Starting phenix.real_space_refine on Fri Sep 19 01:10:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kfg_9972/09_2025/6kfg_9972.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kfg_9972/09_2025/6kfg_9972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kfg_9972/09_2025/6kfg_9972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kfg_9972/09_2025/6kfg_9972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kfg_9972/09_2025/6kfg_9972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kfg_9972/09_2025/6kfg_9972.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 96 5.16 5 C 14704 2.51 5 N 3632 2.21 5 O 3832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22264 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2783 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 326} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 2.40, per 1000 atoms: 0.11 Number of scatterers: 22264 At special positions: 0 Unit cell: (126.896, 126.896, 107.184, 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 96 16.00 O 3832 8.00 N 3632 7.00 C 14704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 265 " distance=2.05 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.05 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 265 " distance=2.05 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.05 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.05 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.05 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.05 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.05 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 76 " - pdb=" SG CYS H 248 " distance=2.03 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: 1.99 Conformation dependent library (CDL) restraints added in 926.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5216 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 8 sheets defined 67.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 29 through 47 removed outlier: 4.140A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.338A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix removed outlier: 3.505A pdb=" N GLY A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 3.780A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 212 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A 302 " --> pdb=" O TRP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.639A pdb=" N TYR A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix removed outlier: 3.504A pdb=" N GLY B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 182 removed outlier: 3.716A pdb=" N ARG B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Proline residue: B 169 - end of helix removed outlier: 3.780A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 212 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B 302 " --> pdb=" O TRP B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 326 through 335 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 29 through 47 removed outlier: 4.140A pdb=" N ARG C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix removed outlier: 3.505A pdb=" N GLY C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 182 removed outlier: 3.718A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Proline residue: C 169 - end of helix removed outlier: 3.781A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 212 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C 275 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU C 302 " --> pdb=" O TRP C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.338A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix removed outlier: 3.505A pdb=" N GLY D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 151 removed outlier: 3.601A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 182 removed outlier: 3.716A pdb=" N ARG D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Proline residue: D 169 - end of helix removed outlier: 3.780A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 212 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 269 through 305 removed outlier: 3.736A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU D 302 " --> pdb=" O TRP D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 326 through 335 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 351 through 365 removed outlier: 3.639A pdb=" N TYR D 356 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 19 Processing helix chain 'E' and resid 29 through 47 removed outlier: 4.140A pdb=" N ARG E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix removed outlier: 3.505A pdb=" N GLY E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 151 removed outlier: 3.601A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 removed outlier: 4.083A pdb=" N LYS E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Proline residue: E 169 - end of helix removed outlier: 3.781A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 212 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS E 275 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU E 302 " --> pdb=" O TRP E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 326 through 335 Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 351 through 365 removed outlier: 3.639A pdb=" N TYR E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 19 Processing helix chain 'F' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL F 37 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU F 47 " --> pdb=" O SER F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 134 removed outlier: 4.452A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix removed outlier: 3.505A pdb=" N GLY F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 182 removed outlier: 3.718A pdb=" N ARG F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Proline residue: F 169 - end of helix removed outlier: 3.779A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 212 Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 269 through 305 removed outlier: 3.736A pdb=" N GLU F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS F 275 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE F 279 " --> pdb=" O LYS F 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR F 301 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU F 302 " --> pdb=" O TRP F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 326 through 335 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR F 356 " --> pdb=" O ILE F 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 19 Processing helix chain 'G' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU G 47 " --> pdb=" O SER G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 134 removed outlier: 4.451A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix removed outlier: 3.504A pdb=" N GLY G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Proline residue: G 169 - end of helix removed outlier: 3.781A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 212 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 269 through 305 removed outlier: 3.736A pdb=" N GLU G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS G 275 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE G 279 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL G 293 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR G 301 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU G 302 " --> pdb=" O TRP G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 326 through 335 Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR G 356 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 19 Processing helix chain 'H' and resid 29 through 47 removed outlier: 4.141A pdb=" N ARG H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU H 47 " --> pdb=" O SER H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 79 removed outlier: 4.339A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 134 removed outlier: 4.452A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix removed outlier: 3.505A pdb=" N GLY H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 151 removed outlier: 3.602A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 4.082A pdb=" N LYS H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 182 removed outlier: 3.717A pdb=" N ARG H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Proline residue: H 169 - end of helix removed outlier: 3.780A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 212 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'H' and resid 269 through 305 removed outlier: 3.737A pdb=" N GLU H 274 " --> pdb=" O ASN H 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS H 275 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE H 279 " --> pdb=" O LYS H 275 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN H 294 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR H 301 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU H 302 " --> pdb=" O TRP H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 326 through 335 Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 351 through 365 removed outlier: 3.640A pdb=" N TYR H 356 " --> pdb=" O ILE H 352 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 removed outlier: 3.930A pdb=" N LEU A 264 " --> pdb=" O TRP A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU B 264 " --> pdb=" O TRP B 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 59 removed outlier: 3.930A pdb=" N LEU C 264 " --> pdb=" O TRP C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU D 264 " --> pdb=" O TRP D 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU E 264 " --> pdb=" O TRP E 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU F 264 " --> pdb=" O TRP F 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 56 through 59 removed outlier: 3.931A pdb=" N LEU G 264 " --> pdb=" O TRP G 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.930A pdb=" N LEU H 264 " --> pdb=" O TRP H 59 " (cutoff:3.500A) 1225 hydrogen bonds defined for protein. 3627 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: 2.96 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6756 1.35 - 1.49: 6983 1.49 - 1.62: 9045 1.62 - 1.76: 8 1.76 - 1.89: 128 Bond restraints: 22920 Sorted by residual: bond pdb=" CB CYS H 58 " pdb=" SG CYS H 58 " ideal model delta sigma weight residual 1.808 1.890 -0.082 3.30e-02 9.18e+02 6.15e+00 bond pdb=" CB CYS C 58 " pdb=" SG CYS C 58 " ideal model delta sigma weight residual 1.808 1.890 -0.082 3.30e-02 9.18e+02 6.13e+00 bond pdb=" CB CYS A 58 " pdb=" SG CYS A 58 " ideal model delta sigma weight residual 1.808 1.890 -0.082 3.30e-02 9.18e+02 6.10e+00 bond pdb=" CB CYS D 58 " pdb=" SG CYS D 58 " ideal model delta sigma weight residual 1.808 1.889 -0.081 3.30e-02 9.18e+02 6.10e+00 bond pdb=" CB CYS E 58 " pdb=" SG CYS E 58 " ideal model delta sigma weight residual 1.808 1.889 -0.081 3.30e-02 9.18e+02 6.07e+00 ... (remaining 22915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 30768 2.55 - 5.10: 392 5.10 - 7.65: 48 7.65 - 10.20: 0 10.20 - 12.75: 8 Bond angle restraints: 31216 Sorted by residual: angle pdb=" CA CYS G 265 " pdb=" CB CYS G 265 " pdb=" SG CYS G 265 " ideal model delta sigma weight residual 114.40 127.15 -12.75 2.30e+00 1.89e-01 3.07e+01 angle pdb=" CA CYS E 265 " pdb=" CB CYS E 265 " pdb=" SG CYS E 265 " ideal model delta sigma weight residual 114.40 127.11 -12.71 2.30e+00 1.89e-01 3.05e+01 angle pdb=" CA CYS C 265 " pdb=" CB CYS C 265 " pdb=" SG CYS C 265 " ideal model delta sigma weight residual 114.40 127.11 -12.71 2.30e+00 1.89e-01 3.05e+01 angle pdb=" CA CYS H 265 " pdb=" CB CYS H 265 " pdb=" SG CYS H 265 " ideal model delta sigma weight residual 114.40 127.10 -12.70 2.30e+00 1.89e-01 3.05e+01 angle pdb=" CA CYS F 265 " pdb=" CB CYS F 265 " pdb=" SG CYS F 265 " ideal model delta sigma weight residual 114.40 127.10 -12.70 2.30e+00 1.89e-01 3.05e+01 ... (remaining 31211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 11402 15.58 - 31.17: 1407 31.17 - 46.75: 287 46.75 - 62.33: 72 62.33 - 77.91: 16 Dihedral angle restraints: 13184 sinusoidal: 5144 harmonic: 8040 Sorted by residual: dihedral pdb=" CB CYS E 58 " pdb=" SG CYS E 58 " pdb=" SG CYS E 265 " pdb=" CB CYS E 265 " ideal model delta sinusoidal sigma weight residual 93.00 39.42 53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS G 58 " pdb=" SG CYS G 58 " pdb=" SG CYS G 265 " pdb=" CB CYS G 265 " ideal model delta sinusoidal sigma weight residual 93.00 39.42 53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS F 58 " pdb=" SG CYS F 58 " pdb=" SG CYS F 265 " pdb=" CB CYS F 265 " ideal model delta sinusoidal sigma weight residual 93.00 39.43 53.57 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 13181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2102 0.038 - 0.076: 951 0.076 - 0.114: 331 0.114 - 0.152: 56 0.152 - 0.190: 8 Chirality restraints: 3448 Sorted by residual: chirality pdb=" CA CYS B 265 " pdb=" N CYS B 265 " pdb=" C CYS B 265 " pdb=" CB CYS B 265 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA CYS E 265 " pdb=" N CYS E 265 " pdb=" C CYS E 265 " pdb=" CB CYS E 265 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA CYS D 265 " pdb=" N CYS D 265 " pdb=" C CYS D 265 " pdb=" CB CYS D 265 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.81e-01 ... (remaining 3445 not shown) Planarity restraints: 3832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 242 " 0.014 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE B 242 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE B 242 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 242 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 242 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 242 " 0.014 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE C 242 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 242 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 242 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 242 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 242 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 242 " 0.014 2.00e-02 2.50e+03 1.10e-02 2.12e+00 pdb=" CG PHE A 242 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 242 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 242 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 242 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 242 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 242 " 0.003 2.00e-02 2.50e+03 ... (remaining 3829 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 604 2.70 - 3.25: 24596 3.25 - 3.80: 35506 3.80 - 4.35: 41354 4.35 - 4.90: 69124 Nonbonded interactions: 171184 Sorted by model distance: nonbonded pdb=" OE1 GLN G 115 " pdb=" NE2 GLN G 206 " model vdw 2.148 3.120 nonbonded pdb=" OE1 GLN