Starting phenix.real_space_refine on Sun Sep 29 08:00:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/09_2024/6kfg_9972.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/09_2024/6kfg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/09_2024/6kfg_9972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/09_2024/6kfg_9972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/09_2024/6kfg_9972.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfg_9972/09_2024/6kfg_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-5461/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: 6.95, per 1000 atoms: 0.31 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=2, 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 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: 5.55 Conformation dependent library (CDL) restraints added in 2.7 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: 2.02 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: 6.02 Time building geometry restraints manager: 6.47 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: 11388 15.58 - 31.17: 1393 31.17 - 46.75: 287 46.75 - 62.33: 58 62.33 - 77.91: 16 Dihedral angle restraints: 13142 sinusoidal: 5102 harmonic: 8040 Sorted by residual: dihedral pdb=" CB CYS A 58 " pdb=" SG CYS A 58 " pdb=" SG CYS A 265 " pdb=" CB CYS A 265 " ideal model delta sinusoidal sigma weight residual 93.00 39.44 53.56 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CA ARG D 29 " pdb=" C ARG D 29 " pdb=" N LEU D 30 " pdb=" CA LEU D 30 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ARG C 29 " pdb=" C ARG C 29 " pdb=" N LEU C 30 " pdb=" CA LEU C 30 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 13139 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: 2.03 - 2.60: 225 2.60 - 3.18: 21287 3.18 - 3.75: 34118 3.75 - 4.33: 43910 4.33 - 4.90: 71686 Nonbonded interactions: 171226 Sorted by model distance: nonbonded pdb=" SG CYS E 76 " pdb=" SG CYS E 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 76 " pdb=" SG CYS C 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS F 76 " pdb=" SG CYS F 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS H 76 " pdb=" SG CYS H 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS G 76 " pdb=" SG CYS G 248 " model vdw 2.029 3.760 ... (remaining 171221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 39.990 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.780 ------------------------------------------------------------------------------- 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 22920 Z= 0.439 Angle : 0.770 12.750 31216 Z= 0.419 Chirality : 0.047 0.190 3448 Planarity : 0.003 0.029 3832 Dihedral : 14.038 77.914 7920 Min Nonbonded Distance : 2.029 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 *********************** 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 fitting. rotamer outliers: 16 poor density : 934 time to evaluate : 2.595 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: 0.3595 time to fit residues: 514.3421 Evaluate side-chains 731 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 723 time to evaluate : 2.280 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22920 Z= 0.200 Angle : 0.683 7.554 31216 Z= 0.356 Chirality : 0.043 0.177 3448 Planarity : 0.004 0.042 3832 Dihedral : 6.094 56.850 2960 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.52 % Allowed : 19.82 % Favored : 75.67 % 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: -2.56 (0.15), residues: 2640 helix: -0.34 (0.12), residues: 1720 sheet: -2.61 (0.38), residues: 144 loop : -4.66 (0.17), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 59 HIS 0.002 0.000 HIS D 247 PHE 0.033 0.001 PHE C 242 TYR 0.027 0.002 TYR D 301 ARG 0.006 0.000 ARG C 186 *********************** 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 fitting. rotamer outliers: 108 poor density : 768 time to evaluate : 2.397 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: 0.8388 (mmp80) cc_final: 0.7241 (mmp80) REVERT: A 127 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7782 (ttmm) REVERT: A 130 ILE cc_start: 0.9011 (tp) cc_final: 0.8632 (tp) REVERT: A 135 TYR cc_start: 0.8785 (t80) cc_final: 0.8424 (t80) REVERT: A 166 GLU cc_start: 0.8803 (tp30) cc_final: 0.8486 (tp30) REVERT: A 213 LEU cc_start: 0.8530 (tp) cc_final: 0.8095 (tt) REVERT: A 344 GLN cc_start: 0.8977 (mm110) cc_final: 0.8770 (mm110) REVERT: B 127 LYS cc_start: 0.8055 (mtmt) cc_final: 0.7810 (ttmm) REVERT: B 130 ILE cc_start: 0.8862 (tp) cc_final: 0.8539 (tp) REVERT: B 153 ASP cc_start: 0.8269 (m-30) cc_final: 0.8057 (m-30) REVERT: B 199 GLN cc_start: 0.8768 (tp40) cc_final: 0.8434 (tt0) REVERT: B 232 GLN cc_start: 0.7819 (mm110) cc_final: 0.7310 (mt0) REVERT: B 313 LYS cc_start: 0.8950 (ttmt) cc_final: 0.8749 (pttp) REVERT: B 328 ASP cc_start: 0.9018 (m-30) cc_final: 0.8811 (p0) REVERT: C 127 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7795 (ttmm) REVERT: C 130 ILE cc_start: 0.9003 (tp) cc_final: 0.8672 (tp) REVERT: C 153 ASP cc_start: 0.8342 (m-30) cc_final: 0.7958 (m-30) REVERT: C 213 LEU cc_start: 0.8442 (tp) cc_final: 0.7996 (tt) REVERT: C 344 GLN cc_start: 0.8946 (mm110) cc_final: 0.8716 (mm110) REVERT: D 127 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7776 (ttmm) REVERT: D 130 ILE cc_start: 0.9000 (tp) cc_final: 0.8669 (tp) REVERT: D 199 GLN cc_start: 0.8785 (tp40) cc_final: 0.8395 (tt0) REVERT: D 244 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7687 (mtm-85) REVERT: E 213 LEU cc_start: 0.8424 (tp) cc_final: 0.8032 (tt) REVERT: E 344 GLN cc_start: 0.8923 (mm110) cc_final: 0.8704 (mm110) REVERT: F 130 ILE cc_start: 0.8855 (tp) cc_final: 0.8528 (tp) REVERT: F 153 ASP cc_start: 0.8294 (m-30) cc_final: 0.8008 (m-30) REVERT: F 166 GLU cc_start: 0.8620 (tp30) cc_final: 0.7711 (tp30) REVERT: F 199 GLN cc_start: 0.8744 (tp40) cc_final: 0.8423 (tt0) REVERT: F 210 LEU cc_start: 0.9344 (tp) cc_final: 0.9039 (tt) REVERT: F 244 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7649 (mtt-85) REVERT: F 328 ASP cc_start: 0.9039 (m-30) cc_final: 0.8815 (p0) REVERT: F 342 MET cc_start: 0.8712 (mmm) cc_final: 0.8505 (mmm) REVERT: F 345 MET cc_start: 0.8852 (tpp) cc_final: 0.8635 (mmp) REVERT: G 328 ASP cc_start: 0.9115 (m-30) cc_final: 0.8708 (p0) REVERT: G 344 GLN cc_start: 0.8913 (mm110) cc_final: 0.8694 (mm110) REVERT: H 127 LYS cc_start: 0.7983 (mtmt) cc_final: 0.7739 (ttmm) REVERT: H 130 ILE cc_start: 0.8847 (tp) cc_final: 0.8516 (tp) REVERT: H 199 GLN cc_start: 0.8754 (tp40) cc_final: 0.8436 (tt0) REVERT: H 210 LEU cc_start: 0.9325 (tp) cc_final: 0.9052 (tt) REVERT: H 328 ASP cc_start: 0.9037 (m-30) cc_final: 0.8808 (p0) REVERT: H 342 MET cc_start: 0.8727 (mmm) cc_final: 0.8480 (mmm) outliers start: 108 