Starting phenix.real_space_refine on Wed Jun 18 23:18:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kfg_9972/06_2025/6kfg_9972.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kfg_9972/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6kfg_9972/06_2025/6kfg_9972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kfg_9972/06_2025/6kfg_9972.map" model { file = "/net/cci-nas-00/data/ceres_data/6kfg_9972/06_2025/6kfg_9972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kfg_9972/06_2025/6kfg_9972.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, H Time building chain proxies: 7.49, per 1000 atoms: 0.34 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 C 58 " - pdb=" SG CYS C 265 " distance=2.05 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.05 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.05 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.05 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.05 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.05 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.05 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 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: 6.08 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.05 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: 6.28 Time building geometry restraints manager: 7.14 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 43.550 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.900 ------------------------------------------------------------------------------- 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 : 13.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (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 TRP 0.012 0.002 TRP A 222 HIS 0.004 0.001 HIS G 241 PHE 0.025 0.002 PHE B 242 TYR 0.012 0.001 TYR F 301 ARG 0.003 0.001 ARG H 161 Details of bonding type rmsd hydrogen bonds : bond 0.14777 ( 1225) hydrogen bonds : angle 6.72421 ( 3627) SS BOND : bond 0.01121 ( 16) SS BOND : angle 4.22989 ( 32) covalent geometry : bond 0.00689 (22920) covalent geometry : angle 0.76960 (31216) *********************** 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 : 2.315 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: 0.3651 time to fit residues: 522.5255 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 : 2.561 ------------------------------------------------------------------------------- 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 222 optimal weight: 0.9980 chunk 200 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 134 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 206 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3572 r_free = 0.3572 target = 0.142552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118711 restraints weight = 30276.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122608 restraints weight = 16689.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125186 restraints weight = 11285.689| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22936 Z= 0.147 Angle : 0.698 8.249 31248 Z= 0.362 Chirality : 0.043 0.168 3448 Planarity : 0.004 0.039 3832 Dihedral : 6.132 57.552 2960 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.93 % Allowed : 19.27 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.15), residues: 2640 helix: -0.44 (0.12), residues: 1728 sheet: -2.47 (0.39), residues: 144 loop : -4.70 (0.17), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 59 HIS 0.002 0.001 HIS F 247 PHE 0.028 0.001 PHE B 242 TYR 0.026 0.002 TYR D 301 ARG 0.006 0.001 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 1225) hydrogen bonds : angle 4.54607 ( 3627) SS BOND : bond 0.01683 ( 16) SS BOND : angle 3.15308 ( 32) covalent geometry : bond 0.00321 (22920) covalent geometry : angle 0.69111 (31216) *********************** 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 876 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 758 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8381 (mmp80) cc_final: 0.7766 (mmp80) REVERT: A 127 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7768 (ttmm) REVERT: A 130 ILE cc_start: 0.8998 (tp) cc_final: 0.8627 (tp) REVERT: A 135 TYR cc_start: 0.8724 (t80) cc_final: 0.8381 (t80) REVERT: A 166 GLU cc_start: 0.8743 (tp30) cc_final: 0.8441 (tp30) REVERT: A 328 ASP cc_start: 0.9000 (m-30) cc_final: 0.8680 (p0) REVERT: B 127 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7800 (ttmm) REVERT: B 130 ILE cc_start: 0.8868 (tp) cc_final: 0.8557 (tp) REVERT: B 153 ASP cc_start: 0.8221 (m-30) cc_final: 0.8000 (m-30) REVERT: B 199 GLN cc_start: 0.8744 (tp40) cc_final: 0.8373 (tt0) REVERT: B 202 ASN cc_start: 0.8716 (t0) cc_final: 0.8492 (t0) REVERT: B 244 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7647 (mtt-85) REVERT: B 313 LYS cc_start: 0.8911 (ttmt) cc_final: 0.8700 (pttp) REVERT: C 127 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7782 (ttmm) REVERT: C 130 ILE cc_start: 0.8986 (tp) cc_final: 0.8661 (tp) REVERT: C 153 ASP cc_start: 0.8320 (m-30) cc_final: 0.7936 (m-30) REVERT: C 213 LEU cc_start: 0.8423 (tp) cc_final: 0.7984 (tt) REVERT: C 343 ASP cc_start: 0.8201 (t70) cc_final: 0.7974 (t70) REVERT: C 344 GLN cc_start: 0.8946 (mm110) cc_final: 0.8724 (mm110) REVERT: D 127 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7804 (ttmm) REVERT: D 130 ILE cc_start: 0.9000 (tp) cc_final: 0.8675 (tp) REVERT: D 199 GLN cc_start: 0.8758 (tp40) cc_final: 0.8346 (tt0) REVERT: D 202 ASN cc_start: 0.8745 (t0) cc_final: 0.8538 (t0) REVERT: D 212 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8398 (mm110) REVERT: D 244 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7700 (mtm-85) REVERT: E 328 ASP cc_start: 0.8976 (m-30) cc_final: 0.8646 (p0) REVERT: E 344 GLN cc_start: 0.8927 (mm110) cc_final: 0.8723 (mm110) REVERT: F 130 ILE cc_start: 0.8865 (tp) cc_final: 0.8545 (tp) REVERT: F 166 GLU cc_start: 0.8602 (tp30) cc_final: 0.7741 (tp30) REVERT: F 199 GLN cc_start: 0.8720 (tp40) cc_final: 0.8377 (tt0) REVERT: F 210 LEU cc_start: 0.9327 (tp) cc_final: 0.9053 (tt) REVERT: F 244 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7617 (mtt-85) REVERT: F 