_work: 0.3202 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12832 Z= 0.253 Angle : 0.610 5.988 17394 Z= 0.343 Chirality : 0.047 0.161 1919 Planarity : 0.005 0.077 2290 Dihedral : 5.200 37.346 1759 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.26 % Allowed : 28.29 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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 aren not related in a simple way. whole: -0.66 (0.21), residues: 1643 helix: -1.35 (0.40), residues: 145 sheet: 0.25 (0.16), residues: 989 loop : -1.40 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 12 TYR 0.015 0.002 TYR C 241 PHE 0.019 0.002 PHE D 73 TRP 0.019 0.002 TRP C 121 HIS 0.010 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00596 (12832) covalent geometry : angle 0.60972 (17394) hydrogen bonds : bond 0.04064 ( 557) hydrogen bonds : angle 5.32628 ( 1553) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 130 time to evaluate : 0.501 Fit side-chains REVERT: A 249 LYS cc_start: 0.7609 (ttmp) cc_final: 0.7269 (mtpp) REVERT: B 204 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7739 (mmm) REVERT: B 219 GLU cc_start: 0.7528 (tt0) cc_final: 0.6652 (tm-30) REVERT: B 253 ASP cc_start: 0.6841 (t0) cc_final: 0.6338 (t70) REVERT: C 116 MET cc_start: 0.6491 (ttt) cc_final: 0.6283 (ptp) REVERT: D 140 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7820 (tttm) REVERT: D 159 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7631 (tp) REVERT: D 179 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: D 227 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8212 (tmm) REVERT: D 249 LYS cc_start: 0.7882 (tttt) cc_final: 0.7368 (tttm) REVERT: D 303 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7981 (ptp-170) REVERT: E 115 LYS cc_start: 0.8404 (ttpt) cc_final: 0.7632 (ttmt) REVERT: E 116 MET cc_start: 0.6211 (OUTLIER) cc_final: 0.5911 (pp-130) REVERT: E 179 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: E 217 GLU cc_start: 0.7059 (tt0) cc_final: 0.6253 (tt0) outliers start: 54 outliers final: 38 residues processed: 168 average time/residue: 0.5482 time to fit residues: 100.9085 Evaluate side-chains 174 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 127 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS C 26 GLN D 238 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119625 restraints weight = 25576.968| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.89 r_work: 0.3209 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12832 Z= 0.125 Angle : 0.505 4.711 17394 Z= 0.286 Chirality : 0.044 0.149 1919 Planarity : 0.004 0.072 2290 Dihedral : 4.750 29.945 1759 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.80 % Allowed : 28.75 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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 aren not related in a simple way. whole: -0.39 (0.21), residues: 1643 helix: -0.99 (0.41), residues: 145 sheet: 0.37 (0.17), residues: 978 loop : -1.13 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 12 TYR 0.016 0.001 TYR C 241 PHE 0.017 0.001 PHE A 21 TRP 0.019 0.001 TRP C 121 HIS 0.006 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00285 (12832) covalent geometry : angle 0.50453 (17394) hydrogen bonds : bond 0.03081 ( 557) hydrogen bonds : angle 5.04621 ( 1553) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.522 Fit side-chains REVERT: A 168 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7481 (mp0) REVERT: A 249 LYS cc_start: 0.7437 (ttmp) cc_final: 0.7118 (mtpp) REVERT: B 204 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7675 (mmm) REVERT: B 219 GLU cc_start: 0.7439 (tt0) cc_final: 0.6550 (tm-30) REVERT: B 234 SER cc_start: 0.8123 (t) cc_final: 0.7550 (m) REVERT: D 140 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7798 (tttm) REVERT: D 159 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7567 (tp) REVERT: D 179 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: D 208 GLU cc_start: 0.7304 (tp30) cc_final: 0.6906 (mm-30) REVERT: D 227 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8237 (tmm) REVERT: D 249 LYS cc_start: 0.7768 (tttt) cc_final: 0.7237 (tttp) REVERT: D 303 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7984 (ptp-170) REVERT: E 116 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5867 (pp-130) REVERT: E 192 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: E 217 GLU cc_start: 0.6981 (tt0) cc_final: 0.6136 (tt0) outliers start: 48 outliers final: 30 residues processed: 163 average time/residue: 0.5650 time to fit residues: 100.9139 Evaluate side-chains 163 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 123 optimal weight: 0.2980 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS C 26 GLN D 238 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.157173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124164 restraints weight = 32400.156| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.65 r_work: 0.3223 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12832 Z= 0.093 Angle : 0.472 4.476 17394 Z= 0.268 Chirality : 0.043 0.144 1919 Planarity : 0.004 0.077 2290 Dihedral : 4.412 24.587 1759 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.89 % Allowed : 29.51 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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 aren not related in a simple way. whole: -0.17 (0.21), residues: 1643 helix: -0.51 (0.42), residues: 145 sheet: 0.41 (0.17), residues: 994 loop : -0.89 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.016 