Starting phenix.real_space_refine on Tue Nov 19 15:39:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/11_2024/8hds_34679.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/11_2024/8hds_34679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/11_2024/8hds_34679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/11_2024/8hds_34679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/11_2024/8hds_34679.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/11_2024/8hds_34679.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 216 5.16 5 C 33540 2.51 5 N 9384 2.21 5 O 10392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 53532 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "a" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L, c, b, e, d, g, f, i, h, k, j, l Time building chain proxies: 13.19, per 1000 atoms: 0.25 Number of scatterers: 53532 At special positions: 0 Unit cell: (161.067, 161.067, 190.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 216 16.00 O 10392 8.00 N 9384 7.00 C 33540 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: 11.65 Conformation dependent library (CDL) restraints added in 6.5 seconds 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12768 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 49 sheets defined 36.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.84 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.563A pdb=" N TYR A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 61 removed outlier: 3.505A pdb=" N VAL A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Proline residue: A 58 - end of helix Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.753A pdb=" N THR A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER A 242 " --> pdb=" O GLU A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 243 through 259 removed outlier: 3.713A pdb=" N ARG A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.619A pdb=" N LEU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 387 " --> pdb=" O HIS A 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Proline residue: B 58 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.753A pdb=" N THR B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 removed outlier: 3.723A pdb=" N SER B 242 " --> pdb=" O GLU B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 243 through 259 removed outlier: 3.715A pdb=" N ARG B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.728A pdb=" N SER B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 387 " --> pdb=" O HIS B 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.502A pdb=" N VAL B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 443 removed outlier: 3.620A pdb=" N SER B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR C 82 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU C 98 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 218 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER C 242 " --> pdb=" O GLU C 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 239 through 242' Processing helix chain 'C' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 295 " --> pdb=" O GLN C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 387 " --> pdb=" O HIS C 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 410 " --> pdb=" O GLY C 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 411 " --> pdb=" O ASN C 407 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 443 removed outlier: 3.618A pdb=" N SER C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Proline residue: D 58 - end of helix Processing helix chain 'D' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR D 82 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU D 83 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 218 " --> pdb=" O ASP D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 removed outlier: 3.723A pdb=" N SER D 242 " --> pdb=" O GLU D 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 239 through 242' Processing helix chain 'D' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS D 249 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE D 293 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 387 " --> pdb=" O HIS D 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 388 " --> pdb=" O ALA D 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.502A pdb=" N VAL D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL D 410 " --> pdb=" O GLY D 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 412 " --> pdb=" O GLN D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Proline residue: E 58 - end of helix Processing helix chain 'E' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR E 82 " --> pdb=" O ARG E 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU E 83 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 102 removed outlier: 3.694A pdb=" N LEU E 98 " --> pdb=" O GLN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 206 through 221 removed outlier: 3.685A pdb=" N SER E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 218 " --> pdb=" O ASP E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER E 242 " --> pdb=" O GLU E 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.713A pdb=" N ARG E 247 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS E 249 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG E 253 " --> pdb=" O LYS E 249 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE E 293 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 335 removed outlier: 3.728A pdb=" N SER E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 384 " --> pdb=" O GLY E 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU E 385 " --> pdb=" O LYS E 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 387 " --> pdb=" O HIS E 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN E 388 " --> pdb=" O ALA E 384 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL E 389 " --> pdb=" O GLU E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL E 410 " --> pdb=" O GLY E 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 411 " --> pdb=" O ASN E 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER E 442 " --> pdb=" O SER E 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 48 removed outlier: 3.563A pdb=" N TYR F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Proline residue: F 58 - end of helix Processing helix chain 'F' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR F 82 " --> pdb=" O ARG F 78 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU F 83 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER F 242 " --> pdb=" O GLU F 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 242' Processing helix chain 'F' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG F 247 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS F 249 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG F 253 " --> pdb=" O LYS F 249 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE F 293 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE F 295 " --> pdb=" O GLN F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 391 removed outlier: 3.621A pdb=" N LEU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 384 " --> pdb=" O GLY F 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU F 385 " --> pdb=" O LYS F 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL F 387 " --> pdb=" O HIS F 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN F 388 " --> pdb=" O ALA F 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL F 410 " --> pdb=" O GLY F 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR F 412 " --> pdb=" O GLN F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER F 442 " --> pdb=" O SER F 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 61 removed outlier: 3.505A pdb=" N VAL G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Proline residue: G 58 - end of helix Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 141 No H-bonds generated for 'chain 'G' and resid 139 through 141' Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER G 242 " --> pdb=" O GLU G 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 239 through 242' Processing helix chain 'G' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG G 247 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS G 249 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG G 253 " --> pdb=" O LYS G 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU G 256 " --> pdb=" O ASP G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE G 293 " --> pdb=" O MET G 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 294 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE G 295 " --> pdb=" O GLN G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU G 382 " --> pdb=" O GLU G 378 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA G 384 " --> pdb=" O GLY G 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU G 385 " --> pdb=" O LYS G 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 387 " --> pdb=" O HIS G 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN G 388 " --> pdb=" O ALA G 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL G 389 " --> pdb=" O GLU G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 412 removed outlier: 3.502A pdb=" N VAL G 404 " --> pdb=" O GLU G 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL G 410 " --> pdb=" O GLY G 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU G 411 " --> pdb=" O ASN G 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR G 412 " --> pdb=" O GLN G 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER G 442 " --> pdb=" O