Starting phenix.real_space_refine on Thu Feb 5 02:14:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dlc_46869/02_2026/9dlc_46869.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dlc_46869/02_2026/9dlc_46869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dlc_46869/02_2026/9dlc_46869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dlc_46869/02_2026/9dlc_46869.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dlc_46869/02_2026/9dlc_46869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dlc_46869/02_2026/9dlc_46869.map" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.050 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 40 5.16 5 C 9165 2.51 5 N 2437 2.21 5 O 2769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14415 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3598 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "B" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3598 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3581 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 21, 'TRANS': 450} Chain: "D" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3598 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'G3H': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'G3H': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'G3H': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'G3H': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.64, per 1000 atoms: 0.25 Number of scatterers: 14415 At special positions: 0 Unit cell: (103.228, 107.168, 105.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 4 15.00 O 2769 8.00 N 2437 7.00 C 9165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 574.6 milliseconds 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3476 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 22 sheets defined 46.9% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 37 through 58 Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 59 through 77 removed outlier: 3.664A pdb=" N TYR A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 92 through 116 removed outlier: 3.734A pdb=" N GLY A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 removed outlier: 4.209A pdb=" N LYS A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Proline residue: A 165 - end of helix removed outlier: 3.664A pdb=" N ALA A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 208 through 219 removed outlier: 6.432A pdb=" N ASP A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 293 through 308 removed outlier: 4.585A pdb=" N ASP A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LYS A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 326 through 343 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.816A pdb=" N SER A 400 " --> pdb=" O PHE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 455 through 463 Processing helix chain 'B' and resid 37 through 56 Proline residue: B 53 - end of helix Processing helix chain 'B' and resid 59 through 77 Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 92 through 115 removed outlier: 3.732A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 101 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.560A pdb=" N SER B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 132 " --> pdb=" O ALA B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 156 through 169 removed outlier: 4.458A pdb=" N LYS B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Proline residue: B 165 - end of helix removed outlier: 3.691A pdb=" N ALA B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 208 through 219 removed outlier: 6.343A pdb=" N ASP B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 293 through 309 removed outlier: 4.637A pdb=" N ASP B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 326 through 343 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.894A pdb=" N SER B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 423 Processing helix chain 'B' and resid 455 through 463 Processing helix chain 'C' and resid 37 through 57 Proline residue: C 53 - end of helix Processing helix chain 'C' and resid 59 through 77 removed outlier: 3.557A pdb=" N TYR C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 90 Processing helix chain 'C' and resid 92 through 115 removed outlier: 3.554A pdb=" N GLY C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 170 removed outlier: 4.267A pdb=" N LYS C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Proline residue: C 165 - end of helix removed outlier: 3.552A pdb=" N ALA C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.585A pdb=" N ALA C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 removed outlier: 3.773A pdb=" N ILE C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 241 removed outlier: 3.587A pdb=" N ARG C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 293 through 309 removed outlier: 4.576A pdb=" N ASP C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LYS C 298 " --> pdb=" O SER C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 326 through 342 Processing helix chain 'C' and resid 389 through 399 Processing helix chain 'C' and resid 412 through 423 Processing helix chain 'C' and resid 455 through 463 Processing helix chain 'D' and resid 37 through 57 Proline residue: D 53 - end of helix Processing helix chain 'D' and resid 59 through 77 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 92 through 114 removed outlier: 