outliers final: 77 residues processed: 794 average time/residue: 0.3143 time to fit residues: 390.2556 Evaluate side-chains 737 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 660 time to evaluate : 2.824 ------------------------------------------------------------------------------- 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 262 THR 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 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 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 177 ILE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 290 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 133 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 chunk 240 optimal weight: 5.9990 chunk 259 optimal weight: 0.0030 chunk 213 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 overall best weight: 2.9796 ------------------------------------------------------------------------------- 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 B 294 ASN B 329 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN 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 73 ASN F 79 HIS F 294 ASN G 199 GLN G 206 GLN G 294 ASN G 348 ASN H 73 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 22920 Z= 0.295 Angle : 0.678 12.766 31216 Z= 0.354 Chirality : 0.044 0.211 3448 Planarity : 0.004 0.045 3832 Dihedral : 5.906 50.704 2960 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 6.69 % Allowed : 21.53 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.16), residues: 2640 helix: 0.07 (0.12), residues: 1752 sheet: -2.68 (0.40), residues: 144 loop : -4.57 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 59 HIS 0.006 0.001 HIS D 79 PHE 0.054 0.001 PHE B 242 TYR 0.016 0.002 TYR D 301 ARG 0.009 0.001 ARG B 362 *********************** 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 845 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 685 time to evaluate : 2.492 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 82 TYR cc_start: 0.8687 (p90) cc_final: 0.8347 (p90) REVERT: A 127 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7838 (ttmm) REVERT: A 213 LEU cc_start: 0.8623 (tp) cc_final: 0.8418 (tp) REVERT: A 244 ARG cc_start: 0.8377 (mtt180) cc_final: 0.7971 (mtm-85) REVERT: A 274 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.5682 (mp0) REVERT: A 328 ASP cc_start: 0.9126 (m-30) cc_final: 0.8762 (p0) REVERT: A 344 GLN cc_start: 0.8996 (mm110) cc_final: 0.8768 (mm110) REVERT: B 127 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7823 (ttmm) REVERT: B 130 ILE cc_start: 0.8976 (tp) cc_final: 0.8587 (tp) REVERT: B 199 GLN cc_start: 0.8777 (tp40) cc_final: 0.8457 (tt0) REVERT: B 313 LYS cc_start: 0.8938 (ttmt) cc_final: 0.8709 (ttmm) REVERT: C 213 LEU cc_start: 0.8545 (tp) cc_final: 0.8341 (tp) REVERT: C 300 TYR cc_start: 0.8357 (t80) cc_final: 0.8155 (t80) REVERT: C 344 GLN cc_start: 0.8980 (mm110) cc_final: 0.8753 (mm110) REVERT: D 127 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7852 (ttmm) REVERT: D 130 ILE cc_start: 0.8962 (tp) cc_final: 0.8623 (tp) REVERT: D 199 GLN cc_start: 0.8783 (tp40) cc_final: 0.8426 (tt0) REVERT: D 274 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.5854 (mp0) REVERT: E 274 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.5777 (mp0) REVERT: E 328 ASP cc_start: 0.9117 (m-30) cc_final: 0.8738 (p0) REVERT: E 344 GLN cc_start: 0.8979 (mm110) cc_final: 0.8757 (mm110) REVERT: F 130 ILE cc_start: 0.8963 (tp) cc_final: 0.8602 (tp) REVERT: F 166 GLU cc_start: 0.8559 (tp30) cc_final: 0.7669 (tp30) REVERT: F 199 GLN cc_start: 0.8771 (tp40) cc_final: 0.8502 (tt0) REVERT: F 210 LEU cc_start: 0.9375 (tp) cc_final: 0.9041 (tt) REVERT: F 244 ARG cc_start: 0.8317 (mtt180) cc_final: 0.8011 (mtt180) REVERT: G 171 VAL cc_start: 0.9228 (t) cc_final: 0.8925 (t) REVERT: G 274 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.5611 (mp0) REVERT: G 328 ASP cc_start: 0.9087 (m-30) cc_final: 0.8633 (p0) REVERT: G 344 GLN cc_start: 0.8943 (mm110) cc_final: 0.8716 (mm110) REVERT: H 58 CYS cc_start: 0.8081 (m) cc_final: 0.7725 (m) REVERT: H 127 LYS cc_start: 0.8067 (mtmt) cc_final: 0.7796 (ttmm) REVERT: H 130 ILE cc_start: 0.8964 (tp) cc_final: 0.8613 (tp) REVERT: H 166 GLU cc_start: 0.8525 (tp30) cc_final: 0.7749 (tp30) REVERT: H 199 GLN cc_start: 0.8784 (tp40) cc_final: 0.8483 (tt0) REVERT: H 210 LEU cc_start: 0.9366 (tp) cc_final: 0.9052 (tt) REVERT: H 364 ILE cc_start: 0.8249 (tp) cc_final: 0.8030 (tp) outliers start: 160 outliers final: 127 residues processed: 735 average time/residue: 0.2912 time to fit residues: 342.5386 Evaluate side-chains 760 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 629 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 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 280 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU 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 329 GLN 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 280 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 205 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 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 D residue 349 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 209 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 274 GLU 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 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 227 LEU 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 277 PHE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 205 ILE 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 280 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 227 LEU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** B 73 ASN C 199 GLN D 73 ASN D 79 HIS D 294 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN F 73 ASN F 79 HIS G 294 ASN H 73 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 22920 Z= 0.283 Angle : 0.659 9.821 31216 Z= 0.343 Chirality : 0.044 0.186 3448 Planarity : 0.003 0.041 3832 Dihedral : 5.569 40.320 2960 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 7.65 % Allowed : 22.87 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.62 (0.16), residues: 2640 helix: 0.37 (0.12), residues: 1752 sheet: None (None), residues: 0 loop : -4.21 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 107 HIS 0.006 0.001 HIS F 79 PHE 0.058 0.001 PHE B 242 TYR 0.016 0.002 TYR H 82 ARG 0.007 0.001 ARG A 362 *********************** 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 859 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 676 time to evaluate : 2.287 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: A 69 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8522 (t) REVERT: A 82 TYR cc_start: 0.8673 (p90) cc_final: 0.8212 (p90) REVERT: A 213 LEU