SER G 438 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR G 443 " --> pdb=" O ALA G 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Proline residue: H 58 - end of helix Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU H 83 " --> pdb=" O ILE H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU H 98 " --> pdb=" O GLN H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 141 No H-bonds generated for 'chain 'H' and resid 139 through 141' Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing helix chain 'H' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER H 213 " --> pdb=" O ALA H 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA H 218 " --> pdb=" O ASP H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER H 242 " --> pdb=" O GLU H 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 239 through 242' Processing helix chain 'H' and resid 243 through 259 removed outlier: 3.713A pdb=" N ARG H 247 " --> pdb=" O SER H 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS H 249 " --> pdb=" O VAL H 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG H 253 " --> pdb=" O LYS H 249 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU H 256 " --> pdb=" O ASP H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE H 293 " --> pdb=" O MET H 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU H 294 " --> pdb=" O GLU H 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE H 295 " --> pdb=" O GLN H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER H 332 " --> pdb=" O ASP H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU H 382 " --> pdb=" O GLU H 378 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA H 384 " --> pdb=" O GLY H 380 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU H 385 " --> pdb=" O LYS H 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL H 387 " --> pdb=" O HIS H 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN H 388 " --> pdb=" O ALA H 384 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL H 389 " --> pdb=" O GLU H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL H 404 " --> pdb=" O GLU H 400 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL H 410 " --> pdb=" O GLY H 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU H 411 " --> pdb=" O ASN H 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER H 442 " --> pdb=" O SER H 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR I 43 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 61 removed outlier: 3.505A pdb=" N VAL I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Proline residue: I 58 - end of helix Processing helix chain 'I' and resid 77 through 87 removed outlier: 3.753A pdb=" N THR I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU I 83 " --> pdb=" O ILE I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 141 No H-bonds generated for 'chain 'I' and resid 139 through 141' Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'I' and resid 206 through 221 removed outlier: 3.683A pdb=" N SER I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA I 218 " --> pdb=" O ASP I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER I 242 " --> pdb=" O GLU I 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 239 through 242' Processing helix chain 'I' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG I 247 " --> pdb=" O SER I 243 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS I 249 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG I 253 " --> pdb=" O LYS I 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 256 " --> pdb=" O ASP I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 300 removed outlier: 3.958A pdb=" N ILE I 293 " --> pdb=" O MET I 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE I 295 " --> pdb=" O GLN I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 335 removed outlier: 3.728A pdb=" N SER I 332 " --> pdb=" O ASP I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU I 382 " --> pdb=" O GLU I 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA I 384 " --> pdb=" O GLY I 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU I 385 " --> pdb=" O LYS I 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL I 387 " --> pdb=" O HIS I 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN I 388 " --> pdb=" O ALA I 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL I 389 " --> pdb=" O GLU I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL I 404 " --> pdb=" O GLU I 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL I 410 " --> pdb=" O GLY I 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU I 411 " --> pdb=" O ASN I 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR I 412 " --> pdb=" O GLN I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER I 442 " --> pdb=" O SER I 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR I 443 " --> pdb=" O ALA I 439 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) Proline residue: J 58 - end of helix Processing helix chain 'J' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR J 82 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU J 83 " --> pdb=" O ILE J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 173 through 175 No H-bonds generated for 'chain 'J' and resid 173 through 175' Processing helix chain 'J' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA J 218 " --> pdb=" O ASP J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 242 removed outlier: 3.723A pdb=" N SER J 242 " --> pdb=" O GLU J 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 239 through 242' Processing helix chain 'J' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG J 247 " --> pdb=" O SER J 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS J 249 " --> pdb=" O VAL J 245 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG J 253 " --> pdb=" O LYS J 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU J 256 " --> pdb=" O ASP J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 300 removed outlier: 3.958A pdb=" N ILE J 293 " --> pdb=" O MET J 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE J 295 " --> pdb=" O GLN J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 335 removed outlier: 3.728A pdb=" N SER J 332 " --> pdb=" O ASP J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU J 382 " --> pdb=" O GLU J 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA J 384 " --> pdb=" O GLY J 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU J 385 " --> pdb=" O LYS J 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL J 387 " --> pdb=" O HIS J 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN J 388 " --> pdb=" O ALA J 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL J 389 " --> pdb=" O GLU J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 400 through 412 removed outlier: 3.502A pdb=" N VAL J 404 " --> pdb=" O GLU J 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL J 410 " --> pdb=" O GLY J 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU J 411 " --> pdb=" O ASN J 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR J 412 " --> pdb=" O GLN J 408 " (cutoff:3.500A) Processing helix chain 'J' and resid 436 through 443 removed outlier: 3.618A pdb=" N SER J 442 " --> pdb=" O SER J 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR J 443 " --> pdb=" O ALA J 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 61 removed outlier: 3.505A pdb=" N VAL K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Proline residue: K 58 - end of helix Processing helix chain 'K' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU K 98 " --> pdb=" O GLN K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 141 No H-bonds generated for 'chain 'K' and resid 139 through 141' Processing helix chain 'K' and resid 173 through 175 No H-bonds generated for 'chain 'K' and resid 173 through 175' Processing helix chain 'K' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA K 218 " --> pdb=" O ASP K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER K 242 " --> pdb=" O GLU K 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 239 through 242' Processing helix chain 'K' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG K 247 " --> pdb=" O SER K 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS K 249 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG K 253 " --> pdb=" O LYS K 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 256 " --> pdb=" O ASP K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE K 293 " --> pdb=" O MET K 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE K 295 " --> pdb=" O GLN K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER K 332 " --> pdb=" O ASP K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 391 removed outlier: 3.619A pdb=" N LEU K 382 " --> pdb=" O GLU K 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA K 384 " --> pdb=" O GLY K 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU K 385 " --> pdb=" O LYS K 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL K 387 " --> pdb=" O HIS K 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN K 388 " --> pdb=" O ALA K 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL K 389 " --> pdb=" O GLU K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 400 through 412 removed outlier: 3.502A pdb=" N VAL K 404 " --> pdb=" O GLU K 400 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL K 410 " --> pdb=" O GLY K 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU K 411 " --> pdb=" O ASN K 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR K 412 " --> pdb=" O GLN K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 