C 115 " pdb=" NE2 GLN C 206 " model vdw 2.148 3.120 nonbonded pdb=" OE1 GLN B 115 " pdb=" NE2 GLN B 206 " model vdw 2.148 3.120 nonbonded pdb=" OE1 GLN F 115 " pdb=" NE2 GLN F 206 " model vdw 2.149 3.120 nonbonded pdb=" OE1 GLN D 115 " pdb=" NE2 GLN D 206 " model vdw 2.149 3.120 ... (remaining 171179 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.970 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.007 0.082 22936 Z= 0.296 Angle : 0.781 12.750 31248 Z= 0.424 Chirality : 0.047 0.190 3448 Planarity : 0.003 0.029 3832 Dihedral : 14.038 77.914 7920 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 0.67 % Allowed : 8.15 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.38 (0.13), residues: 2640 helix: -1.78 (0.11), residues: 1704 sheet: -3.36 (0.47), residues: 88 loop : -5.15 (0.13), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 161 TYR 0.012 0.001 TYR F 301 PHE 0.025 0.002 PHE B 242 TRP 0.012 0.002 TRP A 222 HIS 0.004 0.001 HIS G 241 Details of bonding type rmsd covalent geometry : bond 0.00689 (22920) covalent geometry : angle 0.76960 (31216) SS BOND : bond 0.01121 ( 16) SS BOND : angle 4.22989 ( 32) hydrogen bonds : bond 0.14777 ( 1225) hydrogen bonds : angle 6.72421 ( 3627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 934 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 VAL cc_start: 0.9055 (m) cc_final: 0.8784 (t) REVERT: A 127 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7711 (ttmm) REVERT: A 130 ILE cc_start: 0.9009 (tp) cc_final: 0.8624 (tp) REVERT: A 284 LEU cc_start: 0.8784 (tp) cc_final: 0.8579 (tp) REVERT: A 343 ASP cc_start: 0.8354 (t70) cc_final: 0.8094 (t70) REVERT: A 344 GLN cc_start: 0.9045 (mm110) cc_final: 0.8730 (mm110) REVERT: A 364 ILE cc_start: 0.8755 (tt) cc_final: 0.8466 (tt) REVERT: B 63 GLN cc_start: 0.8001 (pp30) cc_final: 0.7764 (pm20) REVERT: B 127 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7811 (ttmm) REVERT: B 130 ILE cc_start: 0.8881 (tp) cc_final: 0.8543 (tp) REVERT: B 166 GLU cc_start: 0.8445 (tp30) cc_final: 0.7718 (tp30) REVERT: B 202 ASN cc_start: 0.8922 (t0) cc_final: 0.8566 (t0) REVERT: B 210 LEU cc_start: 0.9314 (tp) cc_final: 0.9013 (tt) REVERT: B 211 THR cc_start: 0.9408 (m) cc_final: 0.9180 (p) REVERT: B 212 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8288 (mp10) REVERT: B 271 ILE cc_start: 0.9446 (tt) cc_final: 0.9244 (tt) REVERT: B 313 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8749 (ttmm) REVERT: B 344 GLN cc_start: 0.8991 (mm110) cc_final: 0.8757 (mm110) REVERT: B 364 ILE cc_start: 0.8650 (tt) cc_final: 0.8209 (tt) REVERT: C 105 TYR cc_start: 0.7005 (m-80) cc_final: 0.6802 (m-80) REVERT: C 127 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7768 (ttmm) REVERT: C 130 ILE cc_start: 0.9000 (tp) cc_final: 0.8662 (tp) REVERT: C 328 ASP cc_start: 0.9023 (m-30) cc_final: 0.8758 (p0) REVERT: C 343 ASP cc_start: 0.8305 (t70) cc_final: 0.8072 (t70) REVERT: C 344 GLN cc_start: 0.9050 (mm110) cc_final: 0.8739 (mm110) REVERT: C 364 ILE cc_start: 0.8750 (tt) cc_final: 0.8525 (tt) REVERT: D 63 GLN cc_start: 0.8026 (pp30) cc_final: 0.7760 (pm20) REVERT: D 127 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7794 (ttmm) REVERT: D 130 ILE cc_start: 0.8927 (tp) cc_final: 0.8609 (tp) REVERT: D 166 GLU cc_start: 0.8380 (tp30) cc_final: 0.7666 (tp30) REVERT: D 202 ASN cc_start: 0.8926 (t0) cc_final: 0.8553 (t0) REVERT: D 210 LEU cc_start: 0.9279 (tp) cc_final: 0.9031 (tt) REVERT: D 212 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8375 (mp10) REVERT: D 244 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7947 (mtt180) REVERT: D 271 ILE cc_start: 0.9475 (tt) cc_final: 0.9233 (tt) REVERT: D 344 GLN cc_start: 0.8953 (mm110) cc_final: 0.8710 (mm110) REVERT: D 364 ILE cc_start: 0.8533 (tt) cc_final: 0.8083 (tt) REVERT: E 127 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7740 (ttmm) REVERT: E 130 ILE cc_start: 0.9010 (tp) cc_final: 0.8640 (tp) REVERT: E 343 ASP cc_start: 0.8296 (t70) cc_final: 0.8029 (t70) REVERT: E 344 GLN cc_start: 0.9036 (mm110) cc_final: 0.8723 (mm110) REVERT: F 63 GLN cc_start: 0.8081 (pp30) cc_final: 0.7817 (pm20) REVERT: F 130 ILE cc_start: 0.8872 (tp) cc_final: 0.8553 (tp) REVERT: F 166 GLU cc_start: 0.8488 (tp30) cc_final: 0.7748 (tp30) REVERT: F 202 ASN cc_start: 0.8953 (t0) cc_final: 0.8614 (t0) REVERT: F 210 LEU cc_start: 0.9324 (tp) cc_final: 0.9103 (tt) REVERT: F 211 THR cc_start: 0.9329 (m) cc_final: 0.9024 (p) REVERT: F 212 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8431 (mp10) REVERT: F 271 ILE cc_start: 0.9464 (tt) cc_final: 0.9207 (tt) REVERT: F 344 GLN cc_start: 0.9006 (mm110) cc_final: 0.8746 (mm110) REVERT: F 364 ILE cc_start: 0.8609 (tt) cc_final: 0.8163 (tt) REVERT: G 69 VAL cc_start: 0.9003 (m) cc_final: 0.8546 (t) REVERT: G 105 TYR cc_start: 0.6993 (m-80) cc_final: 0.6787 (m-80) REVERT: G 127 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7818 (ttmm) REVERT: G 343 ASP cc_start: 0.8380 (t70) cc_final: 0.8115 (t70) REVERT: G 344 GLN cc_start: 0.9012 (mm110) cc_final: 0.8704 (mm110) REVERT: G 364 ILE cc_start: 0.8759 (tt) cc_final: 0.8520 (tt) REVERT: H 63 GLN cc_start: 0.8002 (pp30) cc_final: 0.7721 (pm20) REVERT: H 127 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7800 (ttmm) REVERT: H 130 ILE cc_start: 0.8905 (tp) cc_final: 0.8551 (tp) REVERT: H 166 GLU cc_start: 0.8379 (tp30) cc_final: 0.7755 (tp30) REVERT: H 202 ASN cc_start: 0.8936 (t0) cc_final: 0.8734 (t0) REVERT: H 210 LEU cc_start: 0.9323 (tp) cc_final: 0.9096 (tt) REVERT: H 212 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8630 (mp10) REVERT: H 244 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7893 (mtt180) REVERT: H 271 ILE cc_start: 0.9481 (tt) cc_final: 0.9218 (tt) REVERT: H 313 LYS cc_start: 0.8973 (ttmt) cc_final: 0.8740 (ttmm) REVERT: H 344 GLN cc_start: 0.8970 (mm110) cc_final: 0.8701 (mm110) REVERT: H 364 ILE cc_start: 0.8602 (tt) cc_final: 0.8194 (tt) outliers start: 16 outliers final: 8 residues processed: 950 average time/residue: 0.1702 time to fit residues: 244.1427 Evaluate side-chains 731 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 723 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain H residue 225 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.0770 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN B 73 ASN B 329 GLN C 73 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN D 73 ASN D 329 GLN E 73 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN F 73 ASN F 329 GLN G 73 ASN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN H 73 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120545 restraints weight = 30358.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124490 restraints weight = 16645.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127254 restraints weight = 11218.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.129016 restraints weight = 8546.