cc_start: 0.8633 (tp) cc_final: 0.8404 (tp) REVERT: A 274 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.5719 (mp0) REVERT: A 328 ASP cc_start: 0.9111 (m-30) cc_final: 0.8743 (p0) REVERT: A 344 GLN cc_start: 0.8969 (mm110) cc_final: 0.8750 (mm110) REVERT: B 29 ARG cc_start: 0.8355 (mmp80) cc_final: 0.7827 (mmp80) REVERT: B 69 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8521 (t) REVERT: B 127 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7827 (ttmm) REVERT: B 130 ILE cc_start: 0.8952 (tp) cc_final: 0.8576 (tp) REVERT: B 199 GLN cc_start: 0.8780 (tp40) cc_final: 0.8460 (tt0) REVERT: B 210 LEU cc_start: 0.9263 (tp) cc_final: 0.8979 (tt) REVERT: B 329 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8022 (pm20) REVERT: C 213 LEU cc_start: 0.8549 (tp) cc_final: 0.8309 (tp) REVERT: C 344 GLN cc_start: 0.8980 (mm110) cc_final: 0.8754 (mm110) REVERT: D 29 ARG cc_start: 0.8350 (mmp80) cc_final: 0.7908 (mmp80) REVERT: D 69 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8397 (t) REVERT: D 127 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7851 (ttmm) REVERT: D 130 ILE cc_start: 0.8962 (tp) cc_final: 0.8612 (tp) REVERT: D 166 GLU cc_start: 0.8472 (tp30) cc_final: 0.7582 (tp30) REVERT: D 199 GLN cc_start: 0.8759 (tp40) cc_final: 0.8380 (tt0) REVERT: D 244 ARG cc_start: 0.8276 (mtt180) cc_final: 0.8036 (mtt180) REVERT: D 274 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.5838 (mp0) REVERT: D 345 MET cc_start: 0.8918 (mmm) cc_final: 0.8409 (tpp) REVERT: E 69 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8404 (t) REVERT: E 208 TYR cc_start: 0.8233 (t80) cc_final: 0.7983 (t80) REVERT: E 212 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8186 (mp10) REVERT: E 274 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.5745 (mp0) REVERT: E 344 GLN cc_start: 0.8977 (mm110) cc_final: 0.8744 (mm110) REVERT: F 130 ILE cc_start: 0.8926 (tp) cc_final: 0.8521 (tp) REVERT: F 166 GLU cc_start: 0.8555 (tp30) cc_final: 0.7683 (tp30) REVERT: F 199 GLN cc_start: 0.8766 (tp40) cc_final: 0.8484 (tt0) REVERT: F 210 LEU cc_start: 0.9367 (tp) cc_final: 0.9051 (tt) REVERT: F 244 ARG cc_start: 0.8338 (mtt180) cc_final: 0.8037 (mtt180) REVERT: G 59 TRP cc_start: 0.8165 (t-100) cc_final: 0.7828 (t-100) REVERT: G 274 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.5523 (mp0) REVERT: G 328 ASP cc_start: 0.9033 (m-30) cc_final: 0.8661 (p0) REVERT: G 344 GLN cc_start: 0.8949 (mm110) cc_final: 0.8733 (mm110) REVERT: G 345 MET cc_start: 0.8555 (mmp) cc_final: 0.8221 (mmm) REVERT: H 127 LYS cc_start: 0.8067 (mtmt) cc_final: 0.7812 (ttmm) REVERT: H 130 ILE cc_start: 0.8967 (tp) cc_final: 0.8579 (tp) REVERT: H 199 GLN cc_start: 0.8784 (tp40) cc_final: 0.8520 (tt0) REVERT: H 210 LEU cc_start: 0.9355 (tp) cc_final: 0.9048 (tt) outliers start: 183 outliers final: 140 residues processed: 750 average time/residue: 0.2807 time to fit residues: 339.6083 Evaluate side-chains 775 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 625 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 37 VAL 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 144 VAL Chi-restraints excluded: chain A residue 178 ARG 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 280 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 248 CYS 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 329 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 ILE 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 144 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 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 280 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 20 VAL 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 69 VAL 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 205 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 277 PHE 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 D residue 349 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain F residue 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 227 LEU 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 277 PHE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain H residue 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 201 VAL Chi-restraints excluded: chain H residue 227 LEU 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 277 PHE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 3 optimal weight: 0.0020 chunk 190 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 73 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN F 79 HIS H 73 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22920 Z= 0.277 Angle : 0.649 8.254 31216 Z= 0.338 Chirality : 0.044 0.192 3448 Planarity : 0.003 0.040 3832 Dihedral : 5.353 20.598 2955 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 8.32 % Allowed : 23.29 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.31 (0.17), residues: 2640 helix: 0.61 (0.13), residues: 1752 sheet: None (None), residues: 0 loop : -4.11 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 236 HIS 0.006 0.001 HIS F 79 PHE 0.051 0.001 PHE B 242 TYR 0.016 0.002 TYR F 82 ARG 0.007 0.001 ARG G 362 *********************** 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 854 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 655 time to evaluate : 2.776 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: A 69 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8506 (t) REVERT: A 130 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8486 (tp) REVERT: A 274 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.5855 (mp0) REVERT: A 328 ASP cc_start: 0.9072 (m-30) cc_final: 0.8689 (p0) REVERT: A 344 GLN cc_start: 0.8986 (mm110) cc_final: 0.8755 (mm110) REVERT: B 29 ARG cc_start: 0.8332 (mmp80) cc_final: 0.8099 (mmp80) REVERT: B 69 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8417 (t) REVERT: B 127 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7803 (ttmm) REVERT: B 130 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8507 (tp) REVERT: B 199 GLN cc_start: 0.8770 (tp40) cc_final: 0.8419 (tt0) REVERT: B 273 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: B 329 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8571 (pm20) REVERT: C 69 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8600 (t) REVERT: C 130 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8574 (tp) REVERT: C 213 LEU cc_start: 0.8544 (tp) cc_final: 0.8328 (tp) REVERT: C 344 GLN cc_start: 0.8955 (mm110) cc_final: 0.8706 (mm110) REVERT: D 29 ARG cc_start: 0.8339 (mmp80) cc_final: 0.8105 (mmp80) REVERT: D 69 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8485 (t) REVERT: D 127 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7851 (ttmm) REVERT: D 130 ILE cc_start: 0.8965 (tp) cc_final: 0.8605 (tp) REVERT: D 199 GLN cc_start: 0.8758 (tp40) cc_final: 0.8395 (tt0) REVERT: D 274 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.5878 (mp0) REVERT: E 69 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8499 (t) REVERT: E 130 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8584 (tp) REVERT: E 212 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: E 274 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.5669 (mp0) REVERT: E 344 GLN cc_start: 0.8947 (mm110) cc_final: 0.8707 (mm110) REVERT: E 345 MET cc_start: 0.8551 (mmp) cc_final: 0.8152 (mmm) REVERT: F 130 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8493 (tp) REVERT: F 199 GLN cc_start: 0.8782 (tp40) cc_final: 0.8552 (tt0) REVERT: F 210 LEU cc_start: 0.9353 (tp) cc_final: 0.9040 (tt) REVERT: F 284 LEU cc_start: 0.9239 (mt) cc_final: 0.9012 (mt) REVERT: F 345 MET cc_start: 0.8307 (mmp) cc_final: 0.8089 (mmm) REVERT: G 59 TRP cc_start: 0.8267 (t-100) cc_final: 0.7826 (t-100) REVERT: G 130 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8619 (tp) REVERT: G 202 ASN cc_start: 0.8965 (t0) cc_final: 0.8582 (t0) REVERT: G 274 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.5386 (mp0) REVERT: G 328 ASP cc_start: 0.9009 (m-30) cc_final: 0.8640 (p0) REVERT: G 344 GLN cc_start: 0.8965 (mm110) cc_final: 0.8734 (mm110) REVERT: G 345 MET cc_start: 0.8575 (mmp) cc_final: 0.8251 (mmm) REVERT: H 127 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7813 (ttmm) REVERT: H 130 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8493 (tp) REVERT: H 199 GLN cc_start: 0.8793 (tp40) cc_final: 0.8545 (tt0) REVERT: H 210 LEU cc_start: 0.9339 (tp) cc_final: 0.9039 (tt) REVERT: H 284 LEU cc_start: 0.9238 (mt) cc_final: 0.9000 (mt) outliers start: 199 outliers final: 147 residues processed: 731 average time/residue: 0.2865 time to fit residues: 339.4901 Evaluate side-chains 784 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 618 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 37 VAL 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 144 VAL Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 231 LEU 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 277 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 PHE 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 329 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 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 130 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 211 THR 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 280 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 20 VAL 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 69 VAL 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 227 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 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 D residue 349 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 212 GLN 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 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 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 130 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 248 CYS 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 277 PHE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 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 130 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 248 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 79 HIS C 294 ASN D 73 ASN D 79 HIS F 73 ASN F 79 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 0.082 22920 Z= 0.206 Angle : 0.636 10.895 31216 Z= 0.327 Chirality : 0.042 0.190 3448 Planarity : 0.003 0.034 3832 Dihedral : 5.162 19.144 2952 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 7.02 % Allowed : 25.38 % Favored : 67.60 % 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: -1.09 (0.17), residues: 2640 helix: 0.83 (0.13), residues: 1752 sheet: -2.99 (0.40), residues: 144 loop : -4.14 (0.19), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 68 HIS 0.006 0.001 HIS H 79 PHE 0.036 0.001 PHE B 242 TYR 0.018 0.001 TYR B 82 ARG 0.005 0.000 ARG A 362 *********************** 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 855 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 687 time to evaluate : 2.455 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: A 69 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8485 (t) REVERT: A 130 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8517 (tp) REVERT: A 274 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.5589 (mp0) REVERT: A 328 ASP cc_start: 0.9055 (m-30) cc_final: 0.8694 (p0) REVERT: A 344 GLN cc_start: 0.8967 (mm110) cc_final: 0.8717 (mm110) REVERT: B 69 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8426 (t) REVERT: B 127 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7782 (ttmm) REVERT: B 130 ILE cc_start: 0.8916 (tp) cc_final: 0.8552 (tp) REVERT: B 155 ASP cc_start: 0.7974 (t0) cc_final: 0.7539 (t0) REVERT: B 199 GLN cc_start: 0.8696 (tp40) cc_final: 0.8392 (tt0) REVERT: B 273 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: C 69 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8528 (t) REVERT: C 182 LYS cc_start: 0.8477 (tptt) cc_final: 0.8158 (tptt) REVERT: C 213 LEU cc_start: 0.8414 (tp) cc_final: 0.8182 (tp) REVERT: C 329 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: C 345 MET cc_start: 0.8491 (mmp) cc_final: 0.8173 (mmm) REVERT: D 69 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8335 (t) REVERT: D 127 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7867 (ttmm) REVERT: D 130 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8566 (tp) REVERT: D 155 ASP cc_start: 0.8031 (t0) cc_final: 0.7580 (t0) REVERT: D 199 GLN cc_start: 0.8702 (tp40) cc_final: 0.8374 (tt0) REVERT: E 59 TRP cc_start: 0.8203 (t-100) cc_final: 0.7863 (t-100) REVERT: E 69 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8427 (t) REVERT: E 130 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8560 (tp) REVERT: E 274 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.5693 (mp0) REVERT: E 328 ASP cc_start: 0.9047 (m-30) cc_final: 0.8694 (p0) REVERT: E 344 GLN cc_start: 0.8949 (mm110) cc_final: 0.8721 (mm110) REVERT: F 130 ILE cc_start: 0.8933 (tp) cc_final: 0.8563 (tp) REVERT: F 210 LEU cc_start: 0.9337 (tp) cc_final: 0.9038 (tt) REVERT: F 345 MET cc_start: 0.8314 (mmp) cc_final: 0.8093 (mmm) REVERT: G 59 TRP cc_start: 0.8170 (t-100) cc_final: 0.7793 (t-100) REVERT: G 202 ASN cc_start: 0.8917 (t0) cc_final: 0.8647 (t0) REVERT: G 274 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.5430 (mp0) REVERT: G 328 ASP cc_start: 0.8948 (m-30) cc_final: 0.8591 (p0) REVERT: G 344 GLN cc_start: 0.8958 (mm110) cc_final: 0.8717 (mm110) REVERT: G 345 MET cc_start: 0.8513 (mmp) cc_final: 