443 removed outlier: 3.618A pdb=" N SER K 442 " --> pdb=" O SER K 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR K 443 " --> pdb=" O ALA K 439 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) Proline residue: L 58 - end of helix Processing helix chain 'L' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU L 83 " --> pdb=" O ILE L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 102 removed outlier: 3.694A pdb=" N LEU L 98 " --> pdb=" O GLN L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 141 No H-bonds generated for 'chain 'L' and resid 139 through 141' Processing helix chain 'L' and resid 173 through 175 No H-bonds generated for 'chain 'L' and resid 173 through 175' Processing helix chain 'L' and resid 206 through 221 removed outlier: 3.683A pdb=" N SER L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA L 218 " --> pdb=" O ASP L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER L 242 " --> pdb=" O GLU L 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 239 through 242' Processing helix chain 'L' and resid 243 through 259 removed outlier: 3.713A pdb=" N ARG L 247 " --> pdb=" O SER L 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS L 249 " --> pdb=" O VAL L 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG L 253 " --> pdb=" O LYS L 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU L 256 " --> pdb=" O ASP L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE L 293 " --> pdb=" O MET L 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE L 295 " --> pdb=" O GLN L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 335 removed outlier: 3.728A pdb=" N SER L 332 " --> pdb=" O ASP L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA L 384 " --> pdb=" O GLY L 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU L 385 " --> pdb=" O LYS L 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL L 387 " --> pdb=" O HIS L 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN L 388 " --> pdb=" O ALA L 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL L 389 " --> pdb=" O GLU L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL L 404 " --> pdb=" O GLU L 400 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL L 410 " --> pdb=" O GLY L 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU L 411 " --> pdb=" O ASN L 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR L 412 " --> pdb=" O GLN L 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 436 through 443 removed outlier: 3.618A pdb=" N SER L 442 " --> pdb=" O SER L 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR L 443 " --> pdb=" O ALA L 439 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 14 Processing helix chain 'a' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL a 25 " --> pdb=" O SER a 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN a 26 " --> pdb=" O ASP a 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 21 through 26' Processing helix chain 'a' and resid 28 through 33 Processing helix chain 'a' and resid 46 through 60 removed outlier: 3.979A pdb=" N ALA a 54 " --> pdb=" O LEU a 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU a 60 " --> pdb=" O MET a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE a 117 " --> pdb=" O TYR a 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU a 120 " --> pdb=" O THR a 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU a 123 " --> pdb=" O ARG a 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN a 124 " --> pdb=" O LEU a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 14 Processing helix chain 'b' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN b 26 " --> pdb=" O ASP b 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 21 through 26' Processing helix chain 'b' and resid 28 through 33 Processing helix chain 'b' and resid 46 through 60 removed outlier: 3.981A pdb=" N ALA b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU b 60 " --> pdb=" O MET b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE b 117 " --> pdb=" O TYR b 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU b 120 " --> pdb=" O THR b 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU b 123 " --> pdb=" O ARG b 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN b 124 " --> pdb=" O LEU b 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 14 Processing helix chain 'c' and resid 21 through 26 removed outlier: 3.902A pdb=" N VAL c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN c 26 " --> pdb=" O ASP c 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 21 through 26' Processing helix chain 'c' and resid 28 through 33 Processing helix chain 'c' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA c 54 " --> pdb=" O LEU c 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU c 60 " --> pdb=" O MET c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 125 removed outlier: 3.888A pdb=" N PHE c 117 " --> pdb=" O TYR c 113 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU c 120 " --> pdb=" O THR c 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU c 123 " --> pdb=" O ARG c 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN c 124 " --> pdb=" O LEU c 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 14 Processing helix chain 'd' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL d 25 " --> pdb=" O SER d 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN d 26 " --> pdb=" O ASP d 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 21 through 26' Processing helix chain 'd' and resid 28 through 33 Processing helix chain 'd' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA d 54 " --> pdb=" O LEU d 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU d 60 " --> pdb=" O MET d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE d 117 " --> pdb=" O TYR d 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU d 120 " --> pdb=" O THR d 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU d 123 " --> pdb=" O ARG d 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 14 Processing helix chain 'e' and resid 21 through 26 removed outlier: 3.902A pdb=" N VAL e 25 " --> pdb=" O SER e 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN e 26 " --> pdb=" O ASP e 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 21 through 26' Processing helix chain 'e' and resid 28 through 33 Processing helix chain 'e' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA e 54 " --> pdb=" O LEU e 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU e 60 " --> pdb=" O MET e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE e 117 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU e 120 " --> pdb=" O THR e 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU e 123 " --> pdb=" O ARG e 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN e 124 " --> pdb=" O LEU e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 14 Processing helix chain 'f' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL f 25 " --> pdb=" O SER f 21 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN f 26 " --> pdb=" O ASP f 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 21 through 26' Processing helix chain 'f' and resid 28 through 33 Processing helix chain 'f' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA f 54 " --> pdb=" O LEU f 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU f 60 " --> pdb=" O MET f 56 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE f 117 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU f 120 " --> pdb=" O THR f 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU f 123 " --> pdb=" O ARG f 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN f 124 " --> pdb=" O LEU f 120 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 14 Processing helix chain 'g' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL g 25 " --> pdb=" O SER g 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN g 26 " --> pdb=" O ASP g 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 21 through 26' Processing helix chain 'g' and resid 28 through 33 Processing helix chain 'g' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA g 54 " --> pdb=" O LEU g 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU g 60 " --> pdb=" O MET g 56 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 125 removed outlier: 3.888A pdb=" N PHE g 117 " --> pdb=" O TYR g 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU g 120 " --> pdb=" O THR g 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN g 124 " --> pdb=" O LEU g 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 14 Processing helix chain 'h' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL h 25 " --> pdb=" O SER h 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN h 26 " --> pdb=" O ASP h 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 21 through 26' Processing helix chain 'h' and resid 28 through 33 Processing helix chain 'h' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA h 54 " --> pdb=" O LEU h 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU h 60 " --> pdb=" O MET h 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE h 117 " --> pdb=" O TYR h 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU h 120 " --> pdb=" O THR h 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU h 123 " --> pdb=" O ARG h 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN h 124 " --> pdb=" O LEU h 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 14 Processing helix chain 'i' and resid 21 through 26 removed outlier: 3.902A pdb=" N VAL i 25 " --> pdb=" O SER i 