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130441 restraints weight = 7105.744| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22936 Z= 0.148 Angle : 0.693 8.036 31248 Z= 0.360 Chirality : 0.043 0.171 3448 Planarity : 0.004 0.041 3832 Dihedral : 6.116 57.770 2960 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.60 % Allowed : 19.48 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.15), residues: 2640 helix: -0.45 (0.12), residues: 1728 sheet: -2.46 (0.39), residues: 144 loop : -4.69 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 186 TYR 0.026 0.002 TYR D 301 PHE 0.026 0.001 PHE C 242 TRP 0.020 0.001 TRP A 59 HIS 0.002 0.001 HIS F 247 Details of bonding type rmsd covalent geometry : bond 0.00326 (22920) covalent geometry : angle 0.68536 (31216) SS BOND : bond 0.01587 ( 16) SS BOND : angle 3.37878 ( 32) hydrogen bonds : bond 0.04748 ( 1225) hydrogen bonds : angle 4.56727 ( 3627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 755 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7731 (ttmm) REVERT: A 130 ILE cc_start: 0.8975 (tp) cc_final: 0.8633 (tp) REVERT: A 166 GLU cc_start: 0.8748 (tp30) cc_final: 0.8434 (tp30) REVERT: A 328 ASP cc_start: 0.8926 (m-30) cc_final: 0.8648 (p0) REVERT: A 344 GLN cc_start: 0.8996 (mm110) cc_final: 0.8793 (mm110) REVERT: B 127 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7781 (ttmm) REVERT: B 130 ILE cc_start: 0.8851 (tp) cc_final: 0.8548 (tp) REVERT: B 153 ASP cc_start: 0.8169 (m-30) cc_final: 0.7922 (m-30) REVERT: B 199 GLN cc_start: 0.8729 (tp40) cc_final: 0.8341 (tt0) REVERT: B 202 ASN cc_start: 0.8700 (t0) cc_final: 0.8466 (t0) REVERT: B 313 LYS cc_start: 0.8909 (ttmt) cc_final: 0.8693 (pttp) REVERT: C 127 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7751 (ttmm) REVERT: C 130 ILE cc_start: 0.8967 (tp) cc_final: 0.8653 (tp) REVERT: C 153 ASP cc_start: 0.8293 (m-30) cc_final: 0.7910 (m-30) REVERT: C 213 LEU cc_start: 0.8408 (tp) cc_final: 0.7976 (tt) REVERT: C 343 ASP cc_start: 0.8223 (t70) cc_final: 0.7989 (t70) REVERT: C 344 GLN cc_start: 0.8963 (mm110) cc_final: 0.8728 (mm110) REVERT: D 130 ILE cc_start: 0.8986 (tp) cc_final: 0.8664 (tp) REVERT: D 202 ASN cc_start: 0.8724 (t0) cc_final: 0.8473 (t0) REVERT: D 212 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8384 (mm110) REVERT: D 244 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7662 (mtm-85) REVERT: D 284 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8823 (mt) REVERT: E 328 ASP cc_start: 0.8906 (m-30) cc_final: 0.8607 (p0) REVERT: E 344 GLN cc_start: 0.8942 (mm110) cc_final: 0.8731 (mm110) REVERT: F 130 ILE cc_start: 0.8844 (tp) cc_final: 0.8533 (tp) REVERT: F 166 GLU cc_start: 0.8602 (tp30) cc_final: 0.7669 (tp30) REVERT: F 199 GLN cc_start: 0.8712 (tp40) cc_final: 0.8346 (tt0) REVERT: F 210 LEU cc_start: 0.9304 (tp) cc_final: 0.9055 (tt) REVERT: F 244 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7572 (mtt-85) REVERT: F 345 MET cc_start: 0.8801 (tpp) cc_final: 0.8548 (mmp) REVERT: F 364 ILE cc_start: 0.8395 (tt) cc_final: 0.8170 (tp) REVERT: G 344 GLN cc_start: 0.8936 (mm110) cc_final: 0.8721 (mm110) REVERT: H 127 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7709 (ttmm) REVERT: H 130 ILE cc_start: 0.8831 (tp) cc_final: 0.8519 (tp) REVERT: H 199 GLN cc_start: 0.8721 (tp40) cc_final: 0.8356 (tt0) REVERT: H 210 LEU cc_start: 0.9276 (tp) cc_final: 0.9016 (tt) REVERT: H 342 MET cc_start: 0.8680 (mmm) cc_final: 0.8444 (mmm) outliers start: 110 outliers final: 72 residues processed: 790 average time/residue: 0.1548 time to fit residues: 192.2610 Evaluate side-chains 731 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 658 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 304 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 248 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 199 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 348 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN C 348 ASN D 79 HIS E 199 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN E 348 ASN F 79 HIS G 73 ASN G 199 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN G 348 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117428 restraints weight = 30959.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.121193 restraints weight = 17257.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.123676 restraints weight = 11724.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125642 restraints weight = 9025.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126877 restraints weight = 7439.608| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 22936 Z= 0.168 Angle : 0.704 12.667 31248 Z= 0.364 Chirality : 0.044 0.212 3448 Planarity : 0.004 0.035 3832 Dihedral : 5.878 51.444 2960 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 5.98 % Allowed : 21.53 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.90 (0.16), residues: 2640 helix: 0.09 (0.12), residues: 1744 sheet: -1.94 (0.44), residues: 144 loop : -4.41 (0.18), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 362 TYR 0.018 0.002 TYR G 301 PHE 0.038 0.001 PHE B 242 TRP 0.015 0.001 TRP H 59 HIS 0.007 0.001 HIS F 79 Details of bonding type rmsd covalent geometry : bond 0.00400 (22920) covalent geometry : angle 0.69229 (31216) SS BOND : bond 0.01657 ( 16) SS BOND : angle 4.04403 ( 32) hydrogen bonds : bond 0.04649 ( 1225) hydrogen bonds : angle 4.42737 ( 3627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 683 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 VAL cc_start: 0.9216 (t) cc_final: 0.9013 (t) REVERT: A 274 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.5646 (mp0) REVERT: A 328 ASP cc_start: 0.8815 (m-30) cc_final: 0.8592 (p0) REVERT: A 344 GLN cc_start: 0.8992 (mm110) cc_final: 0.8788 (mm110) REVERT: B 69 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8669 (t) REVERT: B 127 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7769 (ttmm) REVERT: B 130 ILE cc_start: 0.8943 (tp) cc_final: 0.8580 (tp) REVERT: B 155 ASP cc_start: 0.7909 (t0) cc_final: 0.7568 (t0) REVERT: B 199 GLN cc_start: 0.8749 (tp40) cc_final: 0.8418 (tt0) REVERT: B 313 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8677 (ttmm) REVERT: C 29 ARG cc_start: 0.8292 (mmp80) cc_final: 0.8035 (mmp80) REVERT: C 153 ASP cc_start: 0.8303 (m-30) cc_final: 0.7978 (m-30) REVERT: C 171 VAL cc_start: 0.9165 (t) cc_final: 0.8953 (t) REVERT: C 300 TYR cc_start: 0.8322 (t80) cc_final: 0.8111 (t80) REVERT: C 343 ASP cc_start: 0.8173 (t70) cc_final: 0.7924 (t70) REVERT: C 344 GLN cc_start: 0.8970 (mm110) cc_final: 0.8736 (mm110) REVERT: D 130 ILE cc_start: 0.8930 (tp) cc_final: 0.8619 (tp) REVERT: D 153 ASP cc_start: 0.8322 (m-30) cc_final: 0.7977 (m-30) REVERT: D 199 GLN cc_start: 0.8758 (tp40) cc_final: 0.8417 (tt0) REVERT: D 244 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7704 (mtm-85) REVERT: E 69 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8598 (t) REVERT: E 213 LEU cc_start: 0.8390 (tp) cc_final: 0.8042 (tt) REVERT: E 274 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.5526 (mp0) REVERT: E 328 ASP cc_start: 0.8806 (m-30) cc_final: 0.8554 (p0) REVERT: E 344 GLN cc_start: 0.8977 (mm110) cc_final: 0.8769 (mm110) REVERT: F 130 ILE cc_start: 0.8928 (tp) cc_final: 0.8588 (tp) REVERT: F 166 GLU cc_start: 0.8637 (tp30) cc_final: 0.7679 (tp30) REVERT: F 199 GLN cc_start: 0.8697 (tp40) cc_final: 0.8370 (tt0) REVERT: F 210 LEU cc_start: 0.9319 (tp) cc_final: 0.9030 (tt) REVERT: F 342 MET cc_start: 0.8558 (mmm) cc_final: 0.8354 (mmm) REVERT: F 345 MET cc_start: 0.8813 (tpp) cc_final: 0.8611 (mmp) REVERT: G 171 VAL cc_start: 0.9122 (t) cc_final: 0.8783 (t) REVERT: G 274 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.5439 (mp0) REVERT: G 328 ASP cc_start: 0.8890 (m-30) cc_final: 0.8540 (p0) REVERT: H 127 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7759 (ttmm) REVERT: H 130 ILE cc_start: 0.8929 (tp) cc_final: 0.8586 (tp) REVERT: H 166 GLU cc_start: 0.8504 (tp30) cc_final: 0.7756 (tp30) REVERT: H 199 GLN cc_start: 0.8703 (tp40) cc_final: 0.8371 (tt0) REVERT: H 210 LEU cc_start: 0.9298 (tp) cc_final: 0.9016 (tt) REVERT: H 364 ILE cc_start: 0.8373 (tp) cc_final: 0.8171 (tp) outliers start: 143 outliers final: 106 residues processed: 718 average time/residue: 0.1408 time to fit residues: 164.2697 Evaluate side-chains 726 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 615 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 304 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 112 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 127 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 173 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 348 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN F 79 HIS F 294 ASN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118917 restraints weight = 30695.