345 MET cc_start: 0.8773 (tpp) cc_final: 0.8533 (mmp) REVERT: F 364 ILE cc_start: 0.8448 (tt) cc_final: 0.8210 (tp) REVERT: G 344 GLN cc_start: 0.8918 (mm110) cc_final: 0.8717 (mm110) REVERT: H 127 LYS cc_start: 0.7979 (mtmt) cc_final: 0.7728 (ttmm) REVERT: H 130 ILE cc_start: 0.8851 (tp) cc_final: 0.8529 (tp) REVERT: H 199 GLN cc_start: 0.8728 (tp40) cc_final: 0.8389 (tt0) REVERT: H 210 LEU cc_start: 0.9302 (tp) cc_final: 0.9035 (tt) REVERT: H 244 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7664 (mtm-85) REVERT: H 342 MET cc_start: 0.8681 (mmm) cc_final: 0.8448 (mmm) outliers start: 118 outliers final: 79 residues processed: 793 average time/residue: 0.3395 time to fit residues: 422.7421 Evaluate side-chains 738 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 659 time to evaluate : 2.549 ------------------------------------------------------------------------------- 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 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 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 262 THR 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 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 225 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU 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 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 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 121 ILE Chi-restraints excluded: chain G residue 177 ILE 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 289 VAL 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 149 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 201 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 199 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 348 ASN B 73 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 F 294 ASN 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** H 294 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.139260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.115306 restraints weight = 31006.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.119207 restraints weight = 16957.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.121896 restraints weight = 11402.246| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22936 Z= 0.177 Angle : 0.712 12.700 31248 Z= 0.368 Chirality : 0.044 0.207 3448 Planarity : 0.003 0.035 3832 Dihedral : 5.927 52.048 2960 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 6.06 % Allowed : 21.91 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.16), residues: 2640 helix: 0.02 (0.12), residues: 1752 sheet: -2.02 (0.43), residues: 144 loop : -4.53 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 59 HIS 0.007 0.001 HIS F 79 PHE 0.049 0.001 PHE B 242 TYR 0.018 0.002 TYR G 301 ARG 0.009 0.001 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 1225) hydrogen bonds : angle 4.44551 ( 3627) SS BOND : bond 0.01281 ( 16) SS BOND : angle 4.55752 ( 32) covalent geometry : bond 0.00429 (22920) covalent geometry : angle 0.69695 (31216) *********************** 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 830 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 685 time to evaluate : 2.498 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 127 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7811 (ttmm) REVERT: A 274 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.5665 (mp0) REVERT: A 328 ASP cc_start: 0.8936 (m-30) cc_final: 0.8663 (p0) REVERT: B 127 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7773 (ttmm) REVERT: B 130 ILE cc_start: 0.8951 (tp) cc_final: 0.8579 (tp) REVERT: B 199 GLN cc_start: 0.8764 (tp40) cc_final: 0.8456 (tt0) REVERT: B 313 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8679 (ttmm) REVERT: B 345 MET cc_start: 0.8897 (mmm) cc_final: 0.8682 (mmp) REVERT: C 153 ASP cc_start: 0.8338 (m-30) cc_final: 0.8048 (m-30) REVERT: C 171 VAL cc_start: 0.9183 (t) cc_final: 0.8981 (t) REVERT: C 343 ASP cc_start: 0.8159 (t70) cc_final: 0.7874 (t70) REVERT: C 344 GLN cc_start: 0.8963 (mm110) cc_final: 0.8715 (mm110) REVERT: D 127 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7800 (ttmm) REVERT: D 130 ILE cc_start: 0.8933 (tp) cc_final: 0.8616 (tp) REVERT: D 155 ASP cc_start: 0.8158 (t0) cc_final: 0.7946 (t0) REVERT: D 199 GLN cc_start: 0.8774 (tp40) cc_final: 0.8428 (tt0) REVERT: E 69 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8647 (t) REVERT: E 213 LEU cc_start: 0.8434 (tp) cc_final: 0.8093 (tt) REVERT: E 274 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.5700 (mp0) REVERT: E 328 ASP cc_start: 0.8915 (m-30) cc_final: 0.8596 (p0) REVERT: E 344 GLN cc_start: 0.8970 (mm110) cc_final: 0.8765 (mm110) REVERT: F 130 ILE cc_start: 0.8937 (tp) cc_final: 0.8585 (tp) REVERT: F 166 GLU cc_start: 0.8642 (tp30) cc_final: 0.7681 (tp30) REVERT: F 199 GLN cc_start: 0.8718 (tp40) cc_final: 0.8433 (tt0) REVERT: F 210 LEU cc_start: 0.9329 (tp) cc_final: 0.9064 (tt) REVERT: F 244 ARG cc_start: 0.8231 (mtt180) cc_final: 0.7996 (mtt180) REVERT: G 274 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.5512 (mp0) REVERT: G 328 ASP cc_start: 0.8967 (m-30) cc_final: 0.8586 (p0) REVERT: H 79 HIS cc_start: 0.8708 (t-90) cc_final: 0.8191 (t-90) REVERT: H 127 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7761 (ttmm) REVERT: H 130 ILE cc_start: 0.8933 (tp) cc_final: 0.8580 (tp) REVERT: H 166 GLU cc_start: 0.8503 (tp30) cc_final: 0.7763 (tp30) REVERT: H 199 GLN cc_start: 0.8724 (tp40) cc_final: 0.8406 (tt0) REVERT: H 210 LEU cc_start: 0.9327 (tp) cc_final: 0.9037 (tt) REVERT: H 364 ILE cc_start: 0.8375 (tp) cc_final: 0.8164 (tp) outliers start: 145 outliers final: 108 residues processed: 720 average time/residue: 0.3005 time to fit residues: 346.0546 Evaluate side-chains 743 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 631 time to evaluate : 2.659 ------------------------------------------------------------------------------- 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 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 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 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 