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN i 26 " --> pdb=" O ASP i 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 21 through 26' Processing helix chain 'i' and resid 28 through 33 Processing helix chain 'i' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA i 54 " --> pdb=" O LEU i 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU i 60 " --> pdb=" O MET i 56 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 125 removed outlier: 3.888A pdb=" N PHE i 117 " --> pdb=" O TYR i 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU i 120 " --> pdb=" O THR i 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN i 124 " --> pdb=" O LEU i 120 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 14 Processing helix chain 'j' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN j 26 " --> pdb=" O ASP j 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 21 through 26' Processing helix chain 'j' and resid 28 through 33 Processing helix chain 'j' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA j 54 " --> pdb=" O LEU j 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU j 60 " --> pdb=" O MET j 56 " (cutoff:3.500A) Processing helix chain 'j' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE j 117 " --> pdb=" O TYR j 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU j 120 " --> pdb=" O THR j 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU j 123 " --> pdb=" O ARG j 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN j 124 " --> pdb=" O LEU j 120 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 14 Processing helix chain 'k' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL k 25 " --> pdb=" O SER k 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN k 26 " --> pdb=" O ASP k 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 21 through 26' Processing helix chain 'k' and resid 28 through 33 Processing helix chain 'k' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA k 54 " --> pdb=" O LEU k 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU k 60 " --> pdb=" O MET k 56 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 125 removed outlier: 3.888A pdb=" N PHE k 117 " --> pdb=" O TYR k 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU k 120 " --> pdb=" O THR k 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU k 123 " --> pdb=" O ARG k 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN k 124 " --> pdb=" O LEU k 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 9 through 14 Processing helix chain 'l' and resid 21 through 26 removed outlier: 3.902A pdb=" N VAL l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN l 26 " --> pdb=" O ASP l 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 26' Processing helix chain 'l' and resid 28 through 33 Processing helix chain 'l' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA l 54 " --> pdb=" O LEU l 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU l 60 " --> pdb=" O MET l 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 111 through 125 removed outlier: 3.888A pdb=" N PHE l 117 " --> pdb=" O TYR l 113 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU l 120 " --> pdb=" O THR l 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN l 124 " --> pdb=" O LEU l 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE A 364 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 137 removed outlier: 3.752A pdb=" N THR A 134 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 107 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 276 through 279 removed outlier: 3.533A pdb=" N THR A 276 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LEU L 267 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP A 230 " --> pdb=" O LEU L 267 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU L 269 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE A 232 " --> pdb=" O LEU L 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR B 276 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE B 364 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 137 removed outlier: 3.752A pdb=" N THR B 134 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 107 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 161 through 162 Processing sheet with id=AA9, first strand: chain 'B' and resid 267 through 270 removed outlier: 3.532A pdb=" N THR C 276 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE C 364 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR C 134 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 107 " --> pdb=" O VAL C 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AB4, first strand: chain 'C' and resid 267 through 270 removed outlier: 3.532A pdb=" N THR D 276 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 68 through 69 removed outlier: 3.575A pdb=" N ILE D 364 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR D 134 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 107 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 161 through 162 Processing sheet with id=AB8, first strand: chain 'D' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR E 276 " --> pdb=" O VAL E 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE E 364 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR E 134 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 107 " --> pdb=" O VAL E 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 161 through 162 Processing sheet with id=AC3, first strand: chain 'E' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR F 276 " --> pdb=" O VAL F 231 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE F 364 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR F 134 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 107 " --> pdb=" O VAL F 178 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 161 through 162 Processing sheet with id=AC7, first strand: chain 'F' and resid 267 through 270 removed outlier: 3.532A pdb=" N THR G 276 " --> pdb=" O VAL G 231 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE G 364 " --> pdb=" O ASP G 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR G 134 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 107 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 161 through 162 Processing sheet with id=AD2, first strand: chain 'G' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR H 276 " --> pdb=" O VAL H 231 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 68 through 69 removed outlier: 3.577A pdb=" N ILE H 364 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 132 through 137 removed outlier: 3.752A pdb=" N THR H 134 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE H 107 " --> pdb=" O VAL H 178 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 161 through 162 Processing sheet with id=AD6, first strand: chain 'H' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR I 276 " --> pdb=" O VAL I 231 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE I 364 " --> pdb=" O ASP I 68 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR I 134 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE I 107 " --> pdb=" O VAL I 178 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 161 through 162 Processing sheet with id=AE1, first strand: chain 'I' and resid 267 through 270 removed outlier: 3.534A pdb=" N THR J 276 " --> pdb=" O VAL J 231 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE J 364 " --> pdb=" O ASP J 68 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR J 134 " --> pdb=" O VAL J 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE J 107 " --> pdb=" O VAL J 178 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 161 through 162 Processing sheet with id=AE5, first strand: chain 'J' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR K 276 " --> pdb=" O VAL K 231 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE K 364 " --> pdb=" O ASP K 68 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 132 through 137 removed outlier: 3.752A pdb=" N THR K 134 " --> pdb=" O VAL K 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE K 107 " --> pdb=" O VAL K 178 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 161 through 162 Processing sheet with id=AE9, first strand: chain 'K' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR L 276 " --> pdb=" O VAL L 231 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE L 364 " --> pdb=" O ASP L 68 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 132 through 137 removed outlier: 3.752A pdb=" N THR L 134 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE L 107 " --> pdb=" O VAL L 178 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 161 through 162 Processing sheet with id=AF4, first strand: chain 'a' and resid 79 through 83 removed outlier: 6.680A pdb=" N THR a 90 " --> pdb=" O LEU a 80 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG a 82 " --> pdb=" O SER a 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER a 88 " --> pdb=" O ARG a 82 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU l 80 " --> pdb=" O PHE a 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR l 90 " --> pdb=" O LEU l 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG l 82 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER l 88 " --> pdb=" O ARG l 82 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU k 80 " --> pdb=" O PHE l 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR k 90 " --> pdb=" O LEU k 80 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG k 82 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER k 88 " --> pdb=" O ARG k 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU j 80 " --> pdb=" O PHE k 91 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR j 90 " --> pdb=" O LEU j 80 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG j 82 " --> pdb=" O SER j 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER j 88 " --> pdb=" O ARG j 82 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU i 80 " --> pdb=" O PHE j 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR i 90 " --> pdb=" O LEU i 80 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG i 82 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER i 88 " --> pdb=" O ARG i 82 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU h 80 " --> pdb=" O PHE i 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR h 90 " --> pdb=" O LEU h 80 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG h 82 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER h 88 " --> pdb=" O ARG h 82 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU g 80 " --> pdb=" O PHE h 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR g 90 " --> pdb=" O LEU g 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG g 82 " --> pdb=" O SER g 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER g 88 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR g 89 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG f 82 " --> pdb=" O THR g 89 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU f 80 " --> pdb=" O PHE g 91 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR f 90 " --> pdb=" O LEU f 80 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG f 82 " --> pdb=" O SER f 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER f 88 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU e 80 " --> pdb=" O PHE f 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR e 90 " --> pdb=" O LEU e 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG e 82 " --> pdb=" O SER e 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER e 88 " --> pdb=" O ARG e 82 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU d 80 " --> pdb=" O PHE e 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR d 90 " --> pdb=" O LEU d 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG d 82 " --> pdb=" O SER d 88 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER d 88 " --> pdb=" O ARG d 82 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU c 80 " --> pdb=" O PHE d 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR c 90 " --> pdb=" O LEU c 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG c 82 " --> pdb=" O SER c 88 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER c 88 " --> pdb=" O ARG c 82 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU b 80 " --> pdb=" O PHE c 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG b 82 " --> pdb=" O SER b 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER b 88 " --> pdb=" O ARG b 82 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU a 80 " --> pdb=" O PHE b 91 " (cutoff:3.500A) 1410 hydrogen bonds defined for protein. 4089 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: 16.59 Time building geometry restraints manager: 13.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14978 1.33 - 1.45: 8920 1.45 - 1.57: 30258 1.57 - 1.69: 0 1.69 - 1.80: 420 Bond restraints: 54576 Sorted by residual: bond pdb=" CB PHE E 30 " pdb=" CG PHE E 30 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.22e+00 bond pdb=" CB PHE G 30 " pdb=" CG PHE G 30 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.21e+00 bond pdb=" CB PHE F 30 " pdb=" CG PHE F 30 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.16e+00 bond pdb=" CB PHE A 30 " pdb=" CG PHE A 30 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.12e+00 bond pdb=" CB PHE C 30 " pdb=" CG PHE C 30 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.11e+00 ... (remaining 54571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 72640 3.27 - 6.55: 1156 6.55 - 9.82: 220 9.82 - 13.10: 0 13.10 - 16.37: 12 Bond angle restraints: 74028 Sorted by residual: angle pdb=" CA LEU G 409 " pdb=" CB LEU G 409 " pdb=" CG LEU G 409 " ideal model delta sigma weight residual 116.30 132.67 -16.37 3.50e+00 8.16e-02 2.19e+01 angle pdb=" CA LEU C 409 " pdb=" CB LEU C 409 " pdb=" CG LEU C 409 " ideal model delta sigma weight residual 116.30 132.67 -16.37 3.50e+00 8.16e-02 2.19e+01 angle pdb=" CA LEU K 409 " pdb=" CB LEU K 409 " pdb=" CG LEU K 409 " ideal model delta sigma weight residual 116.30 132.66 -16.36 3.50e+00 8.16e-02 2.19e+01 angle pdb=" CA LEU F 409 " pdb=" CB LEU F 409 " pdb=" CG LEU F 409 " ideal model delta sigma weight residual 116.30 132.66 -16.36 3.50e+00 8.16e-02 2.19e+01 angle pdb=" CA LEU E 409 " pdb=" CB LEU E 409 " pdb=" CG LEU E 409 " ideal model delta sigma weight residual 116.30 132.65 -16.35 3.50e+00 8.16e-02 2.18e+01 ... (remaining 74023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 30894 15.28 - 30.56: 1722 30.56 - 45.83: 372 45.83 - 61.11: 12 61.11 - 76.39: 48 Dihedral angle restraints: 33048 sinusoidal: 13248 harmonic: 19800 Sorted by residual: dihedral pdb=" CA TYR j 62 " pdb=" C TYR j 62 " pdb=" N PRO j 63 " pdb=" CA PRO j 63 " ideal model delta harmonic sigma weight residual -180.00 -135.44 -44.56 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA TYR f 62 " pdb=" C TYR f 62 " pdb=" N PRO f 63 " pdb=" CA PRO f 63 " ideal model delta harmonic sigma weight residual -180.00 -135.45 -44.55 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA TYR k 62 " pdb=" C TYR k 62 " pdb=" N PRO k 63 " pdb=" CA PRO k 63 " ideal model delta harmonic sigma weight residual -180.00 -135.45 -44.55 0 5.00e+00 4.00e-02 7.94e+01 ... (remaining 33045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4693 0.043 - 0.085: 2500 0.085 - 0.128: 786 0.128 - 0.170: 145 0.170 - 0.213: 72 Chirality restraints: 8196 Sorted by residual: chirality pdb=" CA PHE L 154 " pdb=" N PHE L 154 " pdb=" C PHE L 154 " pdb=" CB PHE L 154 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PHE G 154 " pdb=" N PHE G 154 " pdb=" C PHE G 154 " pdb=" CB PHE G 154 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB VAL l 128 " pdb=" CA VAL l 128 " pdb=" CG1 VAL l 128 " pdb=" CG2 VAL l 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 8193 not shown) Planarity restraints: 9804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 159 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C LYS D 159 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS D 159 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG D 160 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 159 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C LYS F 159 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS F 159 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG F 160 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 159 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C LYS G 159 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS G 159 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG G 160 " 0.017 2.00e-02 2.50e+03 ... (remaining 9801 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 16845 2.83 - 3.35: 46849 3.35 - 3.86: 84411 3.86 - 4.38: 98012 4.38 - 4.90: 167433 Nonbonded interactions: 413550 Sorted by model distance: nonbonded pdb=" OG SER A 316 " pdb=" O SER L 311 " model vdw 2.312 3.040 nonbonded pdb=" O SER B 311 " pdb=" OG SER C 316 " model vdw 2.317 3.040 nonbonded pdb=" O SER I 311 " pdb=" OG SER J 316 " model vdw 2.324 3.040 nonbonded pdb=" O SER D 311 " pdb=" OG SER E 316 " model vdw 2.326 3.040 nonbonded pdb=" O SER H 311 " pdb=" OG SER I 316 " model vdw 2.330 3.040 ... (remaining 413545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.040 Extract box with map and model: 1.780 Check model and map are aligned: 0.340 Set scattering table: 0.430 Process input model: 85.110 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 54576 Z= 0.462 Angle : 1.108 16.375 74028 Z= 0.598 Chirality : 0.057 0.213 8196 Planarity : 0.008 0.070 9804 Dihedral : 10.701 76.391 20280 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 0.63 % Allowed : 5.37 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.41 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.20 (0.07), residues: 6816 helix: -4.89 (0.03), residues: 2472 sheet: -3.18 (0.20), residues: 540 loop : -3.83 (0.07), residues: 3804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP c 40 HIS 0.011 0.003 HIS J 383 PHE 0.021 0.003 PHE A 295 TYR 0.020 0.002 TYR b 113 ARG 0.008 0.001 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2038 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 2002 time to evaluate : 5.