3.568A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 removed outlier: 3.704A pdb=" N LYS D 132 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 169 removed outlier: 4.296A pdb=" N LYS D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Proline residue: D 165 - end of helix removed outlier: 3.667A pdb=" N ALA D 169 " --> pdb=" O PRO D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 196 Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 293 through 309 removed outlier: 4.661A pdb=" N ASP D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS D 298 " --> pdb=" O SER D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 318 Processing helix chain 'D' and resid 326 through 343 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 389 through 399 Processing helix chain 'D' and resid 412 through 423 Processing helix chain 'D' and resid 455 through 463 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.847A pdb=" N GLY A 31 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 346 through 347 removed outlier: 6.456A pdb=" N VAL B 361 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 384 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE B 363 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ARG B 386 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS B 287 " --> pdb=" O PRO B 383 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE B 385 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL B 289 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL B 387 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL B 291 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP B 254 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 255 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER B 406 " --> pdb=" O HIS B 429 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP A 472 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C 428 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N ASP D 472 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ILE C 430 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER C 406 " --> pdb=" O HIS C 429 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA C 255 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE C 409 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU C 257 " --> pdb=" O PHE C 409 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASP C 254 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL C 289 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA C 256 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL C 291 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL C 258 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LYS C 287 " --> pdb=" O PRO C 383 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ILE C 385 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL C 289 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL C 387 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 291 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.719A pdb=" N ILE A 145 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASN A 226 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 147 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N THR A 228 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 149 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.531A pdb=" N VAL A 361 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE A 384 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE A 363 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG A 386 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLN A 365 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LYS A 287 " --> pdb=" O PRO A 383 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ILE A 385 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 289 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL A 387 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 291 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASP A 254 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL A 289 " --> pdb=" O ASP A 254 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA A 256 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL A 291 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 258 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 255 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER A 406 " --> pdb=" O HIS A 429 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 428 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ASP B 472 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE A 430 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA D 255 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N PHE D 409 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 257 " --> pdb=" O PHE D 409 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP D 254 " --> pdb=" O LYS D 287 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL D 289 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA D 256 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL D 291 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL D 258 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ILE D 385 " --> pdb=" O LYS D 287 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL D 289 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL D 387 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL D 291 " --> pdb=" O VAL D 387 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.653A