0.001 TYR C 241 PHE 0.020 0.001 PHE A 21 TRP 0.022 0.001 TRP C 121 HIS 0.008 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00205 (12832) covalent geometry : angle 0.47206 (17394) hydrogen bonds : bond 0.02665 ( 557) hydrogen bonds : angle 4.84391 ( 1553) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.486 Fit side-chains REVERT: A 55 ARG cc_start: 0.7980 (mmt90) cc_final: 0.7779 (mmt180) REVERT: A 168 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7308 (mp0) REVERT: A 249 LYS cc_start: 0.7306 (ttmp) cc_final: 0.6998 (mtpp) REVERT: B 204 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7604 (mmm) REVERT: B 219 GLU cc_start: 0.7344 (tt0) cc_final: 0.6490 (tm-30) REVERT: D 75 GLU cc_start: 0.7722 (tt0) cc_final: 0.7373 (tt0) REVERT: D 140 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7804 (tttm) REVERT: D 159 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7480 (tp) REVERT: D 179 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: D 208 GLU cc_start: 0.7075 (tp30) cc_final: 0.6671 (mm-30) REVERT: D 227 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8010 (tmt) REVERT: D 249 LYS cc_start: 0.7636 (tttt) cc_final: 0.7143 (tttp) REVERT: D 303 ARG cc_start: 0.8101 (ptt90) cc_final: 0.7893 (ptp-170) REVERT: E 116 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.5841 (pp-130) REVERT: E 192 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8037 (mtp) REVERT: E 217 GLU cc_start: 0.6943 (tt0) cc_final: 0.6189 (tt0) outliers start: 36 outliers final: 25 residues processed: 159 average time/residue: 0.5633 time to fit residues: 97.6924 Evaluate side-chains 156 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 115 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 31 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN E 152 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.154851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122910 restraints weight = 34157.655| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.89 r_work: 0.3156 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12832 Z= 0.143 Angle : 0.518 4.632 17394 Z= 0.293 Chirality : 0.044 0.151 1919 Planarity : 0.004 0.074 2290 Dihedral : 4.575 25.689 1758 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.66 % Allowed : 29.89 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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 aren not related in a simple way. whole: -0.24 (0.21), residues: 1643 helix: -0.79 (0.42), residues: 145 sheet: 0.49 (0.17), residues: 967 loop : -1.10 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 303 TYR 0.015 0.001 TYR C 241 PHE 0.015 0.001 PHE A 21 TRP 0.020 0.001 TRP C 121 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00330 (12832) covalent geometry : angle 0.51784 (17394) hydrogen bonds : bond 0.03101 ( 557) hydrogen bonds : angle 4.92038 ( 1553) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.534 Fit side-chains REVERT: A 168 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7415 (mp0) REVERT: A 249 LYS cc_start: 0.7397 (ttmp) cc_final: 0.7071 (mtpp) REVERT: B 140 LYS cc_start: 0.8420 (tttm) cc_final: 0.8218 (tttm) REVERT: B 204 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7650 (mmm) REVERT: B 219 GLU cc_start: 0.7399 (tt0) cc_final: 0.6548 (tm-30) REVERT: D 140 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7855 (tttm) REVERT: D 159 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7551 (tp) REVERT: D 179 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.6837 (tt0) REVERT: D 208 GLU cc_start: 0.7117 (tp30) cc_final: 0.6709 (mm-30) REVERT: D 227 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8136 (tmm) REVERT: D 249 LYS cc_start: 0.7726 (tttt) cc_final: 0.7205 (tttp) REVERT: D 303 ARG cc_start: 0.8141 (ptt90) cc_final: 0.7935 (ptp-170) REVERT: E 116 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5887 (pp-130) REVERT: E 159 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7930 (tt) REVERT: E 192 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8060 (mtp) REVERT: E 217 GLU cc_start: 0.6993 (tt0) cc_final: 0.6218 (tt0) outliers start: 33 outliers final: 23 residues processed: 148 average time/residue: 0.5733 time to fit residues: 92.5456 Evaluate side-chains 153 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN D 238 ASN E 152 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.154701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122073 restraints weight = 30372.587| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.54 r_work: 0.3154 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12832 Z= 0.172 Angle : 0.540 4.763 17394 Z= 0.305 Chirality : 0.045 0.154 1919 Planarity : 0.004 0.075 2290 Dihedral : 4.727 27.876 1758 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.89 % Allowed : 30.04 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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 aren not related in a simple way. whole: -0.35 (0.21), residues: 1643 helix: -0.95 (0.40), residues: 151 sheet: 0.45 (0.17), residues: 962 loop : -1.18 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 303 TYR 0.016 0.001 TYR C 241 PHE 0.016 0.002 PHE B 163 TRP 0.021 0.001 TRP C 121 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00400 (12832) covalent geometry : angle 0.54021 (17394) hydrogen bonds : bond 0.03354 ( 557) hydrogen bonds : angle 5.01794 ( 1553) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4137.02 seconds wall clock time: 71 minutes 36.50 seconds (4296.50 seconds total)