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7223 (mtp180) REVERT: A 52 ARG cc_start: 0.7872 (ttt-90) cc_final: 0.7604 (ttt90) REVERT: A 60 LEU cc_start: 0.8852 (tt) cc_final: 0.8640 (tp) REVERT: A 84 LYS cc_start: 0.8407 (mttt) cc_final: 0.7992 (tttt) REVERT: A 94 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7793 (tm-30) REVERT: A 148 GLN cc_start: 0.7446 (pm20) cc_final: 0.7017 (mt0) REVERT: A 154 PHE cc_start: 0.8411 (p90) cc_final: 0.7929 (p90) REVERT: A 157 ARG cc_start: 0.6768 (mtp180) cc_final: 0.6383 (mtp180) REVERT: A 249 LYS cc_start: 0.8804 (tptt) cc_final: 0.8516 (ttmm) REVERT: A 293 ILE cc_start: 0.8572 (pp) cc_final: 0.8367 (tp) REVERT: A 315 MET cc_start: 0.1214 (ttp) cc_final: 0.0982 (ttm) REVERT: A 371 MET cc_start: 0.8220 (mmm) cc_final: 0.7502 (mmt) REVERT: A 375 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 399 GLU cc_start: 0.6983 (tp30) cc_final: 0.6667 (tp30) REVERT: B 84 LYS cc_start: 0.8485 (mttt) cc_final: 0.8057 (tttt) REVERT: B 136 MET cc_start: 0.7602 (mtt) cc_final: 0.7013 (mtm) REVERT: B 148 GLN cc_start: 0.7574 (pm20) cc_final: 0.7101 (mt0) REVERT: B 154 PHE cc_start: 0.8485 (p90) cc_final: 0.8002 (p90) REVERT: B 157 ARG cc_start: 0.6683 (mtp180) cc_final: 0.6203 (mtp180) REVERT: B 189 MET cc_start: 0.8527 (mmm) cc_final: 0.8324 (mmm) REVERT: B 249 LYS cc_start: 0.8644 (tptt) cc_final: 0.8313 (ttmm) REVERT: B 294 LEU cc_start: 0.8669 (mm) cc_final: 0.8454 (mm) REVERT: B 371 MET cc_start: 0.8206 (mmm) cc_final: 0.7958 (mmt) REVERT: B 397 MET cc_start: 0.7577 (mmm) cc_final: 0.7374 (mmm) REVERT: C 47 ASN cc_start: 0.9026 (m-40) cc_final: 0.8807 (m110) REVERT: C 84 LYS cc_start: 0.8432 (mttt) cc_final: 0.8055 (tttt) REVERT: C 94 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7792 (tm-30) REVERT: C 249 LYS cc_start: 0.8707 (tptt) cc_final: 0.8421 (ttmm) REVERT: C 371 MET cc_start: 0.8008 (mmm) cc_final: 0.7075 (mmt) REVERT: C 399 GLU cc_start: 0.6742 (tp30) cc_final: 0.6256 (tp30) REVERT: D 12 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7232 (mtp180) REVERT: D 52 ARG cc_start: 0.7856 (ttt-90) cc_final: 0.7563 (ttt90) REVERT: D 84 LYS cc_start: 0.8432 (mttt) cc_final: 0.7984 (tttt) REVERT: D 148 GLN cc_start: 0.7511 (pm20) cc_final: 0.7062 (mt0) REVERT: D 154 PHE cc_start: 0.8413 (p90) cc_final: 0.7895 (p90) REVERT: D 157 ARG cc_start: 0.6760 (mtp180) cc_final: 0.6392 (mtp180) REVERT: D 187 ASP cc_start: 0.6427 (t0) cc_final: 0.5826 (p0) REVERT: D 293 ILE cc_start: 0.8583 (pp) cc_final: 0.8357 (tp) REVERT: D 315 MET cc_start: 0.1146 (ttp) cc_final: 0.0922 (ttm) REVERT: D 371 MET cc_start: 0.8251 (mmm) cc_final: 0.7531 (mmt) REVERT: D 375 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6989 (mt-10) REVERT: D 379 ILE cc_start: 0.9168 (mt) cc_final: 0.8953 (mt) REVERT: D 399 GLU cc_start: 0.6880 (tp30) cc_final: 0.6509 (tp30) REVERT: E 84 LYS cc_start: 0.8494 (mttt) cc_final: 0.8062 (tttt) REVERT: E 148 GLN cc_start: 0.7579 (pm20) cc_final: 0.7085 (mt0) REVERT: E 154 PHE cc_start: 0.8414 (p90) cc_final: 0.7719 (p90) REVERT: E 157 ARG cc_start: 0.6777 (mtp180) cc_final: 0.6332 (mtp180) REVERT: E 189 MET cc_start: 0.8543 (mmm) cc_final: 0.8326 (mmm) REVERT: E 249 LYS cc_start: 0.8626 (tptt) cc_final: 0.8296 (ttmm) REVERT: E 273 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7386 (mt-10) REVERT: E 294 LEU cc_start: 0.8671 (mm) cc_final: 0.8430 (mm) REVERT: E 399 GLU cc_start: 0.6927 (tp30) cc_final: 0.6605 (tp30) REVERT: F 47 ASN cc_start: 0.9039 (m-40) cc_final: 0.8832 (m110) REVERT: F 84 LYS cc_start: 0.8469 (mttt) cc_final: 0.8093 (tttt) REVERT: F 249 LYS cc_start: 0.8731 (tptt) cc_final: 0.8319 (tttp) REVERT: F 324 LYS cc_start: 0.7920 (mtpt) cc_final: 0.6845 (mttm) REVERT: F 371 MET cc_start: 0.8036 (mmm) cc_final: 0.7572 (mmt) REVERT: F 399 GLU cc_start: 0.6756 (tp30) cc_final: 0.6224 (tp30) REVERT: G 12 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7233 (mtp180) REVERT: G 52 ARG cc_start: 0.7854 (ttt-90) cc_final: 0.7563 (ttt90) REVERT: G 84 LYS cc_start: 0.8431 (mttt) cc_final: 0.7980 (tttt) REVERT: G 148 GLN cc_start: 0.7514 (pm20) cc_final: 0.7049 (mt0) REVERT: G 154 PHE cc_start: 0.8411 (p90) cc_final: 0.7902 (p90) REVERT: G 157 ARG cc_start: 0.6756 (mtp180) cc_final: 0.6407 (mtp180) REVERT: G 187 ASP cc_start: 0.6425 (t0) cc_final: 0.5808 (p0) REVERT: G 293 ILE cc_start: 0.8579 (pp) cc_final: 0.8354 (tp) REVERT: G 315 MET cc_start: 0.1142 (ttp) cc_final: 0.0916 (ttm) REVERT: G 371 MET cc_start: 0.8251 (mmm) cc_final: 0.7486 (mmt) REVERT: G 375 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7018 (mt-10) REVERT: G 399 GLU cc_start: 0.6882 (tp30) cc_final: 0.6503 (tp30) REVERT: H 84 LYS cc_start: 0.8496 (mttt) cc_final: 0.8084 (tttt) REVERT: H 148 GLN cc_start: 0.7575 (pm20) cc_final: 0.7068 (mt0) REVERT: H 154 PHE cc_start: 0.8411 (p90) cc_final: 0.7760 (p90) REVERT: H 157 ARG cc_start: 0.6781 (mtp180) cc_final: 0.6326 (mtp180) REVERT: H 189 MET cc_start: 0.8542 (mmm) cc_final: 0.8319 (mmm) REVERT: H 249 LYS cc_start: 0.8652 (tptt) cc_final: 0.8320 (ttmm) REVERT: H 294 LEU cc_start: 0.8670 (mm) cc_final: 0.8426 (mm) REVERT: H 397 MET cc_start: 0.7538 (mmm) cc_final: 0.7280 (mmm) REVERT: I 47 ASN cc_start: 0.9051 (m-40) cc_final: 0.8847 (m110) REVERT: I 84 LYS cc_start: 0.8469 (mttt) cc_final: 0.8100 (tttt) REVERT: I 94 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7729 (tm-30) REVERT: I 249 LYS cc_start: 0.8775 (tptt) cc_final: 0.8429 (ttmm) REVERT: I 324 LYS cc_start: 0.7920 (mtpt) cc_final: 0.6876 (mttm) REVERT: I 371 MET cc_start: 0.8044 (mmm) cc_final: 0.7572 (mmt) REVERT: I 399 GLU cc_start: 0.6712 (tp30) cc_final: 0.6224 (tp30) REVERT: J 12 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7225 (mtp180) REVERT: J 52 ARG cc_start: 0.7892 (ttt-90) cc_final: 0.7611 (ttt90) REVERT: J 84 LYS cc_start: 0.8388 (mttt) cc_final: 0.7957 (tttt) REVERT: J 94 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7805 (tm-30) REVERT: J 148 GLN cc_start: 0.7449 (pm20) cc_final: 0.6978 (mt0) REVERT: J 154 PHE cc_start: 0.8402 (p90) cc_final: 0.7925 (p90) REVERT: J 157 ARG cc_start: 0.6736 (mtp180) cc_final: 0.6321 (mtp180) REVERT: J 249 LYS cc_start: 0.8803 (tptt) cc_final: 0.8511 (ttmm) REVERT: J 315 MET cc_start: 0.1280 (ttp) cc_final: 0.1014 (ttm) REVERT: J 371 MET cc_start: 0.8223 (mmm) cc_final: 0.7484 (mmt) REVERT: J 375 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7049 (mt-10) REVERT: J 399 GLU cc_start: 0.6890 (tp30) cc_final: 0.6641 (tp30) REVERT: K 84 LYS cc_start: 0.8481 (mttt) cc_final: 0.8053 (tttt) REVERT: K 136 MET cc_start: 0.7574 (mtt) cc_final: 0.6993 (mtm) REVERT: K 148 GLN cc_start: 0.7572 (pm20) cc_final: 0.7088 (mt0) REVERT: K 154 PHE cc_start: 0.8478 (p90) cc_final: 0.7722 (p90) REVERT: K 157 ARG cc_start: 0.6688 (mtp180) cc_final: 0.6260 (mtp180) REVERT: K 189 MET cc_start: 0.8530 (mmm) cc_final: 0.8324 (mmm) REVERT: K 249 LYS cc_start: 0.8657 (tptt) cc_final: 0.8314 (ttmm) REVERT: K 294 LEU cc_start: 0.8664 (mm) cc_final: 0.8415 (mm) REVERT: K 371 MET cc_start: 0.8131 (mmm) cc_final: 0.7922 (mmt) REVERT: K 397 MET cc_start: 0.7568 (mmm) cc_final: 0.7324 (mmm) REVERT: L 47 ASN cc_start: 0.9054 (m-40) cc_final: 0.8836 (m110) REVERT: L 84 LYS cc_start: 0.8443 (mttt) cc_final: 0.8051 (tttt) REVERT: L 94 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7729 (tm-30) REVERT: L 249 LYS cc_start: 0.8782 (tptt) cc_final: 0.8441 (ttmm) REVERT: L 324 LYS cc_start: 0.7921 (mtpt) cc_final: 0.6856 (mttm) REVERT: L 371 MET cc_start: 0.8046 (mmm) cc_final: 0.7503 (mmt) REVERT: L 399 GLU cc_start: 0.6707 (tp30) cc_final: 0.6216 (tp30) REVERT: a 9 ASP cc_start: 0.7657 (t0) cc_final: 0.7393 (t0) REVERT: a 35 MET cc_start: 0.8256 (mmm) cc_final: 0.8050 (mmt) REVERT: a 91 PHE cc_start: 0.8299 (m-10) cc_final: 0.8096 (m-10) REVERT: b 9 ASP cc_start: 0.7657 (t0) cc_final: 0.7405 (t0) REVERT: c 9 ASP cc_start: 0.7816 (t0) cc_final: 0.7554 (t0) REVERT: d 9 ASP cc_start: 0.7711 (t0) cc_final: 0.7351 (t0) REVERT: e 9 ASP cc_start: 0.7657 (t0) cc_final: 0.7395 (t0) REVERT: e 14 TYR cc_start: 0.8229 (m-10) cc_final: 0.8003 (m-10) REVERT: f 9 ASP cc_start: 0.7736 (t0) cc_final: 0.7483 (t0) REVERT: h 9 ASP cc_start: 0.7662 (t0) cc_final: 0.7412 (t0) REVERT: i 9 ASP cc_start: 0.7775 (t0) cc_final: 0.7496 (t0) REVERT: j 9 ASP cc_start: 0.7689 (t0) cc_final: 0.7434 (t0) REVERT: k 9 ASP cc_start: 0.7666 (t0) cc_final: 0.7420 (t0) REVERT: l 9 ASP cc_start: 0.7813 (t0) cc_final: 0.7541 (t0) outliers start: 36 outliers final: 1 residues processed: 2026 average time/residue: 0.7251 time to fit residues: 2345.7125 Evaluate side-chains 1314 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1313 time to evaluate : 5.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 577 optimal weight: 3.9990 chunk 518 optimal weight: 0.0970 chunk 287 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 349 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 536 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 325 optimal weight: 3.9990 chunk 399 optimal weight: 1.9990 chunk 621 optimal weight: 0.0270 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 47 ASN A 70 GLN A 291 GLN A 321 HIS B 40 GLN B 70 GLN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 HIS C 40 GLN C 70 GLN C 185 HIS D 40 GLN D 47 ASN D 70 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN D 321 HIS E 40 GLN E 70 GLN E 321 HIS F 40 GLN F 70 GLN F 185 HIS F 321 HIS G 40 GLN G 47 ASN G 70 GLN G 291 GLN G 321 HIS H 40 GLN H 70 GLN H 321 HIS I 40 GLN I 70 GLN I 185 HIS I 321 HIS J 40 GLN J 47 ASN J 70 GLN J 291 GLN J 321 HIS K 40 GLN K 70 GLN K 321 HIS L 40 GLN L 70 GLN L 185 HIS ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 321 HIS d 107 ASN g 107 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54576 Z= 0.212 Angle : 0.695 9.757 74028 Z= 0.359 Chirality : 0.044 0.183 8196 Planarity : 0.006 0.070 9804 Dihedral : 6.327 34.364 7465 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.45 % Allowed : 11.45 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.08), residues: 6816 helix: -3.37 (0.07), residues: 2496 sheet: -2.33 (0.22), residues: 420 loop : -3.30 (0.08), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP k 40 HIS 0.008 0.001 HIS F 185 PHE 0.025 0.002 PHE G 30 TYR 0.016 0.001 TYR k 113 ARG 0.007 0.001 ARG j 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1603 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 1406 time to evaluate : 6.