pdb=" N LEU A 357 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 402 through 403 removed outlier: 3.823A pdb=" N GLY A 403 " --> pdb=" O VAL A 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 443 through 444 Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.713A pdb=" N THR B 2 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 31 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 204 removed outlier: 6.233A pdb=" N VAL B 146 " --> pdb=" O MET B 174 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LYS B 176 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 148 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 145 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASN B 226 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 147 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N THR B 228 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 149 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 353 through 354 removed outlier: 3.901A pdb=" N LEU B 357 " --> pdb=" O GLU B 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB5, first strand: chain 'C' and resid 18 through 22 removed outlier: 6.294A pdb=" N ILE C 19 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR C 32 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 21 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 202 through 204 Processing sheet with id=AB7, first strand: chain 'C' and resid 443 through 444 Processing sheet with id=AB8, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AB9, first strand: chain 'D' and resid 18 through 22 removed outlier: 3.847A pdb=" N GLY D 31 " --> pdb=" O ILE D 21 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 202 through 204 removed outlier: 6.414A pdb=" N VAL D 146 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LYS D 176 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA D 148 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE D 145 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ASN D 226 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU D 147 " --> pdb=" O ASN D 226 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR D 228 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE D 149 " --> pdb=" O THR D 228 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 346 through 347 Processing sheet with id=AC3, first strand: chain 'D' and resid 353 through 354 removed outlier: 3.889A pdb=" N LEU D 357 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 443 through 444 736 hydrogen bonds defined for protein. 2085 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2535 1.31 - 1.43: 3414 1.43 - 1.56: 8626 1.56 - 1.68: 4 1.68 - 1.81: 76 Bond restraints: 14655 Sorted by residual: bond pdb=" C ARG D 140 " pdb=" N GLU D 141 " ideal model delta sigma weight residual 1.331 1.256 0.075 1.59e-02 3.96e+03 2.23e+01 bond pdb=" O1P G3H B 501 " pdb=" P G3H B 501 " ideal model delta sigma weight residual 1.713 1.647 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" O1P G3H C 501 " pdb=" P G3H C 501 " ideal model delta sigma weight residual 1.713 1.648 0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" O1P G3H D 501 " pdb=" P G3H D 501 " ideal model delta sigma weight residual 1.713 1.649 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O1P G3H A 501 " pdb=" P G3H A 501 " ideal model delta sigma weight residual 1.713 1.650 0.063 2.00e-02 2.50e+03 1.01e+01 ... (remaining 14650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 19466 2.68 - 5.36: 332 5.36 - 8.04: 48 8.04 - 10.72: 6 10.72 - 13.40: 1 Bond angle restraints: 19853 Sorted by residual: angle pdb=" N VAL C 372 " pdb=" CA VAL C 372 " pdb=" C VAL C 372 " ideal model delta sigma weight residual 113.71 105.97 7.74 9.50e-01 1.11e+00 6.64e+01 angle pdb=" N GLY B 455 " pdb=" CA GLY B 455 " pdb=" C GLY B 455 " ideal model delta sigma weight residual 112.18 104.06 8.12 1.34e+00 5.57e-01 3.67e+01 angle pdb=" N GLY D 455 " pdb=" CA GLY D 455 " pdb=" C GLY D 455 " ideal model delta sigma weight residual 112.18 104.76 7.42 1.34e+00 5.57e-01 3.07e+01 angle pdb=" N VAL A 156 " pdb=" CA VAL A 156 " pdb=" C VAL A 156 " ideal model delta sigma weight residual 113.53 108.25 5.28 9.80e-01 1.04e+00 2.91e+01 angle pdb=" N ASN D 411 " pdb=" CA ASN D 411 " pdb=" C ASN D 411 " ideal model delta sigma weight residual 114.56 108.09 6.47 1.27e+00 6.20e-01 2.60e+01 ... (remaining 19848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7522 17.75 - 35.50: 950 35.50 - 53.25: 307 53.25 - 70.99: 85 70.99 - 88.74: 36 Dihedral angle restraints: 8900 sinusoidal: 3502 harmonic: 5398 Sorted by residual: dihedral pdb=" CA VAL D 446 " pdb=" C VAL D 446 " pdb=" N LYS D 447 " pdb=" CA LYS D 447 " ideal model delta harmonic sigma weight residual -180.00 -138.57 -41.43 0 5.00e+00 4.00e-02 6.87e+01 dihedral pdb=" CA VAL A 446 " pdb=" C VAL A 446 " pdb=" N LYS A 447 " pdb=" CA LYS A 447 " ideal model delta harmonic sigma weight residual -180.00 -139.05 -40.95 0 5.00e+00 4.00e-02 6.71e+01 dihedral pdb=" CA SER B 15 " pdb=" C SER B 15 " pdb=" N GLU B 16 " pdb=" CA GLU B 16 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 8897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1725 0.061 - 0.122: 519 0.122 - 0.182: 43 0.182 - 0.243: 2 0.243 - 0.304: 4 Chirality restraints: 2293 Sorted by residual: chirality pdb=" C2 G3H D 501 " pdb=" C1 G3H D 501 " pdb=" C3 G3H D 501 " pdb=" O2 G3H D 501 " both_signs ideal model delta sigma weight residual False -2.21 -2.52 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C2 G3H C 501 " pdb=" C1 G3H C 501 " pdb=" C3 G3H C 501 " pdb=" O2 G3H C 501 " both_signs ideal model delta sigma weight residual False -2.21 -2.51 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2 G3H B 501 " pdb=" C1 G3H B 501 " pdb=" C3 G3H B 501 " pdb=" O2 G3H B 501 " both_signs ideal model delta sigma weight residual False -2.21 -2.51 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 2290 not shown) Planarity restraints: 2581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 314 " -0.052 5.00e-02 4.00e+02 7.87e-02 9.92e+00 pdb=" N PRO A 315 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 164 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO D 165 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 165 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 165 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 359 " -0.023 2.00e-02 2.50e+03 1.09e-02 3.00e+00 pdb=" CG TRP D 359 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP D 359 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP D 359 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 359 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 359 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 359 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 359 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 359 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 359 " -0.003 2.00e-02 2.50e+03 ... (remaining 2578 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 277 2.65 - 3.21: 13114 3.21 - 3.78: 24237 3.78 - 4.34: 35512 4.34 - 4.90: 56948 Nonbonded interactions: 130088 Sorted by model distance: nonbonded pdb=" OD1 ASP A 42 " pdb=" OH TYR A 215 " model vdw 2.089 3.040 nonbonded pdb=" O GLY B 251 " pdb=" OG SER B 449 " model vdw 2.119 3.040 nonbonded pdb=" OD1 ASP B 326 " pdb=" OG SER B 329 " model vdw 2.179 3.040 nonbonded pdb=" OD2 ASP C 42 " pdb=" OH TYR C 215 " model vdw 2.181 3.040 nonbonded pdb=" OG SER A 15 " pdb=" OE1 GLU A 40 " model vdw 2.200 3.040 ... (remaining 130083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 472 or resid 501)) selection = (chain 'B' and (resid 1 through 472 or resid 501)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 472 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.220 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.010 0.084 14655 Z= 0.415 Angle : 0.919 13.404 19853 Z= 0.538 Chirality : 0.054 0.304 2293 Planarity : 0.005 0.079 2581 Dihedral : 19.041 88.741 5424 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.45 % Favored : 95.33 % Rotamer: Outliers : 4.02 % Allowed : 24.03 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1886 helix: 0.02 (0.18), residues: 803 sheet: -1.52 (0.24), residues: 421 loop : -1.20 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 236 TYR 0.020 0.003 TYR C 154 PHE 0.018 0.003 PHE D 443 TRP 0.023 0.003 TRP D 359 HIS 0.009 0.002 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00956 (14655) covalent geometry : angle 0.91916 (19853) hydrogen bonds : bond 0.16323 ( 736) hydrogen bonds : angle 7.24416 ( 2085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 0.549 Fit side-chains REVERT: A 305 GLU cc_start: 0.6688 (mp0) cc_final: 0.6465 (mm-30) REVERT: B 17 GLN cc_start: 0.7795 (mt0) cc_final: 0.7578 (mt0) REVERT: B 105 ASP cc_start: 0.7981 (p0) cc_final: 0.7709 (p0) REVERT: B 220 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7778 (mppt) REVERT: B 474 LYS cc_start: 0.5858 (OUTLIER) cc_final: 0.5406 (mptt) REVERT: C 42 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7259 (t70) REVERT: C 190 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7266 (mptp) REVERT: C 371 LYS cc_start: 0.8321 (ptpp) cc_final: 0.7939 (ptmt) REVERT: D 174 MET cc_start: 0.8084 (mmm) cc_final: 0.7873 (mmm) outliers start: 60 outliers final: 42 residues processed: 204 average time/residue: 0.6970 time to fit residues: 154.9297 Evaluate side-chains 187 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 417 PHE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 203 ASN B 180 GLN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121801 restraints weight = 15530.340| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.54 r_work: 0.3387 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14655 Z= 0.186 Angle : 0.616 9.495 19853 Z= 0.321 Chirality : 0.045 0.200 2293 Planarity : 0.005 0.059 2581 Dihedral : 7.826 56.423 2091 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.39 % Favored : 96.39 % Rotamer: Outliers : 4.75 % Allowed : 21.35 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1886 helix: 0.70 (0.18), residues: 803 sheet: -1.47 (0.23), residues: 448 loop : -0.93 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 208 TYR 0.010 0.001 TYR B 154 PHE 0.011 0.002 PHE A 316 TRP 0.017 0.002 TRP D 359 HIS 0.002 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00431 (14655) covalent geometry : angle 0.61559 (19853) hydrogen bonds : bond 0.05179 ( 736) hydrogen bonds : angle 5.29875 ( 2085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 161 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7726 (mtp180) REVERT: A 16 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: A 205 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8185 (pt) REVERT: A 305 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6797 (mm-30) REVERT: A 417 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8040 (m-80) REVERT: A 444 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8753 (pt) REVERT: B 220 LYS cc_start: 0.8535 (mmtt) cc_final: 0.7988 (mppt) REVERT: B 329 SER cc_start: 0.8550 (m) cc_final: 0.8258 (t) REVERT: C 85 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6908 (tp) REVERT: C 190 LYS cc_start: 0.8043 (mptp) cc_final: 0.7839 (mmtp) REVERT: C 236 ARG cc_start: 0.7669 (ttt90) cc_final: 0.7458 (ttt90) REVERT: D 75 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7420 (mt-10) REVERT: D 304 GLN cc_start: 0.7385 (tm-30) cc_final: 0.6798 (tm-30) REVERT: D 378 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.7785 (t80) REVERT: D 415 LYS cc_start: 0.7959 (tppt) cc_final: 0.7715 (tptm) outliers start: 71 outliers final: 26 residues processed: 214 average time/residue: 0.7382 time to fit residues: 170.8245 Evaluate side-chains 182 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 6 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 203 ASN B 153 ASN B 157 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119392 restraints weight = 15670.424| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.56 r_work: 0.3354 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 14655 Z= 0.273 Angle : 0.672 10.337 19853 Z= 0.347 Chirality : 0.048 0.212 2293 Planarity : 0.005 0.053 2581 Dihedral : 7.189 57.063 2048 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.14 % Favored : 95.65 % Rotamer: Outliers : 4.69 % Allowed : 21.75 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1886 helix: 0.74 (0.18), residues: 805 sheet: -1.35 (0.24), residues: 421 loop : -0.88 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 208 TYR 0.014 0.002 TYR B 154 PHE 0.014 0.002 PHE D 443 TRP 0.019 0.002 TRP D 359 HIS 0.005 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00651 (14655) covalent geometry : angle 0.67217 (19853) hydrogen bonds : bond 0.05608 ( 736) hydrogen bonds : angle 5.23234 ( 2085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 150 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7762 (mtp180) REVERT: A 16 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: A 116 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.6679 (mtt90) REVERT: A 203 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7767 (m-40) REVERT: A 305 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6848 (mm-30) REVERT: A 417 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8137 (m-80) REVERT: B 220 LYS cc_start: 0.8613 (mmtt) cc_final: 0.8023 (mppt) REVERT: B 329 SER cc_start: 0.8565 (m) cc_final: 0.8275 (t) REVERT: C 236 ARG cc_start: 0.7723 (ttt90) cc_final: 0.7482 (ttt90) REVERT: C 371 LYS cc_start: 0.8330 (ptpp) cc_final: 0.8070 (ptmt) REVERT: D 75 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7519 (mt-10) REVERT: D 134 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7993 (mmtp) REVERT: D 378 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.7969 (t80) REVERT: D 415 LYS cc_start: 0.8054 (tppt) cc_final: 0.7729 (tptm) outliers start: 70 outliers final: 32 residues processed: 200 average time/residue: 0.7015 time to fit residues: 151.8246 Evaluate side-chains 183 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 417 PHE Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 203 ASN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124644 restraints weight = 15569.520| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.57 r_work: 0.3431 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14655 Z= 0.135 Angle : 0.545 8.378 19853 Z= 0.282 Chirality : 0.043 0.190 2293 Planarity : 0.004 0.052 2581 Dihedral : 6.478 59.005 2044 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.02 % Allowed : 22.49 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.20), residues: 1886 helix: 1.14 (0.19), residues: 806 sheet: -1.16 (0.24), residues: 427 loop : -0.64 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 208 TYR 0.007 0.001 TYR B 154 PHE 0.015 0.001 PHE A 202 TRP 0.014 0.001 TRP D 359 HIS 0.002 0.001 HIS D 266 Details of bonding type rmsd covalent geometry : bond 0.00310 (14655) covalent geometry : angle 0.54488 (19853) hydrogen bonds : bond 0.04359 ( 736) hydrogen bonds : angle 4.79989 ( 2085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7782 (mtp180) REVERT: A 205 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8097 (pt) REVERT: A 282 ARG cc_start: 0.8094 (mtm180) cc_final: 0.7714 (mtm-85) REVERT: A 305 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6826 (mm-30) REVERT: A 338 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6771 (mt-10) REVERT: A 417 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: B 17 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: B 42 ASP cc_start: 0.7633 (t70) cc_final: 0.7413 (m-30) REVERT: B 174 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7601 (mtm) REVERT: B 220 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8015 (mppt) REVERT: B 235 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6918 (mt-10) REVERT: C 371 LYS cc_start: 0.8181 (ptpp) cc_final: 0.7972 (ptmt) REVERT: D 18 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7289 (pt0) REVERT: D 75 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7374 (mt-10) REVERT: D 134 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8030 (mmtp) REVERT: D 236 ARG cc_start: 0.8082 (mmm160) cc_final: 0.7847 (ttt-90) REVERT: D 304 GLN cc_start: 0.7361 (tm-30) cc_final: 0.6819 (tm-30) REVERT: D 415 LYS cc_start: 0.7928 (tppt) cc_final: 0.7542 (tptm) REVERT: D 418 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7171 (pt0) outliers start: 60 outliers final: 24 residues processed: 210 average time/residue: 0.6825 time to fit residues: 154.8614 Evaluate side-chains 183 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 34 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120319 restraints weight = 15822.832| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.55 r_work: 0.3367 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14655 Z= 0.258 Angle : 0.648 9.764 19853 Z= 0.333 Chirality : 0.047 0.210 2293 Planarity : 0.005 0.052 2581 Dihedral : 6.672 59.355 2036 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 3.95 % Allowed : 22.29 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1886 helix: 1.09 (0.19), residues: 787 sheet: -1.19 (0.24), residues: 421 loop : -0.74 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 208 TYR 0.013 0.002 TYR B 154 PHE 0.013 0.002 PHE D 443 TRP 0.017 0.002 TRP D 359 HIS 0.005 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00616 (14655) covalent geometry : angle 0.64837 (19853) hydrogen bonds : bond 0.05340 ( 736) hydrogen bonds : angle 5.05109 ( 2085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 3 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7746 (mtp180) REVERT: A 16 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: A 203 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.7833 (m-40) REVERT: A 305 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6847 (mm-30) REVERT: A 417 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: B 220 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8046 (mppt) REVERT: B 235 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6994 (mt-10) REVERT: C 1 MET cc_start: 0.5132 (mtm) cc_final: 0.3808 (tmt) REVERT: C 18 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7152 (mt-10) REVERT: C 93 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7769 (tp) REVERT: C 190 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7881 (mmtt) REVERT: C 371 LYS cc_start: 0.8295 (ptpp) cc_final: 0.8086 (ptmt) REVERT: D 75 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7474 (mt-10) REVERT: D 134 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7991 (mmtp) REVERT: D 378 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.7988 (t80) REVERT: D 415 LYS cc_start: 0.7996 (tppt) cc_final: 0.7686 (tptm) REVERT: D 418 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7594 (pt0) outliers start: 59 outliers final: 33 residues processed: 194 average time/residue: 0.6328 time to fit residues: 132.6395 Evaluate side-chains 190 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 417 PHE Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 125 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 158 optimal weight: 0.0980 chunk 140 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127098 restraints weight = 15494.262| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.57 r_work: 0.3458 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14655 Z= 0.115 Angle : 0.519 8.318 19853 Z= 0.268 Chirality : 0.042 0.184 2293 Planarity : 0.004 0.052 2581 Dihedral : 5.953 58.798 2036 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.28 % Allowed : 22.96 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1886 helix: 1.32 (0.19), residues: 808 sheet: -1.09 (0.24), residues: 431 loop : -0.40 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 208 TYR 0.007 0.001 TYR C 278 PHE 0.024 0.001 PHE A 202 TRP 0.012 0.001 TRP D 359 HIS 0.002 0.000 HIS D 429 Details of bonding type rmsd covalent geometry : bond 0.00259 (14655) covalent geometry : angle 0.51891 (19853) hydrogen bonds : bond 0.04013 ( 736) hydrogen bonds : angle 4.61164 ( 2085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.495 Fit side-chains REVERT: A 1 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6077 (tpt) REVERT: A 3 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7755 (mtp180) REVERT: A 120 GLN cc_start: 0.8524 (mt0) cc_final: 0.8307 (mt0) REVERT: A 205 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8107 (pt) REVERT: A 282 ARG cc_start: 0.8034 (mtm180) cc_final: 0.7680 (mtm-85) REVERT: A 417 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: A 444 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8669 (pt) REVERT: B 42 ASP cc_start: 0.7608 (t70) cc_final: 0.7405 (m-30) REVERT: B 220 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8009 (mppt) REVERT: B 399 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: C 128 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8212 (pt0) REVERT: C 190 LYS cc_start: 0.8056 (mmtp) cc_final: 0.7830 (mmtt) REVERT: D 75 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7350 (mt-10) REVERT: D 134 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8014 (mmtp) REVERT: D 304 GLN cc_start: 0.7341 (tm-30) cc_final: 0.6775 (tm-30) REVERT: D 368 LYS cc_start: 0.7435 (mmtp) cc_final: 0.6723 (mppt) REVERT: D 378 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7599 (t80) REVERT: D 401 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: D 415 LYS cc_start: 0.7758 (tppt) cc_final: 0.7477 (tptm) outliers start: 49 outliers final: 23 residues processed: 195 average time/residue: 0.6394 time to fit residues: 134.8511 Evaluate side-chains 178 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 