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 C residue 349 LEU 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 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 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 262 THR Chi-restraints excluded: chain F residue 264 LEU 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 G residue 37 VAL Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 177 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 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 225 SER Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 16 optimal weight: 0.9980 chunk 222 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 259 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN B 73 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN D 79 HIS D 294 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN F 79 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.120279 restraints weight = 30541.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124127 restraints weight = 17104.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126807 restraints weight = 11580.461| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 22936 Z= 0.140 Angle : 0.658 9.237 31248 Z= 0.340 Chirality : 0.042 0.187 3448 Planarity : 0.003 0.036 3832 Dihedral : 5.309 38.214 2960 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 5.60 % Allowed : 23.58 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.16), residues: 2640 helix: 0.51 (0.13), residues: 1744 sheet: None (None), residues: 0 loop : -3.83 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 236 HIS 0.006 0.001 HIS F 79 PHE 0.016 0.001 PHE B 242 TYR 0.022 0.002 TYR B 82 ARG 0.008 0.000 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 1225) hydrogen bonds : angle 4.18491 ( 3627) SS BOND : bond 0.01223 ( 16) SS BOND : angle 4.08562 ( 32) covalent geometry : bond 0.00329 (22920) covalent geometry : angle 0.64564 (31216) *********************** 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 833 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 699 time to evaluate : 2.392 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 69 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8658 (t) REVERT: A 274 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.5614 (mp0) REVERT: A 328 ASP cc_start: 0.8925 (m-30) cc_final: 0.8558 (p0) REVERT: B 69 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8644 (t) REVERT: B 79 HIS cc_start: 0.8654 (t-90) cc_final: 0.8142 (t-90) REVERT: B 127 LYS cc_start: 0.7958 (mtmt) cc_final: 0.7738 (ttmm) REVERT: B 130 ILE cc_start: 0.8903 (tp) cc_final: 0.8543 (tp) REVERT: B 155 ASP cc_start: 0.7896 (t0) cc_final: 0.7528 (t0) REVERT: B 199 GLN cc_start: 0.8661 (tp40) cc_final: 0.8396 (tt0) REVERT: B 313 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8647 (ttmm) REVERT: C 69 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8631 (t) REVERT: C 153 ASP cc_start: 0.8320 (m-30) cc_final: 0.8003 (m-30) REVERT: C 179 LEU cc_start: 0.9177 (tp) cc_final: 0.8816 (tt) REVERT: C 213 LEU cc_start: 0.8313 (tp) cc_final: 0.7890 (tt) REVERT: C 344 GLN cc_start: 0.8948 (mm110) cc_final: 0.8744 (mm110) REVERT: C 345 MET cc_start: 0.8418 (mmp) cc_final: 0.8094 (mmm) REVERT: D 118 LEU cc_start: 0.8831 (mt) cc_final: 0.8597 (mt) REVERT: D 130 ILE cc_start: 0.9028 (tp) cc_final: 0.8690 (tp) REVERT: D 199 GLN cc_start: 0.8411 (tp40) cc_final: 0.8134 (tt0) REVERT: E 213 LEU cc_start: 0.8357 (tp) cc_final: 0.8083 (tp) REVERT: E 328 ASP cc_start: 0.8923 (m-30) cc_final: 0.8574 (p0) REVERT: E 344 GLN cc_start: 0.8949 (mm110) cc_final: 0.8738 (mm110) REVERT: E 345 MET cc_start: 0.8574 (mmp) cc_final: 0.8221 (mmm) REVERT: F 130 ILE cc_start: 0.8911 (tp) cc_final: 0.8558 (tp) REVERT: F 155 ASP cc_start: 0.8054 (t0) cc_final: 0.7731 (t0) REVERT: F 166 GLU cc_start: 0.8662 (tp30) cc_final: 0.7723 (tp30) REVERT: F 199 GLN cc_start: 0.8662 (tp40) cc_final: 0.8385 (tt0) REVERT: F 210 LEU cc_start: 0.9273 (tp) cc_final: 0.8972 (tt) REVERT: G 274 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.5412 (mp0) REVERT: G 328 ASP cc_start: 0.8954 (m-30) cc_final: 0.8606 (p0) REVERT: G 345 MET cc_start: 0.8544 (mmp) cc_final: 0.8180 (mmm) REVERT: H 127 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7775 (ttmm) REVERT: H 130 ILE cc_start: 0.8895 (tp) cc_final: 0.8531 (tp) REVERT: H 210 LEU cc_start: 0.9275 (tp) cc_final: 0.8987 (tt) REVERT: H 244 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7706 (mtm-85) outliers start: 134 outliers final: 82 residues processed: 750 average time/residue: 0.2896 time to fit residues: 351.4736 Evaluate side-chains 719 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 632 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL 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 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 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 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 56 ILE 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 20 VAL Chi-restraints excluded: chain D residue 56 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 D residue 349 LEU 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 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 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 274 GLU Chi-restraints excluded: chain F residue 277 PHE 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 177 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU 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 118 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS B 294 ASN D 79 HIS E 348 ASN F 70 ASN F 79 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN H 79 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118298 restraints weight = 30843.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122120 restraints weight = 17350.