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8443 (mttt) cc_final: 0.7973 (tttt) REVERT: A 94 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7628 (tm-30) REVERT: A 157 ARG cc_start: 0.6748 (mtp180) cc_final: 0.6282 (mtp180) REVERT: A 160 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7555 (mmm-85) REVERT: A 189 MET cc_start: 0.8620 (mmm) cc_final: 0.8392 (mmm) REVERT: A 371 MET cc_start: 0.8164 (mmm) cc_final: 0.7463 (mmt) REVERT: A 375 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6886 (mt-10) REVERT: A 399 GLU cc_start: 0.6901 (tp30) cc_final: 0.6649 (tp30) REVERT: B 30 PHE cc_start: 0.7635 (m-80) cc_final: 0.7163 (m-80) REVERT: B 84 LYS cc_start: 0.8508 (mttt) cc_final: 0.8077 (tttt) REVERT: B 160 ARG cc_start: 0.7769 (mmm-85) cc_final: 0.7468 (mmm-85) REVERT: B 378 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7588 (mt-10) REVERT: C 30 PHE cc_start: 0.7738 (m-80) cc_final: 0.7509 (m-10) REVERT: C 84 LYS cc_start: 0.8386 (mttt) cc_final: 0.7947 (tttt) REVERT: C 94 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7464 (tm-30) REVERT: C 160 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7383 (mmm-85) REVERT: C 238 MET cc_start: 0.8401 (ttm) cc_final: 0.8171 (ttp) REVERT: C 399 GLU cc_start: 0.6784 (tp30) cc_final: 0.6416 (tp30) REVERT: D 84 LYS cc_start: 0.8474 (mttt) cc_final: 0.7982 (tttt) REVERT: D 94 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7606 (tm-30) REVERT: D 157 ARG cc_start: 0.6832 (mtp180) cc_final: 0.6370 (mtp180) REVERT: D 160 ARG cc_start: 0.7807 (mmm-85) cc_final: 0.7566 (mmm-85) REVERT: D 189 MET cc_start: 0.8611 (mmm) cc_final: 0.8366 (mmm) REVERT: D 371 MET cc_start: 0.8198 (mmm) cc_final: 0.7395 (mmt) REVERT: D 375 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6854 (mt-10) REVERT: D 399 GLU cc_start: 0.6866 (tp30) cc_final: 0.6560 (tp30) REVERT: E 84 LYS cc_start: 0.8487 (mttt) cc_final: 0.8037 (tttt) REVERT: E 160 ARG cc_start: 0.7673 (mmm-85) cc_final: 0.7375 (mmm-85) REVERT: E 162 GLN cc_start: 0.7590 (tt0) cc_final: 0.7325 (tt0) REVERT: E 369 GLU cc_start: 0.6009 (mt-10) cc_final: 0.5146 (tt0) REVERT: E 378 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7675 (mt-10) REVERT: F 30 PHE cc_start: 0.7749 (m-80) cc_final: 0.7507 (m-10) REVERT: F 39 ARG cc_start: 0.7473 (ttm170) cc_final: 0.7267 (ttt180) REVERT: F 84 LYS cc_start: 0.8402 (mttt) cc_final: 0.7989 (tttt) REVERT: F 94 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7445 (tm-30) REVERT: F 160 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7391 (mmm-85) REVERT: F 238 MET cc_start: 0.8433 (ttm) cc_final: 0.8089 (ttp) REVERT: F 371 MET cc_start: 0.7885 (mmm) cc_final: 0.7517 (mmt) REVERT: F 399 GLU cc_start: 0.6713 (tp30) cc_final: 0.6314 (tp30) REVERT: G 84 LYS cc_start: 0.8467 (mttt) cc_final: 0.7979 (tttt) REVERT: G 94 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7605 (tm-30) REVERT: G 157 ARG cc_start: 0.6842 (mtp180) cc_final: 0.6373 (mtp180) REVERT: G 189 MET cc_start: 0.8606 (mmm) cc_final: 0.8376 (mmm) REVERT: G 315 MET cc_start: 0.1108 (ttp) cc_final: 0.0855 (ttm) REVERT: G 371 MET cc_start: 0.8124 (mmm) cc_final: 0.7410 (mmt) REVERT: G 375 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6844 (mt-10) REVERT: G 399 GLU cc_start: 0.6865 (tp30) cc_final: 0.6574 (tp30) REVERT: H 84 LYS cc_start: 0.8490 (mttt) cc_final: 0.8035 (tttt) REVERT: H 160 ARG cc_start: 0.7668 (mmm-85) cc_final: 0.7341 (mmm-85) REVERT: H 162 GLN cc_start: 0.7578 (tt0) cc_final: 0.7317 (tt0) REVERT: H 378 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7675 (mt-10) REVERT: I 30 PHE cc_start: 0.7721 (m-80) cc_final: 0.7478 (m-10) REVERT: I 39 ARG cc_start: 0.7477 (ttm170) cc_final: 0.7274 (ttt180) REVERT: I 84 LYS cc_start: 0.8402 (mttt) cc_final: 0.7993 (tttt) REVERT: I 94 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7424 (tm-30) REVERT: I 160 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7368 (mmm-85) REVERT: I 238 MET cc_start: 0.8405 (ttm) cc_final: 0.8171 (ttp) REVERT: I 371 MET cc_start: 0.7873 (mmm) cc_final: 0.7518 (mmt) REVERT: I 399 GLU cc_start: 0.6695 (tp30) cc_final: 0.6269 (tp30) REVERT: J 84 LYS cc_start: 0.8450 (mttt) cc_final: 0.7944 (tttt) REVERT: J 157 ARG cc_start: 0.6820 (mtp180) cc_final: 0.6339 (mtp180) REVERT: J 160 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7551 (mmm-85) REVERT: J 189 MET cc_start: 0.8602 (mmm) cc_final: 0.8392 (mmm) REVERT: J 315 MET cc_start: 0.1027 (ttp) cc_final: 0.0755 (ttm) REVERT: J 371 MET cc_start: 0.8195 (mmm) cc_final: 0.7451 (mmt) REVERT: J 375 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6969 (mt-10) REVERT: J 399 GLU cc_start: 0.6840 (tp30) cc_final: 0.6632 (tp30) REVERT: K 84 LYS cc_start: 0.8507 (mttt) cc_final: 0.8066 (tttt) REVERT: K 160 ARG cc_start: 0.7752 (mmm-85) cc_final: 0.7451 (mmm-85) REVERT: K 378 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7604 (mt-10) REVERT: L 30 PHE cc_start: 0.7725 (m-80) cc_final: 0.7485 (m-10) REVERT: L 39 ARG cc_start: 0.7470 (ttm170) cc_final: 0.7188 (ttt180) REVERT: L 84 LYS cc_start: 0.8400 (mttt) cc_final: 0.7989 (tttt) REVERT: L 94 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7441 (tm-30) REVERT: L 160 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7375 (mmm-85) REVERT: L 238 MET cc_start: 0.8406 (ttm) cc_final: 0.8179 (ttp) REVERT: L 371 MET cc_start: 0.7763 (mmm) cc_final: 0.7490 (mmt) REVERT: L 399 GLU cc_start: 0.6691 (tp30) cc_final: 0.6273 (tp30) REVERT: g 35 MET cc_start: 0.8387 (mmm) cc_final: 0.8127 (mmt) REVERT: g 65 ARG cc_start: 0.6757 (ttm170) cc_final: 0.6435 (mtm-85) REVERT: h 14 TYR cc_start: 0.8139 (m-10) cc_final: 0.7926 (m-80) REVERT: h 16 GLU cc_start: 0.7931 (pm20) cc_final: 0.7498 (pm20) outliers start: 197 outliers final: 121 residues processed: 1518 average time/residue: 0.6842 time to fit residues: 1685.3253 Evaluate side-chains 1270 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 1149 time to evaluate : 5.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 350 ILE Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 68 ASP Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 68 ASP Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 345 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 516 optimal weight: 0.9990 chunk 422 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 622 optimal weight: 6.9990 chunk 672 optimal weight: 9.9990 chunk 554 optimal weight: 5.9990 chunk 617 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 499 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN C 185 HIS C 408 GLN D 408 GLN ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 GLN ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 GLN F 408 GLN G 408 GLN ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 408 GLN ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN J 408 GLN K 408 GLN L 47 ASN ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 GLN a 107 ASN b 107 ASN h 107 ASN j 107 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 54576 Z= 0.268 Angle : 0.689 9.206 74028 Z= 0.358 Chirality : 0.044 0.173 8196 Planarity : 0.005 0.074 9804 Dihedral : 5.943 30.876 7465 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 4.62 % Allowed : 13.11 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.31 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.08), residues: 6816 helix: -2.45 (0.08), residues: 2508 sheet: -2.91 (0.19), residues: 588 loop : -3.26 (0.08), residues: 3720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 32 HIS 0.010 0.002 HIS C 185 PHE 0.036 0.002 PHE A 30 TYR 0.014 0.001 TYR c 14 ARG 0.008 0.001 ARG b 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1517 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 1253 time to evaluate : 6.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8401 (mttt) cc_final: 0.7970 (tttt) REVERT: A 157 ARG cc_start: 0.7198 (mtp180) cc_final: 0.6960 (mtp180) REVERT: A 160 ARG cc_start: 0.7742 (mmm-85) cc_final: 0.7497 (mmm-85) REVERT: A 371 MET cc_start: 0.8046 (mmm) cc_final: 0.7774 (mmt) REVERT: A 399 GLU cc_start: 0.6704 (tp30) cc_final: 0.6212 (tp30) REVERT: B 84 LYS cc_start: 0.8438 (mttt) cc_final: 0.7974 (tttt) REVERT: B 157 ARG cc_start: 0.7197 (mtp180) cc_final: 0.6830 (mtp180) REVERT: B 268 MET cc_start: 0.7991 (tpp) cc_final: 0.7694 (mtm) REVERT: B 378 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7469 (mt-10) REVERT: B 397 MET cc_start: 0.7453 (mmm) cc_final: 0.7011 (mmm) REVERT: C 84 LYS cc_start: 0.8441 (mttt) cc_final: 0.8061 (tttt) REVERT: C 160 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7293 (mmm-85) REVERT: C 238 MET cc_start: 0.8457 (ttm) cc_final: 0.8225 (ttp) REVERT: C 399 GLU cc_start: 0.6628 (tp30) cc_final: 0.6133 (tp30) REVERT: D 84 LYS cc_start: 0.8410 (mttt) cc_final: 0.7965 (tttt) REVERT: D 160 ARG cc_start: 0.7744 (mmm-85) cc_final: 0.7482 (mmm-85) REVERT: D 371 MET cc_start: 0.8075 (mmm) cc_final: 0.7765 (mmt) REVERT: D 378 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7223 (mt-10) REVERT: E 23 ARG cc_start: 0.7992 (tpt90) cc_final: 0.7286 (tpt-90) REVERT: E 84 LYS cc_start: 0.8451 (mttt) cc_final: 0.7982 (tttt) REVERT: E 157 ARG cc_start: 0.7176 (mtp180) cc_final: 0.6699 (mtp180) REVERT: E 162 GLN cc_start: 0.7804 (tt0) cc_final: 0.7593 (tt0) REVERT: E 268 MET cc_start: 0.7995 (tpp) cc_final: 0.7675 (mtm) REVERT: E 369 GLU cc_start: 0.6005 (mt-10) cc_final: 0.5689 (tt0) REVERT: E 378 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7564 (mt-10) REVERT: E 397 MET cc_start: 0.7487 (mmm) cc_final: 0.7285 (mmm) REVERT: F 39 ARG cc_start: 0.7520 (ttm170) cc_final: 0.7305 (ttt180) REVERT: F 84 LYS cc_start: 0.8417 (mttt) cc_final: 0.8049 (tttt) REVERT: F 160 ARG cc_start: 0.7505 (mmm-85) cc_final: 