0.8155 (mmm) REVERT: H 127 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7846 (ttmm) REVERT: H 130 ILE cc_start: 0.8907 (tp) cc_final: 0.8539 (tp) REVERT: H 210 LEU cc_start: 0.9330 (tp) cc_final: 0.9029 (tt) outliers start: 168 outliers final: 111 residues processed: 761 average time/residue: 0.2909 time to fit residues: 357.6941 Evaluate side-chains 754 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 630 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 179 LEU 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 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 248 CYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 273 TYR Chi-restraints excluded: chain B residue 277 PHE 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 329 GLN 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 78 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 179 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 329 GLN 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 69 VAL 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 130 ILE Chi-restraints excluded: chain D residue 177 ILE 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 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 334 LEU 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 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 248 CYS 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 G residue 20 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 205 ILE 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 290 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 248 CYS 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 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 246 optimal weight: 8.9990 chunk 28 optimal weight: 0.0170 chunk 145 optimal weight: 0.0970 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.9618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN B 73 ASN B 237 GLN D 79 HIS E 329 GLN F 79 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 329 GLN H 73 ASN H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 22920 Z= 0.188 Angle : 0.642 10.952 31216 Z= 0.328 Chirality : 0.042 0.194 3448 Planarity : 0.003 0.036 3832 Dihedral : 5.027 18.368 2952 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 6.77 % Allowed : 26.13 % 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: -0.84 (0.17), residues: 2640 helix: 1.06 (0.13), residues: 1720 sheet: -2.93 (0.41), residues: 144 loop : -3.96 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 68 HIS 0.006 0.001 HIS H 79 PHE 0.018 0.001 PHE C 242 TYR 0.019 0.001 TYR C 172 ARG 0.013 0.000 ARG A 362 *********************** 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 828 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 666 time to evaluate : 2.565 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: A 69 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8505 (t) REVERT: A 130 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8415 (tp) REVERT: A 274 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.5515 (mp0) REVERT: A 328 ASP cc_start: 0.9034 (m-30) cc_final: 0.8701 (p0) REVERT: A 344 GLN cc_start: 0.8963 (mm110) cc_final: 0.8726 (mm110) REVERT: B 69 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8305 (t) REVERT: B 127 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7794 (ttmm) REVERT: B 328 ASP cc_start: 0.7860 (p0) cc_final: 0.7412 (p0) REVERT: B 329 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: C 69 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8393 (t) REVERT: C 130 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8472 (tp) REVERT: C 213 LEU cc_start: 0.8356 (tp) cc_final: 0.8109 (tp) REVERT: C 345 MET cc_start: 0.8527 (mmp) cc_final: 0.8241 (mmm) REVERT: D 69 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8508 (t) REVERT: D 127 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7849 (ttmm) REVERT: D 130 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8562 (tp) REVERT: D 199 GLN cc_start: 0.8377 (tp40) cc_final: 0.8146 (tt0) REVERT: D 244 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7819 (mtm-85) REVERT: D 345 MET cc_start: 0.8250 (mmp) cc_final: 0.7983 (mmm) REVERT: E 59 TRP cc_start: 0.8175 (t-100) cc_final: 0.7898 (t-100) REVERT: E 69 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8429 (t) REVERT: E 130 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8423 (tp) REVERT: E 274 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.5511 (mp0) REVERT: E 328 ASP cc_start: 0.9032 (m-30) cc_final: 0.8658 (p0) REVERT: E 344 GLN cc_start: 0.8953 (mm110) cc_final: 0.8717 (mm110) REVERT: F 29 ARG cc_start: 0.8006 (mmp80) cc_final: 0.7779 (mmp80) REVERT: F 166 GLU cc_start: 0.8557 (tp30) cc_final: 0.7977 (tp30) REVERT: G 59 TRP cc_start: 0.8106 (t-100) cc_final: 0.7771 (t-100) REVERT: G 72 VAL cc_start: 0.9099 (p) cc_final: 0.8842 (p) REVERT: G 202 ASN cc_start: 0.8881 (t0) cc_final: 0.8612 (t0) REVERT: G 274 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.5484 (mp0) REVERT: G 328 ASP cc_start: 0.8924 (m-30) cc_final: 0.8591 (p0) REVERT: G 344 GLN cc_start: 0.8955 (mm110) cc_final: 0.8732 (mm110) REVERT: G 345 MET cc_start: 0.8497 (mmp) cc_final: 0.8160 (mmm) REVERT: H 28 ASP cc_start: 0.8570 (m-30) cc_final: 0.8291 (m-30) REVERT: H 155 ASP cc_start: 0.8190 (t0) cc_final: 0.7768 (t0) REVERT: H 345 MET cc_start: 0.8295 (mmp) cc_final: 0.8038 (mmm) outliers start: 162 outliers final: 110 residues processed: 738 average time/residue: 0.2905 time to fit residues: 346.0023 Evaluate side-chains 746 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 623 time to evaluate : 2.382 ------------------------------------------------------------------------------- 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 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 196 THR 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 280 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 329 GLN 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 248 CYS 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 329 GLN 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 78 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 130 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 196 THR 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 280 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 69 VAL 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 130 ILE Chi-restraints excluded: chain D residue 177 ILE 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 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 69 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 277 PHE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 334 LEU 