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124615 restraints weight = 11797.993| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 22936 Z= 0.144 Angle : 0.674 12.100 31248 Z= 0.346 Chirality : 0.042 0.184 3448 Planarity : 0.003 0.062 3832 Dihedral : 5.105 19.891 2954 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.93 % Allowed : 25.04 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2640 helix: 0.71 (0.13), residues: 1752 sheet: -1.67 (0.46), residues: 144 loop : -4.05 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 59 HIS 0.007 0.001 HIS H 79 PHE 0.013 0.001 PHE G 64 TYR 0.016 0.001 TYR C 301 ARG 0.007 0.000 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 1225) hydrogen bonds : angle 4.21531 ( 3627) SS BOND : bond 0.01428 ( 16) SS BOND : angle 5.17918 ( 32) covalent geometry : bond 0.00341 (22920) covalent geometry : angle 0.65341 (31216) *********************** 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 788 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 670 time to evaluate : 2.507 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 69 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8741 (t) REVERT: A 179 LEU cc_start: 0.9150 (tp) cc_final: 0.8891 (tp) REVERT: A 274 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.5568 (mp0) REVERT: A 300 TYR cc_start: 0.8542 (t80) cc_final: 0.8309 (t80) REVERT: A 328 ASP cc_start: 0.8946 (m-30) cc_final: 0.8599 (p0) REVERT: B 29 ARG cc_start: 0.8288 (mmp80) cc_final: 0.7710 (mmp80) REVERT: B 69 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8685 (t) REVERT: B 127 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7713 (ttmm) REVERT: B 130 ILE cc_start: 0.8876 (tp) cc_final: 0.8522 (tp) REVERT: B 199 GLN cc_start: 0.8391 (tp40) cc_final: 0.8056 (tt0) REVERT: B 313 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8531 (ttmm) REVERT: C 69 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8659 (t) REVERT: C 153 ASP cc_start: 0.8277 (m-30) cc_final: 0.7998 (m-30) REVERT: C 179 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8878 (tt) REVERT: C 213 LEU cc_start: 0.8338 (tp) cc_final: 0.8014 (tp) REVERT: C 344 GLN cc_start: 0.8938 (mm110) cc_final: 0.8725 (mm110) REVERT: D 29 ARG cc_start: 0.8293 (mmp80) cc_final: 0.7692 (mmp80) REVERT: D 118 LEU cc_start: 0.8813 (mt) cc_final: 0.8582 (mt) REVERT: D 130 ILE cc_start: 0.9027 (tp) cc_final: 0.8677 (tp) REVERT: D 199 GLN cc_start: 0.8393 (tp40) cc_final: 0.8040 (tt0) REVERT: E 213 LEU cc_start: 0.8398 (tp) cc_final: 0.8106 (tp) REVERT: E 328 ASP cc_start: 0.8884 (m-30) cc_final: 0.8591 (p0) REVERT: E 344 GLN cc_start: 0.8952 (mm110) cc_final: 0.8711 (mm110) REVERT: F 130 ILE cc_start: 0.8865 (tp) cc_final: 0.8517 (tp) REVERT: F 210 LEU cc_start: 0.9305 (tp) cc_final: 0.8998 (tt) REVERT: G 179 LEU cc_start: 0.9123 (tp) cc_final: 0.8801 (tp) REVERT: G 274 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.5234 (mp0) REVERT: H 130 ILE cc_start: 0.8906 (tp) cc_final: 0.8547 (tp) REVERT: H 210 LEU cc_start: 0.9299 (tp) cc_final: 0.9000 (tt) outliers start: 118 outliers final: 94 residues processed: 710 average time/residue: 0.2876 time to fit residues: 331.3159 Evaluate side-chains 734 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 634 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 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 274 GLU 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 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 69 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 277 PHE 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 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 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 277 PHE 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 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 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 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 277 PHE 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 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 277 PHE 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 33 ARG 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 274 GLU Chi-restraints excluded: chain H residue 277 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 34 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 3 optimal weight: 0.0570 chunk 118 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 198 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- 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 C 348 ASN D 79 HIS F 79 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117547 restraints weight = 30600.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121371 restraints weight = 17334.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124032 restraints weight = 11814.630| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 22936 Z= 0.151 Angle : 0.681 11.258 31248 Z= 0.348 Chirality : 0.043 0.190 3448 Planarity : 0.003 0.033 3832 Dihedral : 5.007 19.239 2952 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 6.31 % Allowed : 24.79 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2640 helix: 0.86 (0.13), residues: 1752 sheet: -1.67 (0.44), residues: 144 loop : -4.05 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 59 HIS 0.007 0.001 HIS H 79 PHE 0.010 0.001 PHE F 242 TYR 0.025 0.001 TYR F 82 ARG 0.007 0.000 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 1225) hydrogen bonds : angle 4.17354 ( 3627) SS BOND : bond 0.01513 ( 16) SS BOND : angle 5.83504 ( 32) covalent geometry : bond 0.00360 (22920) covalent geometry : angle 0.65514 (31216) *********************** 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 828 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 677 time to evaluate : 2.606 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: A 69 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8728 (t) REVERT: A 130 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8429 (tp) REVERT: A 274 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.5503 (mp0) REVERT: A 300 TYR cc_start: 0.8570 (t80) cc_final: 0.8334 (t80) REVERT: A 328 ASP cc_start: 0.8849 (m-30) cc_final: 0.8590 (p0) REVERT: B 29 ARG cc_start: 0.8237 (mmp80) cc_final: 0.7780 (mmp80) REVERT: B 69 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8698 (t) REVERT: B 199 GLN cc_start: 0.8634 (tp40) cc_final: 0.8401 (tt0) REVERT: B 345 MET cc_start: 0.8231 (mmp) cc_final: 0.7955 (mmm) REVERT: C 69 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8730 (t) REVERT: C 179 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8876 (tt) REVERT: C 182 LYS cc_start: 0.8450 (tptt) cc_final: 0.8163 (tptt) REVERT: C 213 LEU cc_start: 0.8390 (tp) cc_final: 0.8172 (tp) REVERT: C 344 GLN cc_start: 0.8901 (mm110) cc_final: 0.8667 (mm110) REVERT: D 29 ARG cc_start: 0.8206 (mmp80) cc_final: 0.7870 (mmp80) REVERT: D 130 ILE cc_start: 0.8906 (tp) cc_final: 0.8552 (tp) REVERT: D 199 GLN cc_start: 0.8393 (tp40) cc_final: 0.8087 (tt0) REVERT: D 244 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7354 (mtm-85) REVERT: D 345 MET cc_start: 0.8214 (mmp) cc_final: 0.7928 (mmm) REVERT: E 328 ASP cc_start: 0.8828 (m-30) cc_final: 0.8591 (p0) REVERT: E 344 GLN cc_start: 0.8911 (mm110) cc_final: 0.8667 (mm110) REVERT: F 210 LEU cc_start: 0.9317 (tp) cc_final: 0.9003 (tt) REVERT: G 166 GLU cc_start: 0.8469 (tp30) cc_final: 0.8239 (tp30) REVERT: G 202 ASN cc_start: 0.8911 (t0) cc_final: 0.8552 (t0) REVERT: G 274 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.5257 (mp0) REVERT: G 328 ASP cc_start: 0.8884 (m-30) cc_final: 0.8605 (p0) REVERT: H 28 ASP cc_start: 0.8686 (m-30) cc_final: 0.8363 (m-30) REVERT: H 210 LEU cc_start: 0.9270 (tp) cc_final: 0.8964 (tt) REVERT: H 244 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7776 (mtm-85) outliers start: 151 outliers final: 116 residues processed: 728 average time/residue: 0.3127 time to fit residues: 368.3669 Evaluate side-chains 757 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 634 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU 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 178 ARG 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 A residue 316 LEU 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 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 179 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 341 ILE 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 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 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 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 277 PHE 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 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 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 262 THR Chi-restraints excluded: chain F residue 264 LEU 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 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 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 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 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 262 THR 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 Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 121 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 151 optimal weight: 0.0980 chunk 182 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 197 optimal weight: 0.0170 chunk 170 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 overall best weight: 0.6222 ------------------------------------------------------------------------------- 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 237 GLN C 237 GLN D 70 ASN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS G 348 ASN H 79 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120944 restraints weight = 30578.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124762 restraints weight = 17304.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127451 restraints weight = 11770.155| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 22936 Z= 0.138 Angle : 0.693 10.850 31248 Z= 0.350 Chirality : 0.042 0.189 3448 Planarity : 0.003 0.043 3832 Dihedral : 4.875 19.088 2952 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 5.18 % Allowed : 25.96 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2640 helix: 1.05 (0.13), residues: 1720 sheet: -1.82 (0.41), residues: 144 loop : -3.86 (0.18), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 59 HIS 0.006 0.001 HIS H 79 PHE 0.017 0.001 PHE B 242 TYR 0.016 0.001 TYR D 301 ARG 0.012 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 1225) hydrogen bonds : angle 4.07289 ( 3627) SS BOND : bond 0.01621 ( 16) SS BOND : angle 6.17295 ( 32) covalent geometry : bond 0.00315 (22920) covalent geometry : angle 0.66446 (31216) *********************** 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 817 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 693 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8699 (t) REVERT: A 171 VAL cc_start: 0.9083 (t) cc_final: 0.8787 (t) REVERT: A 300 TYR cc_start: 0.8567 (t80) cc_final: 0.8332 (t80) REVERT: A 328 ASP cc_start: 0.8835 (m-30) cc_final: 0.8582 (p0) REVERT: B 29 ARG cc_start: 0.8176 (mmp80) cc_final: 0.7811 (mmp80) REVERT: B 69 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8560 (t) REVERT: B 178 ARG cc_start: 0.8534 (ttm-80) cc_final: 0.8274 (ttp80) REVERT: C 69 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8509 (t) REVERT: C 166 GLU cc_start: 0.8405 (tp30) cc_final: 0.8196 (tp30) REVERT: C 171 VAL cc_start: 0.9040 (t) cc_final: 0.8808 (t) REVERT: C 182 LYS cc_start: 0.8397 (tptt) cc_final: 0.7894 (tppt) REVERT: C 344 GLN cc_start: 0.8862 (mm110) cc_final: 0.8662 (mm110) REVERT: C 345 MET cc_start: 0.8369 (mmp) cc_final: 0.8126 (mmm) REVERT: D 29 ARG cc_start: 0.8153 (mmp80) cc_final: 0.7867 (mmp80) REVERT: D 130 ILE cc_start: 0.8985 (tp) cc_final: 0.8664 (tp) REVERT: D 199 GLN cc_start: 0.8313 (tp40) cc_final: 0.8037 (tt0) REVERT: E 300 TYR cc_start: 0.8580 (t80) cc_final: 0.8357 (t80) REVERT: E 328 ASP cc_start: 0.8796 (m-30) cc_final: 0.8543 (p0) REVERT: E 344 GLN cc_start: 0.8876 (mm110) cc_final: 0.8654 (mm110) REVERT: F 28 ASP cc_start: 0.8447 (m-30) cc_final: 0.8170 (m-30) REVERT: F 210 LEU cc_start: 0.9290 (tp) cc_final: 0.8985 (tt) REVERT: G 166 GLU cc_start: 0.8390 (tp30) cc_final: 0.7320 (tp30) REVERT: G 202 ASN cc_start: 0.8856 (t0) cc_final: 0.8567 (t0) REVERT: G 274 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.5223 (mp0) REVERT: G 300 TYR cc_start: 0.8585 (t80) cc_final: 0.8377 (t80) REVERT: G 