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122732 restraints weight = 17156.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125480 restraints weight = 11613.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127346 restraints weight = 8805.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128534 restraints weight = 7248.984| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 22936 Z= 0.140 Angle : 0.659 9.362 31248 Z= 0.340 Chirality : 0.042 0.179 3448 Planarity : 0.003 0.036 3832 Dihedral : 5.228 36.043 2960 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 5.02 % Allowed : 24.37 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.17), residues: 2640 helix: 0.56 (0.13), residues: 1744 sheet: -1.95 (0.44), residues: 144 loop : -4.12 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 362 TYR 0.024 0.002 TYR F 82 PHE 0.042 0.001 PHE F 242 TRP 0.015 0.001 TRP F 236 HIS 0.006 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00324 (22920) covalent geometry : angle 0.64492 (31216) SS BOND : bond 0.02041 ( 16) SS BOND : angle 4.28987 ( 32) hydrogen bonds : bond 0.03960 ( 1225) hydrogen bonds : angle 4.15172 ( 3627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 699 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8659 (t) REVERT: A 274 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.5551 (mp0) REVERT: A 328 ASP cc_start: 0.8824 (m-30) cc_final: 0.8532 (p0) REVERT: A 345 MET cc_start: 0.8611 (mmp) cc_final: 0.8275 (mmm) REVERT: B 130 ILE cc_start: 0.8996 (tp) cc_final: 0.8632 (tp) REVERT: B 199 GLN cc_start: 0.8386 (tp40) cc_final: 0.8145 (tt0) REVERT: C 69 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8557 (t) REVERT: C 179 LEU cc_start: 0.9173 (tp) cc_final: 0.8840 (tt) REVERT: D 130 ILE cc_start: 0.9016 (tp) cc_final: 0.8690 (tp) REVERT: D 153 ASP cc_start: 0.8241 (m-30) cc_final: 0.7948 (m-30) REVERT: D 199 GLN cc_start: 0.8378 (tp40) cc_final: 0.8134 (tt0) REVERT: D 244 ARG cc_start: 0.8071 (mtt180) cc_final: 0.7683 (mtm-85) REVERT: E 213 LEU cc_start: 0.8369 (tp) cc_final: 0.8002 (tt) REVERT: E 274 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.5284 (mp0) REVERT: E 328 ASP cc_start: 0.8804 (m-30) cc_final: 0.8520 (p0) REVERT: E 344 GLN cc_start: 0.8954 (mm110) cc_final: 0.8728 (mm110) REVERT: E 345 MET cc_start: 0.8556 (mmp) cc_final: 0.8194 (mmm) REVERT: F 118 LEU cc_start: 0.8785 (mt) cc_final: 0.8523 (mt) REVERT: F 130 ILE cc_start: 0.9023 (tp) cc_final: 0.8665 (tp) REVERT: F 199 GLN cc_start: 0.8623 (tp40) cc_final: 0.8356 (tt0) REVERT: F 210 LEU cc_start: 0.9266 (tp) cc_final: 0.8967 (tt) REVERT: G 274 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.5192 (mp0) REVERT: G 328 ASP cc_start: 0.8823 (m-30) cc_final: 0.8520 (p0) REVERT: G 345 MET cc_start: 0.8401 (mmp) cc_final: 0.8059 (mmm) REVERT: H 130 ILE cc_start: 0.9005 (tp) cc_final: 0.8642 (tp) REVERT: H 166 GLU cc_start: 0.8542 (tp30) cc_final: 0.7727 (tp30) REVERT: H 199 GLN cc_start: 0.8394 (tp40) cc_final: 0.8152 (tt0) REVERT: H 210 LEU cc_start: 0.9231 (tp) cc_final: 0.8946 (tt) REVERT: H 364 ILE cc_start: 0.8228 (tp) cc_final: 0.7989 (tp) outliers start: 120 outliers final: 74 residues processed: 737 average time/residue: 0.1358 time to fit residues: 163.3758 Evaluate side-chains 704 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 625 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 PHE Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 304 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 219 optimal weight: 0.0270 chunk 10 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS B 79 HIS B 294 ASN C 348 ASN D 79 HIS D 206 GLN D 294 ASN F 79 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.119420 restraints weight = 30518.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.123115 restraints weight = 17181.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125930 restraints weight = 11712.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.127756 restraints weight = 8924.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129049 restraints weight = 7348.903| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 22936 Z= 0.136 Angle : 0.663 11.870 31248 Z= 0.340 Chirality : 0.042 0.182 3448 Planarity : 0.003 0.067 3832 Dihedral : 4.986 20.108 2953 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 5.02 % Allowed : 25.50 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.17), residues: 2640 helix: 0.77 (0.13), residues: 1752 sheet: -1.73 (0.44), residues: 144 loop : -3.99 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 362 TYR 0.017 0.001 TYR E 110 PHE 0.022 0.001 PHE F 242 TRP 0.029 0.001 TRP G 59 HIS 0.006 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00313 (22920) covalent geometry : angle 0.64583 (31216) SS BOND : bond 0.01288 ( 16) SS BOND : angle 4.73609 ( 32) hydrogen bonds : bond 0.03798 ( 1225) hydrogen bonds : angle 4.10921 ( 3627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 675 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8612 (t) REVERT: A 171 VAL cc_start: 0.9012 (t) cc_final: 0.8796 (t) REVERT: A 179 LEU cc_start: 0.9132 (tp) cc_final: 0.8885 (tp) REVERT: A 300 TYR cc_start: 0.8544 (t80) cc_final: 0.8307 (t80) REVERT: B 29 ARG cc_start: 0.8177 (mmp80) cc_final: 0.7605 (mmp80) REVERT: B 69 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8600 (t) REVERT: B 130 ILE cc_start: 0.8856 (tp) cc_final: 0.8515 (tp) REVERT: B 199 GLN cc_start: 0.8383 (tp40) cc_final: 0.8072 (tt0) REVERT: C 69 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8601 (t) REVERT: C 166 GLU cc_start: 0.8540 (tp30) cc_final: 0.7979 (mt-10) REVERT: C 171 VAL cc_start: 0.8961 (t) cc_final: 0.8744 (t) REVERT: C 179 LEU cc_start: 0.9106 (tp) cc_final: 0.8867 (tt) REVERT: C 213 LEU cc_start: 0.8252 (tp) cc_final: 0.7976 (tp) REVERT: C 342 MET cc_start: 0.8733 (mmm) cc_final: 0.8515 (mmm) REVERT: C 344 GLN cc_start: 0.8839 (mm110) cc_final: 0.8601 (mm110) REVERT: D 29 ARG cc_start: 0.8227 (mmp80) cc_final: 0.7689 (mmp80) REVERT: D 130 ILE cc_start: 0.9009 (tp) cc_final: 0.8663 (tp) REVERT: D 199 GLN cc_start: 0.8366 (tp40) cc_final: 0.8014 (tt0) REVERT: D 244 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7719 (mtm-85) REVERT: E 166 GLU cc_start: 0.8542 (tp30) cc_final: 0.7972 (mt-10) REVERT: E 274 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.5239 (mp0) REVERT: E 