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 227 LEU Chi-restraints excluded: chain F residue 248 CYS 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 56 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 205 ILE 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 329 GLN Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 248 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 0.0040 chunk 76 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 348 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 GLN E 348 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 348 ASN H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 22920 Z= 0.179 Angle : 0.661 10.869 31216 Z= 0.330 Chirality : 0.042 0.204 3448 Planarity : 0.003 0.035 3832 Dihedral : 4.885 18.552 2952 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 6.48 % Allowed : 26.46 % Favored : 67.06 % 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: -0.67 (0.17), residues: 2640 helix: 1.18 (0.13), residues: 1720 sheet: -2.92 (0.40), residues: 144 loop : -3.86 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 236 HIS 0.006 0.001 HIS H 79 PHE 0.024 0.001 PHE C 242 TYR 0.018 0.001 TYR B 82 ARG 0.007 0.000 ARG A 362 *********************** 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 818 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 663 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7376 (m-30) REVERT: A 69 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8528 (t) REVERT: A 130 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8394 (tp) REVERT: A 182 LYS cc_start: 0.8433 (tptt) cc_final: 0.8138 (tptt) REVERT: A 274 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.5473 (mp0) REVERT: A 300 TYR cc_start: 0.8612 (t80) cc_final: 0.8329 (t80) REVERT: A 328 ASP cc_start: 0.9023 (m-30) cc_final: 0.8700 (p0) REVERT: A 344 GLN cc_start: 0.9001 (mm110) cc_final: 0.8761 (mm110) REVERT: B 28 ASP cc_start: 0.8431 (m-30) cc_final: 0.8170 (m-30) REVERT: B 69 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8490 (t) REVERT: B 127 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7798 (ttmm) REVERT: B 130 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8423 (tp) REVERT: B 182 LYS cc_start: 0.8623 (tptt) cc_final: 0.8398 (tptt) REVERT: B 300 TYR cc_start: 0.8613 (t80) cc_final: 0.8404 (t80) REVERT: B 328 ASP cc_start: 0.7961 (p0) cc_final: 0.7687 (p0) REVERT: B 339 LEU cc_start: 0.9086 (mt) cc_final: 0.8865 (mt) REVERT: C 59 TRP cc_start: 0.8439 (t-100) cc_final: 0.7992 (t-100) REVERT: C 69 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8429 (t) REVERT: C 130 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8419 (tp) REVERT: C 213 LEU cc_start: 0.8260 (tp) cc_final: 0.8019 (tp) REVERT: C 328 ASP cc_start: 0.8268 (p0) cc_final: 0.7898 (p0) REVERT: D 69 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8403 (t) REVERT: D 127 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7824 (ttmm) REVERT: D 130 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8538 (tp) REVERT: D 244 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7801 (mtm-85) REVERT: D 345 MET cc_start: 0.8294 (mmp) cc_final: 0.8067 (mmm) REVERT: E 59 TRP cc_start: 0.8186 (t-100) cc_final: 0.7900 (t-100) REVERT: E 69 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8377 (t) REVERT: E 130 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8397 (tp) REVERT: E 328 ASP cc_start: 0.9025 (m-30) cc_final: 0.8700 (p0) REVERT: E 344 GLN cc_start: 0.9002 (mm110) cc_final: 0.8731 (mm110) REVERT: F 130 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8461 (tp) REVERT: F 166 GLU cc_start: 0.8457 (tp30) cc_final: 0.7759 (tp30) REVERT: F 339 LEU cc_start: 0.9088 (mt) cc_final: 0.8887 (mt) REVERT: G 59 TRP cc_start: 0.7958 (t-100) cc_final: 0.7687 (t-100) REVERT: G 171 VAL cc_start: 0.9102 (t) cc_final: 0.8792 (t) REVERT: G 202 ASN cc_start: 0.8839 (t0) cc_final: 0.8581 (t0) REVERT: G 274 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.5598 (mp0) REVERT: G 344 GLN cc_start: 0.8992 (mm110) cc_final: 0.8704 (mm110) REVERT: G 345 MET cc_start: 0.8496 (mmp) cc_final: 0.8137 (mmm) REVERT: H 28 ASP cc_start: 0.8476 (m-30) cc_final: 0.8181 (m-30) REVERT: H 130 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8444 (tp) REVERT: H 274 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: H 300 TYR cc_start: 0.8615 (t80) cc_final: 0.8405 (t80) REVERT: H 345 MET cc_start: 0.8291 (mmp) cc_final: 0.8066 (mmm) outliers start: 155 outliers final: 108 residues processed: 723 average time/residue: 0.2815 time to fit residues: 329.6220 Evaluate side-chains 776 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 652 time to evaluate : 2.382 ------------------------------------------------------------------------------- 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 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 196 THR 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 280 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 334 LEU 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 130 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 262 THR 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 56 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 78 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 130 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 69 VAL 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 130 ILE Chi-restraints excluded: chain D residue 177 ILE 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 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 69 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU 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 329 GLN 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 130 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 248 CYS 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 334 LEU 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 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 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 130 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 248 CYS 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 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 Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 237 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 186 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 237 GLN C 247 HIS ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN G 73 ASN H 73 ASN H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 22920 Z= 0.190 Angle : 0.669 11.113 31216 Z= 0.332 Chirality : 0.042 0.198 3448 Planarity : 0.003 0.033 3832 Dihedral : 4.812 18.206 2952 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.60 % Allowed : 26.80 % Favored : 67.60 % 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: 1.24 (0.13), residues: 1720 sheet: -3.05 (0.39), residues: 144 loop : -3.80 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 59 HIS 0.005 0.001 HIS H 79 PHE 0.020 0.001 PHE C 242 TYR 0.018 0.001 TYR D 300 ARG 0.006 0.000 ARG A 362 *********************** 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 816 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 682 time to evaluate : 2.263 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 54 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: A 69 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8528 (t) REVERT: A 130 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8397 (tp) REVERT: A 274 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.5491 (mp0) REVERT: A 300 TYR cc_start: 0.8630 (t80) cc_final: 0.8353 (t80) REVERT: A 328 ASP cc_start: 0.9014 (m-30) cc_final: 0.8623 (p0) REVERT: A 344 GLN cc_start: 0.9080 (mm110) cc_final: 0.8797 (mm110) REVERT: B 28 ASP cc_start: 0.8511 (m-30) cc_final: 0.8306 (m-30) REVERT: B 69 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8474 (t) REVERT: B 127 LYS cc_start: 0.8013 (mtmt) cc_final: 0.7773 (ttmm) REVERT: B 130 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8422 (tp) REVERT: B 182 LYS cc_start: 0.8635 (tptt) cc_final: 0.8407 (tptt) REVERT: B 300 TYR cc_start: 0.8623 (t80) cc_final: 0.8413 (t80) REVERT: B 345 MET cc_start: 0.8388 (mmp) cc_final: 0.8134 (mmm) REVERT: C 28 ASP cc_start: 0.8729 (m-30) cc_final: 0.8464 (m-30) REVERT: C 59 TRP cc_start: 0.8373 (t-100) cc_final: 0.7966 (t-100) REVERT: C 69 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8416 (t) REVERT: C 130 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8416 (tp) REVERT: C 213 LEU cc_start: 0.8267 (tp) cc_final: 0.8023 (tt) REVERT: D 28 ASP cc_start: 0.8466 (m-30) cc_final: 0.8214 (m-30) REVERT: D 69 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8489 (t) REVERT: D 127 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7814 (ttmm) REVERT: D 130 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8473 (tp) REVERT: E 28 ASP cc_start: 0.8766 (m-30) cc_final: 0.8504 (m-30) REVERT: E 59 TRP cc_start: 0.8019 (t-100) cc_final: 0.7812 (t-100) REVERT: E 69 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8358 (t) REVERT: E 130 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8399 (tp) REVERT: E 328 ASP cc_start: 0.9016 (m-30) cc_final: 0.8637 (p0) REVERT: E 344 GLN cc_start: 0.9022 (mm110) cc_final: 0.8744 (mm110) REVERT: F 28 ASP cc_start: 0.8629 (m-30) cc_final: 0.8059 (m-30) REVERT: F 29 ARG cc_start: 0.7948 (mmp80) cc_final: 0.7674 (mmp80) REVERT: F 130 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8456 (tp) REVERT: F 166 GLU cc_start: 0.8428 (tp30) cc_final: 0.7727 (tp30) REVERT: F 182 LYS cc_start: 0.8681 (tptt) cc_final: 0.8440 (tptt) REVERT: F 310 LYS cc_start: 0.8739 (tppt) cc_final: 0.8359 (tptp) REVERT: F 339 LEU cc_start: 0.9118 (mt) cc_final: 0.8917 (mt) REVERT: F 345 MET cc_start: 0.8236 (mmp) cc_final: 0.7981 (mmm) REVERT: G 28 ASP cc_start: 0.8754 (m-30) cc_final: 0.8450 (m-30) REVERT: G 59 TRP cc_start: 0.8049 (t-100) cc_final: 0.7719 (t-100) REVERT: G 166 GLU cc_start: 0.8505 (tp30) cc_final: 0.7878 (tp30) REVERT: G 182 LYS cc_start: 0.8573 (tptt) cc_final: 0.8333 (tptt) REVERT: G 202 ASN cc_start: 0.8833 (t0) cc_final: 0.8591 (t0) REVERT: G 274 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.5575 (mp0) REVERT: G 344 GLN cc_start: 0.8995 (mm110) cc_final: 0.8708 (mm110) REVERT: G 345 MET cc_start: 0.8507 (mmp) cc_final: 0.8145 (mmm) REVERT: H 28 ASP cc_start: 0.8593 (m-30) cc_final: 0.8295 (m-30) REVERT: H 130 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8446 (tp) REVERT: H 182 LYS cc_start: 0.8712 (tptt) cc_final: 0.8471 (tptt) REVERT: H 329 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8437 (mp10) REVERT: H 345 MET cc_start: 0.8299 (mmp) cc_final: 0.8057 (mmm) outliers start: 134 outliers final: 113 residues processed: 724 average time/residue: 0.2820 time to fit residues: 330.6384 Evaluate side-chains 779 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 650 time to evaluate : 2.528 ------------------------------------------------------------------------------- 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 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 196 THR 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 A residue 329 GLN 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 130 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 262 THR 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 329 GLN 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 78 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 130 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 69 VAL 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 130 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 268 THR 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 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 69 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 262 THR 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 E residue 329 GLN 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 130 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 248 CYS 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 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 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 130 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 248 CYS 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 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 Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 118 optimal weight: 0.3980 chunk 174 optimal weight: 0.9990 chunk 263 optimal weight: 0.0670 chunk 242 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 overall best weight: 0.