345 MET cc_start: 0.8486 (mmp) cc_final: 0.8128 (mmm) REVERT: H 28 ASP cc_start: 0.8632 (m-30) cc_final: 0.8361 (m-30) REVERT: H 210 LEU cc_start: 0.9250 (tp) cc_final: 0.8923 (tt) REVERT: H 213 LEU cc_start: 0.8254 (tp) cc_final: 0.7994 (tp) REVERT: H 214 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6435 (mm) outliers start: 124 outliers final: 92 residues processed: 729 average time/residue: 0.2911 time to fit residues: 341.5413 Evaluate side-chains 749 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 652 time to evaluate : 2.313 ------------------------------------------------------------------------------- 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 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 316 LEU Chi-restraints excluded: chain A residue 341 ILE 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 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 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 264 LEU 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 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR 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 334 LEU 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 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 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 214 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 242 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 249 optimal weight: 0.7980 chunk 220 optimal weight: 0.0970 chunk 152 optimal weight: 0.8980 chunk 1 optimal weight: 0.0970 chunk 244 optimal weight: 1.9990 chunk 231 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 348 ASN E 348 ASN F 79 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120722 restraints weight = 30416.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124625 restraints weight = 17067.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127258 restraints weight = 11599.690| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3666 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= 0.138 Angle : 0.706 11.045 31248 Z= 0.352 Chirality : 0.042 0.181 3448 Planarity : 0.003 0.037 3832 Dihedral : 4.796 19.387 2952 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.35 % Allowed : 27.09 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2640 helix: 1.13 (0.13), residues: 1720 sheet: -1.89 (0.41), residues: 144 loop : -3.79 (0.18), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP G 59 HIS 0.007 0.001 HIS H 79 PHE 0.025 0.001 PHE B 242 TYR 0.017 0.001 TYR C 172 ARG 0.012 0.000 ARG H 362 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1225) hydrogen bonds : angle 4.04024 ( 3627) SS BOND : bond 0.01672 ( 16) SS BOND : angle 6.08061 ( 32) covalent geometry : bond 0.00314 (22920) covalent geometry : angle 0.67926 (31216) *********************** 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 780 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 676 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8778 (t) REVERT: A 178 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8212 (ptp-110) REVERT: A 300 TYR cc_start: 0.8573 (t80) cc_final: 0.8319 (t80) REVERT: A 328 ASP cc_start: 0.8841 (m-30) cc_final: 0.8636 (p0) REVERT: B 28 ASP cc_start: 0.8231 (m-30) cc_final: 0.7777 (m-30) REVERT: B 69 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8698 (t) REVERT: B 182 LYS cc_start: 0.8674 (tptt) cc_final: 0.8440 (tptt) REVERT: C 54 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: C 59 TRP cc_start: 0.8090 (t-100) cc_final: 0.7716 (t60) REVERT: C 69 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8617 (t) REVERT: C 166 GLU cc_start: 0.8350 (tp30) cc_final: 0.8086 (tp30) REVERT: C 182 LYS cc_start: 0.8417 (tptt) cc_final: 0.8096 (tptt) REVERT: C 344 GLN cc_start: 0.8900 (mm110) cc_final: 0.8659 (mm110) REVERT: C 345 MET cc_start: 0.8401 (mmp) cc_final: 0.8136 (mmm) REVERT: D 28 ASP cc_start: 0.8271 (m-30) cc_final: 0.7821 (m-30) REVERT: D 130 ILE cc_start: 0.8944 (tp) cc_final: 0.8576 (tp) REVERT: D 182 LYS cc_start: 0.8559 (tptt) cc_final: 0.8359 (tptt) REVERT: D 199 GLN cc_start: 0.8329 (tp40) cc_final: 0.8103 (tt0) REVERT: E 182 LYS cc_start: 0.8563 (tptt) cc_final: 0.8274 (tptt) REVERT: E 202 ASN cc_start: 0.8702 (t0) cc_final: 0.8382 (t0) REVERT: E 300 TYR cc_start: 0.8603 (t80) cc_final: 0.8374 (t80) REVERT: E 344 GLN cc_start: 0.8915 (mm110) cc_final: 0.8673 (mm110) REVERT: F 210 LEU cc_start: 0.9331 (tp) cc_final: 0.8995 (tt) REVERT: F 345 MET cc_start: 0.8235 (mmp) cc_final: 0.7961 (mmm) REVERT: G 166 GLU cc_start: 0.8441 (tp30) cc_final: 0.7539 (tp30) REVERT: G 274 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.5470 (mp0) REVERT: G 300 TYR cc_start: 0.8604 (t80) cc_final: 0.8353 (t80) REVERT: G 328 ASP cc_start: 0.8882 (m-30) cc_final: 0.8643 (p0) REVERT: H 210 LEU cc_start: 0.9244 (tp) cc_final: 0.8918 (tt) REVERT: H 345 MET cc_start: 0.8286 (mmp) cc_final: 0.8035 (mmm) outliers start: 104 outliers final: 83 residues processed: 704 average time/residue: 0.3075 time to fit residues: 349.3485 Evaluate side-chains 747 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 658 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 264 LEU 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 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 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 304 ASN Chi-restraints excluded: chain C residue 341 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 177 ILE Chi-restraints excluded: chain D residue 264 LEU 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 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 264 LEU Chi-restraints excluded: chain E residue 268 THR 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 177 ILE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 271 ILE 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 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 162 LEU 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 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 274 GLU 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 148 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 189 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 220 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN D 237 GLN F 79 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.147013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122408 restraints weight = 30338.