107 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 160 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN D 281 GLN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121674 restraints weight = 15480.402| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.57 r_work: 0.3385 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14655 Z= 0.210 Angle : 0.608 9.088 19853 Z= 0.311 Chirality : 0.045 0.202 2293 Planarity : 0.005 0.051 2581 Dihedral : 6.308 59.374 2033 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.82 % Favored : 96.02 % Rotamer: Outliers : 3.15 % Allowed : 23.36 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1886 helix: 1.34 (0.19), residues: 786 sheet: -1.13 (0.24), residues: 448 loop : -0.55 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 208 TYR 0.012 0.002 TYR B 154 PHE 0.012 0.002 PHE A 202 TRP 0.016 0.002 TRP D 359 HIS 0.004 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00497 (14655) covalent geometry : angle 0.60829 (19853) hydrogen bonds : bond 0.04932 ( 736) hydrogen bonds : angle 4.85456 ( 2085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 0.479 Fit side-chains REVERT: A 3 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7789 (mtp180) REVERT: A 16 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: A 205 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8131 (pt) REVERT: A 282 ARG cc_start: 0.8097 (mtm180) cc_final: 0.7703 (mtm-85) REVERT: A 305 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: A 417 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: B 42 ASP cc_start: 0.7611 (t70) cc_final: 0.7398 (m-30) REVERT: B 174 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7621 (mtm) REVERT: B 220 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8032 (mppt) REVERT: C 1 MET cc_start: 0.5130 (mtm) cc_final: 0.3790 (tmt) REVERT: C 18 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7205 (mt-10) REVERT: C 128 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8240 (pt0) REVERT: C 190 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7828 (mmtt) REVERT: D 75 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7497 (mt-10) REVERT: D 120 GLN cc_start: 0.8180 (mt0) cc_final: 0.7966 (mp-120) REVERT: D 134 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7996 (mmtp) REVERT: D 174 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7768 (mmm) REVERT: D 368 LYS cc_start: 0.7518 (mmtp) cc_final: 0.6761 (mppt) REVERT: D 378 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.7906 (t80) REVERT: D 415 LYS cc_start: 0.7944 (tppt) cc_final: 0.7696 (tptm) outliers start: 47 outliers final: 30 residues processed: 181 average time/residue: 0.6701 time to fit residues: 131.1113 Evaluate side-chains 187 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 109 optimal weight: 0.0470 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 203 ASN B 157 ASN B 431 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129299 restraints weight = 15333.812| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.55 r_work: 0.3479 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14655 Z= 0.107 Angle : 0.507 8.073 19853 Z= 0.260 Chirality : 0.042 0.179 2293 Planarity : 0.004 0.053 2581 Dihedral : 5.676 58.943 2033 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.68 % Allowed : 23.96 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1886 helix: 1.58 (0.19), residues: 790 sheet: -0.94 (0.25), residues: 437 loop : -0.32 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 208 TYR 0.007 0.001 TYR D 4 PHE 0.031 0.001 PHE A 202 TRP 0.011 0.001 TRP D 359 HIS 0.002 0.000 HIS D 429 Details of bonding type rmsd covalent geometry : bond 0.00235 (14655) covalent geometry : angle 0.50676 (19853) hydrogen bonds : bond 0.03806 ( 736) hydrogen bonds : angle 4.49732 ( 2085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.426 Fit side-chains REVERT: A 3 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7731 (mtp180) REVERT: A 93 ILE cc_start: 0.7553 (tp) cc_final: 0.7329 (tp) REVERT: A 120 GLN cc_start: 0.8489 (mt0) cc_final: 0.8274 (mt0) REVERT: A 205 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7943 (pt) REVERT: A 282 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7596 (mtm-85) REVERT: A 329 SER cc_start: 0.8309 (t) cc_final: 0.8092 (p) REVERT: A 444 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8570 (pt) REVERT: B 42 ASP cc_start: 0.7581 (t70) cc_final: 0.7377 (m-30) REVERT: B 220 LYS cc_start: 0.8595 (mmtt) cc_final: 0.7994 (mppt) REVERT: C 190 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7775 (mmtt) REVERT: D 75 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7267 (mt-10) REVERT: D 120 GLN cc_start: 0.8140 (mt0) cc_final: 0.7922 (mp-120) REVERT: D 304 GLN cc_start: 0.7284 (tm-30) cc_final: 0.6736 (tm-30) REVERT: D 368 LYS cc_start: 0.7257 (mmtp) cc_final: 0.6672 (mppt) REVERT: D 378 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7408 (t80) REVERT: D 401 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: D 415 LYS cc_start: 0.7839 (tppt) cc_final: 0.7522 (tptm) outliers start: 40 outliers final: 21 residues processed: 199 average time/residue: 0.6734 time to fit residues: 144.9684 Evaluate side-chains 181 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 78 optimal weight: 0.0040 chunk 75 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN B 157 ASN C 120 GLN D 153 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123099 