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN E 329 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 22920 Z= 0.185 Angle : 0.678 11.386 31216 Z= 0.335 Chirality : 0.042 0.203 3448 Planarity : 0.003 0.046 3832 Dihedral : 4.753 17.898 2952 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 5.60 % Allowed : 26.96 % 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: -0.54 (0.17), residues: 2640 helix: 1.28 (0.13), residues: 1720 sheet: -3.13 (0.37), residues: 144 loop : -3.74 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 236 HIS 0.005 0.001 HIS H 79 PHE 0.016 0.001 PHE G 330 TYR 0.018 0.001 TYR H 300 ARG 0.012 0.000 ARG G 362 ********************** 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 791 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 657 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8736 (m-30) cc_final: 0.8490 (m-30) REVERT: A 54 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: A 69 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8506 (t) REVERT: A 130 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8390 (tp) REVERT: A 274 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.5563 (mp0) REVERT: A 300 TYR cc_start: 0.8635 (t80) cc_final: 0.8366 (t80) REVERT: A 328 ASP cc_start: 0.8941 (m-30) cc_final: 0.8654 (p0) REVERT: A 344 GLN cc_start: 0.9076 (mm110) cc_final: 0.8790 (mm110) REVERT: B 69 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8470 (t) REVERT: B 127 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7758 (ttmm) REVERT: B 130 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8413 (tp) REVERT: B 182 LYS cc_start: 0.8658 (tptt) cc_final: 0.8449 (tptt) REVERT: B 300 TYR cc_start: 0.8626 (t80) cc_final: 0.8420 (t80) REVERT: B 310 LYS cc_start: 0.8650 (tppt) cc_final: 0.8262 (tptp) REVERT: B 329 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: B 345 MET cc_start: 0.8379 (mmp) cc_final: 0.8123 (mmm) REVERT: C 28 ASP cc_start: 0.8702 (m-30) cc_final: 0.8466 (m-30) REVERT: C 59 TRP cc_start: 0.8372 (t-100) cc_final: 0.8041 (t-100) REVERT: C 69 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8434 (t) REVERT: C 130 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8410 (tp) REVERT: C 213 LEU cc_start: 0.8197 (tp) cc_final: 0.7904 (tt) REVERT: D 28 ASP cc_start: 0.8472 (m-30) cc_final: 0.8268 (m-30) REVERT: D 69 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8482 (t) REVERT: D 127 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7808 (ttmm) REVERT: D 130 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8465 (tp) REVERT: D 182 LYS cc_start: 0.8609 (tptt) cc_final: 0.8404 (tptt) REVERT: D 274 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: D 310 LYS cc_start: 0.8690 (tppt) cc_final: 0.8272 (tptp) REVERT: D 329 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8419 (mp10) REVERT: E 28 ASP cc_start: 0.8752 (m-30) cc_final: 0.8472 (m-30) REVERT: E 69 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8366 (t) REVERT: E 130 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8431 (tp) REVERT: E 182 LYS cc_start: 0.8551 (tptt) cc_final: 0.8301 (tptt) REVERT: E 328 ASP cc_start: 0.8941 (m-30) cc_final: 0.8663 (p0) REVERT: E 344 GLN cc_start: 0.9039 (mm110) cc_final: 0.8759 (mm110) REVERT: F 28 ASP cc_start: 0.8620 (m-30) cc_final: 0.8096 (m-30) REVERT: F 130 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8450 (tp) REVERT: F 166 GLU cc_start: 0.8426 (tp30) cc_final: 0.7711 (tp30) REVERT: F 182 LYS cc_start: 0.8717 (tptt) cc_final: 0.8470 (tptt) REVERT: F 310 LYS cc_start: 0.8707 (tppt) cc_final: 0.8317 (tptp) REVERT: F 329 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8414 (mp10) REVERT: F 345 MET cc_start: 0.8220 (mmp) cc_final: 0.7965 (mmm) REVERT: G 28 ASP cc_start: 0.8732 (m-30) cc_final: 0.8456 (m-30) REVERT: G 59 TRP cc_start: 0.7984 (t-100) cc_final: 0.7747 (t-100) REVERT: G 130 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8585 (tp) REVERT: G 202 ASN cc_start: 0.8817 (t0) cc_final: 0.8604 (t0) REVERT: G 274 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.5630 (mp0) REVERT: G 344 GLN cc_start: 0.8987 (mm110) cc_final: 0.8703 (mm110) REVERT: G 345 MET cc_start: 0.8497 (mmp) cc_final: 0.8145 (mmm) REVERT: H 28 ASP cc_start: 0.8581 (m-30) cc_final: 0.8029 (m-30) REVERT: H 130 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8432 (tp) REVERT: H 182 LYS cc_start: 0.8617 (tptt) cc_final: 0.8173 (tppt) REVERT: H 345 MET cc_start: 0.8270 (mmp) cc_final: 0.8021 (mmm) outliers start: 134 outliers final: 106 residues processed: 698 average time/residue: 0.2983 time to fit residues: 339.5944 Evaluate side-chains 766 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 640 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 121 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 196 THR 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 A residue 329 GLN 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 130 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 262 THR 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 329 GLN 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 78 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 130 ILE Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 277 PHE Chi-restraints excluded: chain C residue 280 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 58 CYS Chi-restraints excluded: chain D residue 69 VAL 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 130 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 268 THR 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 299 ILE Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 262 THR 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 E residue 329 GLN Chi-restraints excluded: chain E residue 334 LEU 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 130 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 248 CYS 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 329 GLN Chi-restraints excluded: chain F residue 364 ILE 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 130 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 277 PHE Chi-restraints excluded: chain G residue 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 130 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 248 CYS 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 290 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 304 ASN Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 329 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN C 73 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN E 73 ASN E 329 GLN F 206 GLN H 79 HIS H 348 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117046 restraints weight = 30634.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121119 restraints weight = 16672.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123925 restraints weight = 11223.044| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 22920 Z= 0.229 Angle : 0.691 11.424 31216 Z= 0.343 Chirality : 0.043 0.197 3448 Planarity : 0.003 0.049 3832 Dihedral : 4.787 19.384 2952 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.64 % Allowed : 27.17 % Favored : 67.18 % 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: -0.53 (0.17), residues: 2640 helix: 1.30 (0.13), residues: 1720 sheet: -3.22 (0.36), residues: 144 loop : -3.74 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP E 59 HIS 0.005 0.001 HIS H 79 PHE 0.020 0.001 PHE C 242 TYR 0.020 0.002 TYR E 208 ARG 0.011 0.000 ARG G 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5845.01 seconds wall clock time: 104 minutes 5.71 seconds (6245.71 seconds total)