328 ASP cc_start: 0.8745 (m-30) cc_final: 0.8537 (p0) REVERT: E 344 GLN cc_start: 0.8934 (mm110) cc_final: 0.8701 (mm110) REVERT: F 118 LEU cc_start: 0.8807 (mt) cc_final: 0.8552 (mt) REVERT: F 130 ILE cc_start: 0.8982 (tp) cc_final: 0.8625 (tp) REVERT: F 199 GLN cc_start: 0.8359 (tp40) cc_final: 0.8119 (tt0) REVERT: F 210 LEU cc_start: 0.9273 (tp) cc_final: 0.9002 (tt) REVERT: F 273 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: F 345 MET cc_start: 0.8371 (mmt) cc_final: 0.8082 (tpp) REVERT: G 166 GLU cc_start: 0.8541 (tp30) cc_final: 0.7940 (mt-10) REVERT: G 274 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.5092 (mp0) REVERT: H 130 ILE cc_start: 0.9005 (tp) cc_final: 0.8639 (tp) REVERT: H 155 ASP cc_start: 0.8063 (t0) cc_final: 0.7773 (t0) REVERT: H 199 GLN cc_start: 0.8361 (tp40) cc_final: 0.8119 (tt0) REVERT: H 210 LEU cc_start: 0.9256 (tp) cc_final: 0.8956 (tt) outliers start: 120 outliers final: 86 residues processed: 716 average time/residue: 0.1375 time to fit residues: 162.9724 Evaluate side-chains 720 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 628 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 304 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 124 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS F 70 ASN F 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117944 restraints weight = 30914.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.121744 restraints weight = 17496.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.124247 restraints weight = 11930.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126226 restraints weight = 9201.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127510 restraints weight = 7576.481| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 22936 Z= 0.141 Angle : 0.676 11.753 31248 Z= 0.345 Chirality : 0.042 0.190 3448 Planarity : 0.003 0.033 3832 Dihedral : 4.950 18.961 2952 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 5.35 % Allowed : 26.00 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.82 (0.17), residues: 2640 helix: 0.90 (0.13), residues: 1752 sheet: -1.61 (0.44), residues: 144 loop : -3.96 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 362 TYR 0.024 0.001 TYR H 82 PHE 0.025 0.001 PHE H 242 TRP 0.020 0.001 TRP E 59 HIS 0.006 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00335 (22920) covalent geometry : angle 0.64848 (31216) SS BOND : bond 0.01609 ( 16) SS BOND : angle 5.99158 ( 32) hydrogen bonds : bond 0.03741 ( 1225) hydrogen bonds : angle 4.10734 ( 3627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 663 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8671 (t) REVERT: A 300 TYR cc_start: 0.8570 (t80) cc_final: 0.8325 (t80) REVERT: B 29 ARG cc_start: 0.8174 (mmp80) cc_final: 0.7747 (mmp80) REVERT: B 69 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8631 (t) REVERT: B 130 ILE cc_start: 0.8884 (tp) cc_final: 0.8530 (tp) REVERT: B 199 GLN cc_start: 0.8337 (tp40) cc_final: 0.7997 (tt0) REVERT: C 69 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8614 (t) REVERT: C 166 GLU cc_start: 0.8513 (tp30) cc_final: 0.7977 (mt-10) REVERT: C 179 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8814 (tt) REVERT: C 213 LEU cc_start: 0.8269 (tp) cc_final: 0.7974 (tp) REVERT: C 342 MET cc_start: 0.8807 (mmm) cc_final: 0.8523 (mmm) REVERT: C 344 GLN cc_start: 0.8853 (mm110) cc_final: 0.8621 (mm110) REVERT: D 29 ARG cc_start: 0.8181 (mmp80) cc_final: 0.7716 (mmp80) REVERT: D 130 ILE cc_start: 0.8998 (tp) cc_final: 0.8665 (tp) REVERT: D 199 GLN cc_start: 0.8343 (tp40) cc_final: 0.7998 (tt0) REVERT: D 244 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7749 (mtm-85) REVERT: D 345 MET cc_start: 0.8233 (mmp) cc_final: 0.7971 (mmm) REVERT: E 166 GLU cc_start: 0.8554 (tp30) cc_final: 0.7955 (tp30) REVERT: E 274 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.5169 (mp0) REVERT: E 344 GLN cc_start: 0.8910 (mm110) cc_final: 0.8671 (mm110) REVERT: F 130 ILE cc_start: 0.8824 (tp) cc_final: 0.8448 (tp) REVERT: F 199 GLN cc_start: 0.8598 (tp40) cc_final: 0.8332 (tt0) REVERT: F 210 LEU cc_start: 0.9362 (tp) cc_final: 0.9040 (tt) REVERT: F 273 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: G 179 LEU cc_start: 0.9182 (tp) cc_final: 0.8947 (tp) REVERT: G 274 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.5145 (mp0) REVERT: H 199 GLN cc_start: 0.8598 (tp40) cc_final: 0.8316 (tt0) REVERT: H 210 LEU cc_start: 0.9291 (tp) cc_final: 0.9013 (tt) REVERT: H 345 MET cc_start: 0.8238 (mmp) cc_final: 0.7956 (mmm) outliers start: 128 outliers final: 96 residues processed: 698 average time/residue: 0.1417 time to fit residues: 162.1286 Evaluate side-chains 735 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 632 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 304 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 248 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 46 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN B 79 HIS B 206 GLN C 348 ASN D 70 ASN E 348 ASN G 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114445 restraints weight = 31022.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118089 restraints weight = 17277.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120818 restraints weight = 11817.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122520 restraints weight = 9046.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123924 restraints weight = 7536.640| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 22936 Z= 0.217 Angle : 0.744 12.217 31248 Z= 0.380 Chirality : 0.046 0.177 3448 Planarity : 0.003 0.036 3832 Dihedral : 5.181 21.635 2952 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 6.15 % Allowed : 25.75 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.17), residues: 2640 helix: 0.88 (0.13), residues: 1760 sheet: None (None), residues: 0 loop : -3.74 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 362 TYR 0.017 0.002 TYR C 172 PHE 0.043 0.001 PHE H 242 TRP 0.042 0.001 TRP G 59 HIS 0.006 0.002 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00527 (22920) covalent geometry : angle 0.71555 (31216) SS BOND : bond 0.01504 ( 16) SS BOND : angle 6.45603 ( 32) hydrogen bonds : bond 0.04415 ( 1225) hydrogen bonds : angle 4.29605 ( 3627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 635 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8797 (t) REVERT: A 130 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8503 (tp) REVERT: A 182 LYS cc_start: 0.8519 (tptt) cc_final: 0.8236 (tptt) REVERT: B 69 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8824 (t) REVERT: B 199 GLN cc_start: 0.8744 (tp40) cc_final: 0.8377 (tt0) REVERT: B 345 MET cc_start: 0.8278 (mmp) cc_final: 0.7975 (mmm) REVERT: C 69 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8779 (t) REVERT: C 182 LYS cc_start: 0.8512 (tptt) cc_final: 0.8206 (tptt) REVERT: C 342 MET cc_start: 0.8931 (mmm) cc_final: 0.8642 (mmm) REVERT: C 344 GLN cc_start: 0.8931 (mm110) cc_final: 0.8713 (mm110) REVERT: D 130 ILE cc_start: 0.8905 (tp) cc_final: 0.8546 (tp) REVERT: D 182 LYS cc_start: 0.8708 (tptt) cc_final: 0.8330 (tptt) REVERT: D 199 GLN cc_start: 0.8736 (tp40) cc_final: 0.8365 (tt0) REVERT: D 244 ARG cc_start: 0.8322 (mtt180) cc_final: 0.7866 (mtm-85) REVERT: D 274 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.5776 (mp0) REVERT: E 179 LEU