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.126677 restraints weight = 16158.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129645 restraints weight = 10641.400| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 22936 Z= 0.140 Angle : 0.715 10.992 31248 Z= 0.356 Chirality : 0.042 0.197 3448 Planarity : 0.003 0.035 3832 Dihedral : 4.730 19.649 2952 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.26 % Allowed : 27.72 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2640 helix: 1.18 (0.13), residues: 1720 sheet: -1.90 (0.41), residues: 144 loop : -3.73 (0.18), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 59 HIS 0.007 0.001 HIS H 79 PHE 0.024 0.001 PHE B 242 TYR 0.019 0.001 TYR C 172 ARG 0.014 0.001 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 1225) hydrogen bonds : angle 4.04350 ( 3627) SS BOND : bond 0.01691 ( 16) SS BOND : angle 6.37163 ( 32) covalent geometry : bond 0.00326 (22920) covalent geometry : angle 0.68597 (31216) *********************** 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 790 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 688 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7980 (mmp80) cc_final: 0.7737 (mmp80) REVERT: A 69 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8823 (t) REVERT: A 130 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8299 (tp) REVERT: A 178 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8083 (ptp-110) REVERT: A 300 TYR cc_start: 0.8605 (t80) cc_final: 0.8351 (t80) REVERT: A 328 ASP cc_start: 0.8894 (m-30) cc_final: 0.8663 (p0) REVERT: B 28 ASP cc_start: 0.8365 (m-30) cc_final: 0.8159 (m-30) REVERT: B 69 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8680 (t) REVERT: B 182 LYS cc_start: 0.8630 (tptt) cc_final: 0.8419 (tptt) REVERT: B 300 TYR cc_start: 0.8589 (t80) cc_final: 0.8370 (t80) REVERT: B 345 MET cc_start: 0.8330 (mmp) cc_final: 0.8059 (mmm) REVERT: C 54 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: C 69 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8551 (t) REVERT: C 182 LYS cc_start: 0.8567 (tptt) cc_final: 0.8304 (tptt) REVERT: C 344 GLN cc_start: 0.8910 (mm110) cc_final: 0.8652 (mm110) REVERT: D 28 ASP cc_start: 0.8092 (m-30) cc_final: 0.7806 (m-30) REVERT: D 130 ILE cc_start: 0.8893 (tp) cc_final: 0.8551 (tp) REVERT: D 199 GLN cc_start: 0.8342 (tp40) cc_final: 0.8109 (tt0) REVERT: D 345 MET cc_start: 0.8417 (mmp) cc_final: 0.8206 (mmm) REVERT: E 166 GLU cc_start: 0.8764 (tp30) cc_final: 0.8061 (mt-10) REVERT: E 182 LYS cc_start: 0.8573 (tptt) cc_final: 0.8244 (tppt) REVERT: E 202 ASN cc_start: 0.8676 (t0) cc_final: 0.8377 (t0) REVERT: E 300 TYR cc_start: 0.8647 (t80) cc_final: 0.8391 (t80) REVERT: E 344 GLN cc_start: 0.8931 (mm110) cc_final: 0.8692 (mm110) REVERT: F 130 ILE cc_start: 0.8755 (tp) cc_final: 0.8415 (tp) REVERT: F 182 LYS cc_start: 0.8726 (tptt) cc_final: 0.8470 (tptt) REVERT: F 210 LEU cc_start: 0.9300 (tp) cc_final: 0.8971 (tt) REVERT: F 300 TYR cc_start: 0.8591 (t80) cc_final: 0.8367 (t80) REVERT: F 310 LYS cc_start: 0.8652 (tppt) cc_final: 0.8287 (tptp) REVERT: F 345 MET cc_start: 0.8328 (mmp) cc_final: 0.8076 (mmm) REVERT: G 171 VAL cc_start: 0.8930 (t) cc_final: 0.8645 (t) REVERT: G 182 LYS cc_start: 0.8581 (tptt) cc_final: 0.8371 (tptt) REVERT: G 186 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7564 (mmt180) REVERT: G 274 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.5463 (mp0) REVERT: G 300 TYR cc_start: 0.8641 (t80) cc_final: 0.8399 (t80) REVERT: G 328 ASP cc_start: 0.8927 (m-30) cc_final: 0.8669 (p0) REVERT: H 182 LYS cc_start: 0.8704 (tptt) cc_final: 0.8479 (tptt) REVERT: H 345 MET cc_start: 0.8319 (mmp) cc_final: 0.8046 (mmm) outliers start: 102 outliers final: 88 residues processed: 710 average time/residue: 0.3095 time to fit residues: 355.0157 Evaluate side-chains 754 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 659 time to evaluate : 3.274 ------------------------------------------------------------------------------- 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 130 ILE Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 264 LEU 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 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 173 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 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 304 ASN Chi-restraints excluded: chain C residue 341 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 177 ILE Chi-restraints excluded: chain D residue 264 LEU 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 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 341 ILE 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 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 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 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 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 188 MET Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 164 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 242 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 70 ASN B 79 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN C 348 ASN D 70 ASN D 79 HIS D 348 ASN F 79 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN H 70 ASN H 79 HIS H 348 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118180 restraints weight = 30878.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122118 restraints weight = 17028.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.124883 restraints weight = 11517.391| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3732 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= 0.165 Angle : 0.744 11.412 31248 Z= 0.369 Chirality : 0.044 0.184 3448 Planarity : 0.003 0.032 3832 Dihedral : 4.822 20.713 2952 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.26 % Allowed : 28.