restraints weight = 15706.051| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.54 r_work: 0.3398 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14655 Z= 0.191 Angle : 0.596 9.083 19853 Z= 0.304 Chirality : 0.045 0.197 2293 Planarity : 0.005 0.052 2581 Dihedral : 6.118 59.712 2032 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 2.34 % Allowed : 24.70 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1886 helix: 1.47 (0.19), residues: 787 sheet: -0.90 (0.25), residues: 433 loop : -0.38 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 208 TYR 0.015 0.002 TYR D 4 PHE 0.012 0.002 PHE A 202 TRP 0.015 0.002 TRP D 359 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00448 (14655) covalent geometry : angle 0.59572 (19853) hydrogen bonds : bond 0.04733 ( 736) hydrogen bonds : angle 4.76160 ( 2085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.562 Fit side-chains REVERT: A 16 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: A 205 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7970 (pt) REVERT: A 282 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7656 (mtm-85) REVERT: A 305 GLU cc_start: 0.7147 (mp0) cc_final: 0.6813 (mm-30) REVERT: A 338 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6767 (mt-10) REVERT: B 174 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7572 (mtm) REVERT: B 220 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8026 (mppt) REVERT: C 1 MET cc_start: 0.5062 (mtm) cc_final: 0.3796 (tmt) REVERT: C 190 LYS cc_start: 0.8104 (mmtp) cc_final: 0.7832 (mmtt) REVERT: D 75 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7432 (mt-10) REVERT: D 120 GLN cc_start: 0.8168 (mt0) cc_final: 0.7966 (mp-120) REVERT: D 368 LYS cc_start: 0.7534 (mmtp) cc_final: 0.6832 (mppt) REVERT: D 378 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.7899 (t80) REVERT: D 415 LYS cc_start: 0.7955 (tppt) cc_final: 0.7696 (tptm) outliers start: 35 outliers final: 24 residues processed: 169 average time/residue: 0.7020 time to fit residues: 128.2236 Evaluate side-chains 172 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 29 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 70 optimal weight: 0.0970 chunk 72 optimal weight: 0.2980 chunk 100 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN B 157 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.149073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126613 restraints weight = 15489.020| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.53 r_work: 0.3447 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14655 Z= 0.126 Angle : 0.537 8.350 19853 Z= 0.274 Chirality : 0.043 0.185 2293 Planarity : 0.004 0.054 2581 Dihedral : 5.836 58.952 2032 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.01 % Allowed : 24.77 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 1886 helix: 1.55 (0.19), residues: 791 sheet: -0.92 (0.25), residues: 425 loop : -0.26 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 208 TYR 0.012 0.001 TYR D 4 PHE 0.013 0.001 PHE A 202 TRP 0.013 0.001 TRP D 359 HIS 0.002 0.000 HIS D 429 Details of bonding type rmsd covalent geometry : bond 0.00285 (14655) covalent geometry : angle 0.53705 (19853) hydrogen bonds : bond 0.04131 ( 736) hydrogen bonds : angle 4.59587 ( 2085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.636 Fit side-chains REVERT: A 120 GLN cc_start: 0.8534 (mt0) cc_final: 0.8300 (mt0) REVERT: A 205 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7907 (pt) REVERT: A 282 ARG cc_start: 0.7977 (mtm180) cc_final: 0.7598 (mtm-85) REVERT: A 305 GLU cc_start: 0.7091 (mp0) cc_final: 0.6740 (mm-30) REVERT: B 220 LYS cc_start: 0.8580 (mmtt) cc_final: 0.7984 (mppt) REVERT: C 1 MET cc_start: 0.5053 (mtm) cc_final: 0.3768 (tmt) REVERT: C 190 LYS cc_start: 0.8052 (mmtp) cc_final: 0.7796 (mmtt) REVERT: D 75 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7332 (mt-10) REVERT: D 120 GLN cc_start: 0.8158 (mt0) cc_final: 0.7921 (mp-120) REVERT: D 368 LYS cc_start: 0.7415 (mmtp) cc_final: 0.6737 (mppt) REVERT: D 378 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7649 (t80) REVERT: D 415 LYS cc_start: 0.7864 (tppt) cc_final: 0.7532 (tptm) outliers start: 30 outliers final: 23 residues processed: 169 average time/residue: 0.6755 time to fit residues: 123.2060 Evaluate side-chains 168 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 453 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN B 157 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123704 restraints weight = 15638.957| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.54 r_work: 0.3406 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14655 Z= 0.178 Angle : 0.587 9.649 19853 Z= 0.299 Chirality : 0.045 0.195 2293 Planarity : 0.005 0.053 2581 Dihedral : 6.062 59.136 2032 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 2.48 % Allowed : 24.56 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1886 helix: 1.49 (0.19), residues: 787 sheet: -0.78 (0.25), residues: 406 loop : -0.38 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 236 TYR 0.013 0.002 TYR D 4 PHE 0.011 0.002 PHE A 316 TRP 0.015 0.001 TRP D 359 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00416 (14655) covalent geometry : angle 0.58734 (19853) hydrogen bonds : bond 0.04622 ( 736) hydrogen bonds : angle 4.73121 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4548.92 seconds wall clock time: 78 minutes 17.53 seconds (4697.53 seconds total)