cc_start: 0.9218 (tp) cc_final: 0.9017 (tp) REVERT: E 274 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.5385 (mp0) REVERT: E 344 GLN cc_start: 0.8940 (mm110) cc_final: 0.8721 (mm110) REVERT: F 199 GLN cc_start: 0.8747 (tp40) cc_final: 0.8478 (tt0) REVERT: F 210 LEU cc_start: 0.9372 (tp) cc_final: 0.9128 (tt) REVERT: F 273 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: F 310 LYS cc_start: 0.8695 (tppt) cc_final: 0.8354 (tptp) REVERT: G 166 GLU cc_start: 0.8663 (tp30) cc_final: 0.8299 (tp30) REVERT: G 274 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.5371 (mp0) REVERT: G 328 ASP cc_start: 0.8832 (m-30) cc_final: 0.8579 (p0) REVERT: H 199 GLN cc_start: 0.8742 (tp40) cc_final: 0.8463 (tt0) REVERT: H 210 LEU cc_start: 0.9347 (tp) cc_final: 0.9117 (tt) REVERT: H 273 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.8086 (m-80) outliers start: 147 outliers final: 120 residues processed: 690 average time/residue: 0.1409 time to fit residues: 160.0213 Evaluate side-chains 740 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 611 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 304 ASN Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 67 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 188 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 63 optimal weight: 10.0000 chunk 165 optimal weight: 30.0000 chunk 100 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN B 79 HIS E 348 ASN G 348 ASN H 70 ASN H 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117443 restraints weight = 30625.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121192 restraints weight = 17534.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123633 restraints weight = 12060.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125532 restraints weight = 9374.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126812 restraints weight = 7774.213| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 22936 Z= 0.159 Angle : 0.735 12.350 31248 Z= 0.367 Chirality : 0.043 0.170 3448 Planarity : 0.003 0.036 3832 Dihedral : 5.063 19.482 2952 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 5.35 % Allowed : 27.22 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.71 (0.17), residues: 2640 helix: 0.97 (0.13), residues: 1752 sheet: None (None), residues: 0 loop : -3.63 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 362 TYR 0.016 0.001 TYR C 172 PHE 0.020 0.001 PHE B 124 TRP 0.025 0.001 TRP G 59 HIS 0.006 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00381 (22920) covalent geometry : angle 0.70661 (31216) SS BOND : bond 0.01533 ( 16) SS BOND : angle 6.31306 ( 32) hydrogen bonds : bond 0.04060 ( 1225) hydrogen bonds : angle 4.15135 ( 3627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 661 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8806 (t) REVERT: A 182 LYS cc_start: 0.8404 (tptt) cc_final: 0.8163 (tptt) REVERT: A 300 TYR cc_start: 0.8573 (t80) cc_final: 0.8345 (t80) REVERT: B 69 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8662 (t) REVERT: B 130 ILE cc_start: 0.8894 (tp) cc_final: 0.8550 (tp) REVERT: B 182 LYS cc_start: 0.8649 (tptt) cc_final: 0.8398 (tptt) REVERT: B 345 MET cc_start: 0.8191 (mmp) cc_final: 0.7930 (mmm) REVERT: C 69 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8727 (t) REVERT: C 166 GLU cc_start: 0.8436 (tp30) cc_final: 0.7826 (mt-10) REVERT: C 182 LYS cc_start: 0.8425 (tptt) cc_final: 0.8219 (tptt) REVERT: C 344 GLN cc_start: 0.8951 (mm110) cc_final: 0.8703 (mm110) REVERT: D 130 ILE cc_start: 0.8912 (tp) cc_final: 0.8596 (tp) REVERT: D 182 LYS cc_start: 0.8632 (tptt) cc_final: 0.8359 (tptt) REVERT: D 345 MET cc_start: 0.8187 (mmp) cc_final: 0.7904 (mmm) REVERT: E 274 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.5390 (mp0) REVERT: E 344 GLN cc_start: 0.8955 (mm110) cc_final: 0.8727 (mm110) REVERT: E 364 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7727 (mm) REVERT: F 199 GLN cc_start: 0.8690 (tp40) cc_final: 0.8381 (tt0) REVERT: F 210 LEU cc_start: 0.9348 (tp) cc_final: 0.9029 (tt) REVERT: F 248 CYS cc_start: 0.7992 (p) cc_final: 0.7755 (p) REVERT: F 273 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: G 274 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.5315 (mp0) REVERT: G 328 ASP cc_start: 0.8838 (m-30) cc_final: 0.8551 (p0) REVERT: H 130 ILE cc_start: 0.8908 (tp) cc_final: 0.8574 (tp) REVERT: H 199 GLN cc_start: 0.8677 (tp40) cc_final: 0.8359 (tt0) REVERT: H 210 LEU cc_start: 0.9340 (tp) cc_final: 0.9057 (tt) REVERT: H 273 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: H 345 MET cc_start: 0.8195 (mmp) cc_final: 0.7902 (mmm) outliers start: 128 outliers final: 108 residues processed: 705 average time/residue: 0.1421 time to fit residues: 164.6104 Evaluate side-chains 750 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 634 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 304 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 89 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 198 optimal weight: 30.0000 chunk 120 optimal weight: 0.0570 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS H 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.118096 restraints weight = 30648.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.121778 restraints weight = 17390.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124385 restraints weight = 11960.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126117 restraints weight = 9214.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127447 restraints weight = 7671.069| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 22936 Z= 0.159 Angle : 0.740 12.356 31248 Z= 0.369 Chirality : 0.043 0.168 3448 Planarity : 0.003 0.033 3832 Dihedral : 5.008 18.906 2952 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.52 % Allowed : 27.13 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.63 (0.17), residues: 2640 helix: 1.03 (0.13), residues: 1752 sheet: None (None), residues: 0 loop : -3.56 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 362 TYR 0.017 0.001 TYR H 82 PHE 0.018 0.001 PHE H 242 TRP 0.031 0.001 TRP C 59 HIS 0.007 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00379 (22920) covalent geometry : angle 0.71107 (31216) SS BOND : bond 0.01561 ( 16) SS BOND : angle 6.39557 ( 32) hydrogen bonds : bond 0.04013 ( 1225) hydrogen bonds : angle 4.15923 ( 3627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 656 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8846 (t) REVERT: A 130 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8440 (tp) REVERT: A 182 LYS cc_start: 0.8385 (tptt) cc_final: 0.8120 (tptt) REVERT: A 300 TYR cc_start: 0.8567 (t80) cc_final: 0.8309 (t80) REVERT: B 28 ASP cc_start: 0.8552 (m-30) cc_final: 0.8246 (m-30) REVERT: B 69 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8775 (t) REVERT: B 182 LYS cc_start: 0.8581 (tptt) cc_final: 0.8352 (tptt) REVERT: B 345 MET cc_start: 0.8183 (mmp) cc_final: 0.7921 (mmm) REVERT: C 69 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8790 (t) REVERT: C 344 GLN cc_start: 0.8936 (mm110) cc_final: 0.8705 (mm110) REVERT: D 28 ASP cc_start: 0.8596 (m-30) cc_final: 0.8299 (m-30) REVERT: D 130 ILE cc_start: 0.8907 (tp) cc_final: 0.8586 (tp) REVERT: D 182 LYS cc_start: 0.8603 (tptt) cc_final: 0.8375 (tptt) REVERT: D 244 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7851 (mtm-85) REVERT: D 345 MET cc_start: 0.8191 (mmp) cc_final: 0.7908 (mmm) REVERT: E 182 LYS cc_start: 0.8473 (tptt) cc_final: 0.8240 (tptt) REVERT: E 274 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.5310 (mp0) REVERT: E 344 GLN cc_start: 0.8956 (mm110) cc_final: 0.8726 (mm110) REVERT: F 182 LYS cc_start: 0.8657 (tptt) cc_final: 0.8354 (tptt) REVERT: F 199 GLN cc_start: 0.8681 (tp40) cc_final: 0.8369 (tt0) REVERT: F 210 LEU cc_start: 0.9357 (tp) cc_final: 0.9036 (tt) REVERT: F 248 CYS cc_start: 0.7837 (p) cc_final: 0.7626 (p) REVERT: F 273 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: G 274 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.5281 (mp0) REVERT: G 328 ASP cc_start: 0.8833 (m-30) cc_final: 0.8552 (p0) REVERT: H 182 LYS cc_start: 0.8692 (tptt) cc_final: 0.8453 (tptt) REVERT: H 199 GLN cc_start: 0.8675 (tp40) cc_final: 0.8374 (tt0) REVERT: H 210 LEU cc_start: 0.9337 (tp) cc_final: 0.9031 (tt) REVERT: H 273 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: H 345 MET cc_start: 0.8239 (mmp) cc_final: 0.7969 (mmm) outliers start: 132 outliers final: 118 residues processed: 701 average time/residue: 0.1411 time to fit residues: 162.3481 Evaluate side-chains 747 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 621 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 304 ASN Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 72 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 226 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117277 restraints weight = 30780.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120975 restraints weight = 17577.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.123395 restraints weight = 12111.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125293 restraints weight = 9436.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.126453 restraints weight = 7834.833| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 22936 Z= 0.172 Angle : 0.761 11.725 31248 Z= 0.379 Chirality : 0.044 0.173 3448 Planarity : 0.003 0.033 3832 Dihedral : 5.020 19.876 2952 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 5.39 % Allowed : 28.22 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.17), residues: 2640 helix: 1.01 (0.13), residues: 1752 sheet: None (None), residues: 0 loop : -3.53 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 362 TYR 0.019 0.002 TYR G 300 PHE 0.018 0.001 PHE D 124 TRP 0.054 0.001 TRP E 59 HIS 0.008 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00417 (22920) covalent geometry : angle 0.73082 (31216) SS BOND : bond 0.01583 ( 16) SS BOND : angle 6.71194 ( 32) hydrogen bonds : bond 0.04080 ( 1225) hydrogen bonds : angle 4.18009 ( 3627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 652 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8849 (t) REVERT: A 130 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8467 (tp) REVERT: A 182 LYS cc_start: 0.8412 (tptt) cc_final: 0.8115 (tptt) REVERT: A 300 TYR cc_start: 0.8569 (t80) cc_final: 0.8306 (t80) REVERT: B 28 ASP cc_start: 0.8643 (m-30) cc_final: 0.8391 (m-30) REVERT: B 69 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8747 (t) REVERT: B 182 LYS cc_start: 0.8574 (tptt) cc_final: 0.8353 (tptt) REVERT: B 310 LYS cc_start: 0.8648 (tppt) cc_final: 0.8281 (tptp) REVERT: B 345 MET cc_start: 0.8197 (mmp) cc_final: 0.7943 (mmm) REVERT: C 69 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8837 (t) REVERT: C 202 ASN cc_start: 0.8848 (t0) cc_final: 0.8425 (t0) REVERT: C 344 GLN cc_start: 0.8945 (mm110) cc_final: 0.8711 (mm110) REVERT: D 28 ASP cc_start: 0.8620 (m-30) cc_final: 0.8345 (m-30) REVERT: D 130 ILE cc_start: 0.8882 (tp) cc_final: 0.8527 (tp) REVERT: D 182 LYS cc_start: 0.8595 (tptt) cc_final: 0.8372 (tptt) REVERT: D 244 ARG cc_start: 0.8310 (mtt180) cc_final: 0.7902 (mtm-85) REVERT: D 310 LYS cc_start: 0.8671 (tppt) cc_final: 0.8241 (tptp) REVERT: D 345 MET cc_start: 0.8200 (mmp) cc_final: 0.7916 (mmm) REVERT: E 130 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8654 (tp) REVERT: E 166 GLU cc_start: 0.8324 (tp30) cc_final: 0.8036 (tp30) REVERT: E 182 LYS cc_start: 0.8474 (tptt) cc_final: 0.8217 (tptt) REVERT: E 274 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.5336 (mp0) REVERT: E 344 GLN cc_start: 0.8958 (mm110) cc_final: 0.8725 (mm110) REVERT: F 182 LYS cc_start: 0.8640 (tptt) cc_final: 0.8366 (tptt) REVERT: F 199 GLN cc_start: 0.8691 (tp40) cc_final: 0.8398 (tt0) REVERT: F 210 LEU cc_start: 0.9343 (tp) cc_final: 0.9031 (tt) REVERT: F 273 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: F 310 LYS cc_start: 0.8637 (tppt) cc_final: 0.8243 (tptp) REVERT: F 345 MET cc_start: 0.8105 (mmp) cc_final: 0.7811 (mmm) REVERT: G 182 LYS cc_start: 0.8518 (tptt) cc_final: 0.8299 (tptt) REVERT: G 274 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.5381 (mp0) REVERT: G 328 ASP cc_start: 0.8845 (m-30) cc_final: 0.8557 (p0) REVERT: H 182 LYS cc_start: 0.8697 (tptt) cc_final: 0.8463 (tptt) REVERT: H 199 GLN cc_start: 0.8698 (tp40) cc_final: 0.8387 (tt0) REVERT: H 210 LEU cc_start: 0.9331 (tp) cc_final: 0.9018 (tt) REVERT: H 273 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8156 (m-80) REVERT: H 345 MET cc_start: 0.8256 (mmp) cc_final: 0.7985 (mmm) outliers start: 129 outliers final: 115 residues processed: 698 average time/residue: 0.1390 time to fit residues: 159.4098 Evaluate side-chains 754 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 630 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 248 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 273 TYR Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 TYR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 304 ASN Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 231 optimal weight: 4.9990 chunk 222 optimal weight: 0.5980 chunk 145 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 chunk 103 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS F 79 HIS H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.143084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119524 restraints weight = 30708.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123260 restraints weight = 17465.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125734 restraints weight = 12016.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127674 restraints weight = 9346.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.128855 restraints weight = 7750.194| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 22936 Z= 0.152 Angle : 0.747 11.456 31248 Z= 0.371 Chirality : 0.043 0.169 3448 Planarity : 0.003 0.031 3832 Dihedral : 4.935 19.874 2952 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.18 % Allowed : 28.26 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.53 (0.17), residues: 2640 helix: 1.08 (0.13), residues: 1752 sheet: None (None), residues: 0 loop : -3.46 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 362 TYR 0.017 0.001 TYR C 301 PHE 0.022 0.001 PHE H 124 TRP 0.035 0.001 TRP E 59 HIS 0.008 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00363 (22920) covalent geometry : angle 0.72057 (31216) SS BOND : bond 0.01659 ( 16) SS BOND : angle 6.18386 ( 32) hydrogen bonds : bond 0.03895 ( 1225) hydrogen bonds : angle 4.14627 ( 3627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3918.54 seconds wall clock time: 68 minutes 27.66 seconds (4107.66 seconds total)