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2640 helix: 1.18 (0.13), residues: 1720 sheet: None (None), residues: 0 loop : -3.38 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 236 HIS 0.007 0.001 HIS B 79 PHE 0.031 0.001 PHE B 242 TYR 0.016 0.001 TYR C 172 ARG 0.011 0.001 ARG H 362 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 1225) hydrogen bonds : angle 4.11025 ( 3627) SS BOND : bond 0.01633 ( 16) SS BOND : angle 6.19850 ( 32) covalent geometry : bond 0.00400 (22920) covalent geometry : angle 0.71740 (31216) ********************** 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 758 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 656 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8051 (mmp80) cc_final: 0.7835 (mmp80) REVERT: A 69 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8875 (t) REVERT: A 130 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8392 (tp) REVERT: A 171 VAL cc_start: 0.8970 (t) cc_final: 0.8747 (t) REVERT: A 178 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7873 (ptm160) REVERT: A 300 TYR cc_start: 0.8614 (t80) cc_final: 0.8352 (t80) REVERT: A 328 ASP cc_start: 0.8864 (m-30) cc_final: 0.8644 (p0) REVERT: A 344 GLN cc_start: 0.9033 (mm110) cc_final: 0.8806 (mm110) REVERT: B 69 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8673 (t) REVERT: B 182 LYS cc_start: 0.8613 (tptt) cc_final: 0.8411 (tptt) REVERT: B 300 TYR cc_start: 0.8599 (t80) cc_final: 0.8379 (t80) REVERT: B 310 LYS cc_start: 0.8664 (tppt) cc_final: 0.8313 (tptp) REVERT: B 345 MET cc_start: 0.8264 (mmp) cc_final: 0.8006 (mmm) REVERT: C 54 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: C 182 LYS cc_start: 0.8526 (tptt) cc_final: 0.8251 (tptt) REVERT: C 213 LEU cc_start: 0.8251 (tp) cc_final: 0.8004 (tp) REVERT: C 344 GLN cc_start: 0.8886 (mm110) cc_final: 0.8653 (mm110) REVERT: D 166 GLU cc_start: 0.8511 (tp30) cc_final: 0.7549 (tp30) REVERT: D 199 GLN cc_start: 0.8645 (tp40) cc_final: 0.8325 (tt0) REVERT: D 310 LYS cc_start: 0.8602 (tppt) cc_final: 0.8209 (tptp) REVERT: D 345 MET cc_start: 0.8352 (mmp) cc_final: 0.8101 (mmm) REVERT: D 364 ILE cc_start: 0.8278 (tp) cc_final: 0.7972 (tp) REVERT: E 171 VAL cc_start: 0.9023 (t) cc_final: 0.8743 (t) REVERT: E 182 LYS cc_start: 0.8532 (tptt) cc_final: 0.8283 (tptt) REVERT: E 202 ASN cc_start: 0.8721 (t0) cc_final: 0.8439 (t0) REVERT: E 300 TYR cc_start: 0.8638 (t80) cc_final: 0.8375 (t80) REVERT: E 344 GLN cc_start: 0.8969 (mm110) cc_final: 0.8743 (mm110) REVERT: F 182 LYS cc_start: 0.8652 (tptt) cc_final: 0.8410 (tptt) REVERT: F 210 LEU cc_start: 0.9345 (tp) cc_final: 0.9018 (tt) REVERT: F 345 MET cc_start: 0.8282 (mmp) cc_final: 0.8030 (mmm) REVERT: G 182 LYS cc_start: 0.8568 (tptt) cc_final: 0.8299 (tptt) REVERT: G 186 ARG cc_start: 0.7865 (tpp-160) cc_final: 0.7578 (mmt180) REVERT: G 274 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.5384 (mp0) REVERT: G 300 TYR cc_start: 0.8662 (t80) cc_final: 0.8404 (t80) REVERT: G 328 ASP cc_start: 0.8900 (m-30) cc_final: 0.8646 (p0) REVERT: H 182 LYS cc_start: 0.8695 (tptt) cc_final: 0.8470 (tptt) REVERT: H 210 LEU cc_start: 0.9289 (tp) cc_final: 0.9002 (tt) REVERT: H 345 MET cc_start: 0.8343 (mmp) cc_final: 0.8066 (mmm) outliers start: 102 outliers final: 89 residues processed: 686 average time/residue: 0.3162 time to fit residues: 350.6063 Evaluate side-chains 738 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 643 time to evaluate : 2.920 ------------------------------------------------------------------------------- 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 130 ILE Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 277 PHE 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 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 54 ASP 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 304 ASN Chi-restraints excluded: chain C residue 341 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 177 ILE Chi-restraints excluded: chain D residue 264 LEU 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 248 CYS Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 THR 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 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 262 THR Chi-restraints excluded: chain F residue 264 LEU 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 30 LEU 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 248 CYS 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 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 341 ILE 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 188 MET Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 74 optimal weight: 0.1980 chunk 85 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 147 optimal weight: 6.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN C 348 ASN D 70 ASN D 79 HIS F 79 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN H 79 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.145315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121116 restraints weight = 30393.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125138 restraints weight = 16751.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127946 restraints weight = 11284.444| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3898 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= 0.142 Angle : 0.732 11.185 31248 Z= 0.362 Chirality : 0.043 0.184 3448 Planarity : 0.003 0.031 3832 Dihedral : 4.726 19.970 2952 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.26 % Allowed : 28.64 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2640 helix: 1.25 (0.13), residues: 1720 sheet: None (None), residues: 0 loop : -3.35 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 236 HIS 0.008 0.001 HIS B 79 PHE 0.022 0.001 PHE B 124 TYR 0.020 0.001 TYR C 172 ARG 0.011 0.000 ARG H 362 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1225) hydrogen bonds : angle 4.04738 ( 3627) SS BOND : bond 0.01640 ( 16) SS BOND : angle 5.95231 ( 32) covalent geometry : bond 0.00331 (22920) covalent geometry : angle 0.70664 (31216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8566.13 seconds wall clock time: 151 minutes 30.02 seconds (9090.02 seconds total)