0.7243 (mmm-85) REVERT: F 238 MET cc_start: 0.8535 (ttm) cc_final: 0.8272 (ttp) REVERT: F 399 GLU cc_start: 0.6642 (tp30) cc_final: 0.6057 (tp30) REVERT: G 84 LYS cc_start: 0.8438 (mttt) cc_final: 0.8007 (tttt) REVERT: G 157 ARG cc_start: 0.7199 (mtp180) cc_final: 0.6962 (mtp180) REVERT: G 371 MET cc_start: 0.8062 (mmm) cc_final: 0.7781 (mmt) REVERT: G 399 GLU cc_start: 0.6744 (tp30) cc_final: 0.6228 (tp30) REVERT: H 84 LYS cc_start: 0.8455 (mttt) cc_final: 0.7983 (tttt) REVERT: H 157 ARG cc_start: 0.7224 (mtp180) cc_final: 0.6747 (mtp180) REVERT: H 162 GLN cc_start: 0.7794 (tt0) cc_final: 0.7590 (tt0) REVERT: H 171 PHE cc_start: 0.7226 (m-10) cc_final: 0.6981 (m-80) REVERT: H 268 MET cc_start: 0.7974 (tpp) cc_final: 0.7680 (mtm) REVERT: H 378 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7556 (mt-10) REVERT: I 84 LYS cc_start: 0.8449 (mttt) cc_final: 0.8083 (tttt) REVERT: I 160 ARG cc_start: 0.7475 (mmm-85) cc_final: 0.7218 (mmm-85) REVERT: I 238 MET cc_start: 0.8448 (ttm) cc_final: 0.8237 (ttp) REVERT: I 399 GLU cc_start: 0.6631 (tp30) cc_final: 0.6045 (tp30) REVERT: J 84 LYS cc_start: 0.8453 (mttt) cc_final: 0.8018 (tttt) REVERT: J 157 ARG cc_start: 0.7178 (mtp180) cc_final: 0.6435 (mtp180) REVERT: J 160 ARG cc_start: 0.7720 (mmm-85) cc_final: 0.7464 (mmm-85) REVERT: J 371 MET cc_start: 0.8013 (mmm) cc_final: 0.7716 (mmt) REVERT: J 378 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7261 (mt-10) REVERT: J 399 GLU cc_start: 0.6692 (tp30) cc_final: 0.6230 (tp30) REVERT: K 84 LYS cc_start: 0.8438 (mttt) cc_final: 0.7955 (tttt) REVERT: K 157 ARG cc_start: 0.7181 (mtp180) cc_final: 0.6824 (mtp180) REVERT: K 378 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7534 (mt-10) REVERT: K 397 MET cc_start: 0.7460 (mmm) cc_final: 0.7009 (mmm) REVERT: K 420 ASP cc_start: 0.7091 (p0) cc_final: 0.6855 (p0) REVERT: L 39 ARG cc_start: 0.7519 (ttm170) cc_final: 0.7277 (ttt180) REVERT: L 84 LYS cc_start: 0.8449 (mttt) cc_final: 0.8084 (tttt) REVERT: L 160 ARG cc_start: 0.7480 (mmm-85) cc_final: 0.7241 (mmm-85) REVERT: L 238 MET cc_start: 0.8485 (ttm) cc_final: 0.8263 (ttp) REVERT: L 399 GLU cc_start: 0.6622 (tp30) cc_final: 0.6165 (tp30) REVERT: a 35 MET cc_start: 0.8463 (mmm) cc_final: 0.8236 (mmt) REVERT: c 110 SER cc_start: 0.8711 (p) cc_final: 0.8390 (t) REVERT: e 65 ARG cc_start: 0.6468 (mtp180) cc_final: 0.5591 (mtp180) REVERT: g 35 MET cc_start: 0.8386 (mmm) cc_final: 0.8184 (mmt) REVERT: l 16 GLU cc_start: 0.7817 (mp0) cc_final: 0.7527 (mp0) REVERT: l 110 SER cc_start: 0.8747 (p) cc_final: 0.8411 (t) outliers start: 264 outliers final: 171 residues processed: 1387 average time/residue: 0.7037 time to fit residues: 1578.6256 Evaluate side-chains 1305 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 1134 time to evaluate : 5.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 424 GLN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 424 GLN Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 390 ILE Chi-restraints excluded: chain H residue 424 GLN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 116 MET Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 116 MET Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 116 MET Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 424 GLN Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 42 VAL Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 42 VAL Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 614 optimal weight: 5.9990 chunk 467 optimal weight: 3.9990 chunk 322 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 417 optimal weight: 2.9990 chunk 624 optimal weight: 2.9990 chunk 661 optimal weight: 0.8980 chunk 326 optimal weight: 0.0870 chunk 591 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54576 Z= 0.200 Angle : 0.626 6.508 74028 Z= 0.325 Chirality : 0.042 0.184 8196 Planarity : 0.005 0.082 9804 Dihedral : 5.533 28.261 7465 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.71 % Allowed : 16.02 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.09), residues: 6816 helix: -1.67 (0.09), residues: 2436 sheet: -2.63 (0.19), residues: 588 loop : -3.09 (0.08), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 49 HIS 0.007 0.001 HIS C 185 PHE 0.040 0.002 PHE G 30 TYR 0.015 0.001 TYR e 62 ARG 0.008 0.001 ARG d 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 1210 time to evaluate : 5.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8403 (mttt) cc_final: 0.8010 (tttt) REVERT: A 239 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7913 (mp0) REVERT: A 256 LEU cc_start: 0.9045 (mt) cc_final: 0.8812 (mt) REVERT: B 84 LYS cc_start: 0.8373 (mttt) cc_final: 0.7957 (tttt) REVERT: B 160 ARG cc_start: 0.7410 (mmm-85) cc_final: 0.6816 (mmm-85) REVERT: B 268 MET cc_start: 0.8005 (tpp) cc_final: 0.7678 (mtm) REVERT: B 378 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7305 (mt-10) REVERT: C 84 LYS cc_start: 0.8508 (mttt) cc_final: 0.8134 (tttt) REVERT: C 160 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.7312 (mmm-85) REVERT: C 399 GLU cc_start: 0.6530 (tp30) cc_final: 0.6122 (tp30) REVERT: D 84 LYS cc_start: 0.8409 (mttt) cc_final: 0.8005 (tttt) REVERT: D 256 LEU cc_start: 0.9035 (mt) cc_final: 0.8825 (mt) REVERT: D 378 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7230 (mt-10) REVERT: E 84 LYS cc_start: 0.8383 (mttt) cc_final: 0.7959 (tttt) REVERT: E 160 ARG cc_start: 0.7272 (mmm-85) cc_final: 0.6710 (mmm-85) REVERT: E 162 GLN cc_start: 0.7751 (tt0) cc_final: 0.7219 (tp40) REVERT: E 268 MET cc_start: 0.7987 (tpp) cc_final: 0.7571 (mtm) REVERT: E 369 GLU cc_start: 0.5883 (mt-10) cc_final: 0.5558 (tt0) REVERT: E 378 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7412 (mt-10) REVERT: F 39 ARG cc_start: 0.7497 (ttm170) cc_final: 0.7286 (ttt180) REVERT: F 84 LYS cc_start: 0.8429 (mttt) cc_final: 0.8067 (tttt) REVERT: F 94 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8229 (tm-30) REVERT: F 399 GLU cc_start: 0.6526 (tp30) cc_final: 0.6088 (tp30) REVERT: G 84 LYS cc_start: 0.8401 (mttt) cc_final: 0.8004 (tttt) REVERT: G 256 LEU cc_start: 0.9035 (mt) cc_final: 0.8825 (mt) REVERT: H 84 LYS cc_start: 0.8408 (mttt) cc_final: 0.7982 (tttt) REVERT: H 160 ARG cc_start: 0.7432 (mmm-85) cc_final: 0.6757 (mmm-85) REVERT: H 162 GLN cc_start: 0.7720 (tt0) cc_final: 0.7512 (tt0) REVERT: H 268 MET cc_start: 0.7973 (tpp) cc_final: 0.7587 (mtm) REVERT: H 378 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7326 (mt-10) REVERT: H 397 MET cc_start: 0.7404 (mmm) cc_final: 0.7111 (mmm) REVERT: I 84 LYS cc_start: 0.8426 (mttt) cc_final: 0.8064 (tttt) REVERT: I 94 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8242 (tm-30) REVERT: I 160 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.7316 (mmm-85) REVERT: I 399 GLU cc_start: 0.6541 (tp30) cc_final: 0.6106 (tp30) REVERT: J 84 LYS cc_start: 0.8404 (mttt) cc_final: 0.8012 (tttt) REVERT: J 256 LEU cc_start: 0.9016 (mt) cc_final: 0.8782 (mt) REVERT: J 378 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7193 (mt-10) REVERT: K 84 LYS cc_start: 0.8366 (mttt) cc_final: 0.7943 (tttt) REVERT: K 160 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.6820 (mmm-85) REVERT: K 162 GLN cc_start: 0.7900 (tt0) cc_final: 0.7450 (tp-100) REVERT: K 378 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7355 (mt-10) REVERT: K 420 ASP cc_start: 0.7107 (p0) cc_final: 0.6869 (p0) REVERT: L 39 ARG cc_start: 0.7512 (ttm170) cc_final: 0.7251 (ttt180) REVERT: L 84 LYS cc_start: 0.8431 (mttt) cc_final: 0.8065 (tttt) REVERT: L 94 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8241 (tm-30) REVERT: L 160 ARG cc_start: 0.7570 (mmm-85) cc_final: 0.7322 (mmm-85) REVERT: L 399 GLU cc_start: 0.6558 (tp30) cc_final: 0.6124 (tp30) REVERT: a 65 ARG cc_start: 0.6868 (mmm-85) cc_final: 0.6409 (mtm-85) REVERT: c 110 SER cc_start: 0.8723 (p) cc_final: 0.8498 (t) REVERT: g 65 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6518 (ttp80) REVERT: l 110 SER cc_start: 0.8739 (p) cc_final: 0.8528 (t) outliers start: 212 outliers final: 154 residues processed: 1313 average time/residue: 0.7166 time to fit residues: 1536.1321 Evaluate side-chains 1282 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 1127 time to evaluate : 5.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 424 GLN Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 424 GLN Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 110 SER Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 65 ARG Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 550 optimal weight: 20.0000 chunk 375 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 492 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 564 optimal weight: 10.0000 chunk 457 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 337 optimal weight: 1.9990 chunk 593 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54576 Z= 0.178 Angle : 0.601 7.660 74028 Z= 0.310 Chirality : 0.041 0.170 8196 Planarity : 0.004 0.076 9804 Dihedral : 5.236 25.389 7465 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.83 % Allowed : 16.26 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.09), residues: 6816 helix: -1.12 (0.10), residues: 2460 sheet: -1.78 (0.24), residues: 444 loop : -3.01 (0.08), residues: 3912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 32 HIS 0.005 0.001 HIS C 185 PHE 0.039 0.002 PHE F 30 TYR 0.017 0.001 TYR e 62 ARG 0.006 0.001 ARG K 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 1249 time to evaluate : 5.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8337 (mttt) cc_final: 0.7969 (tttt) REVERT: A 373 GLU cc_start: 0.7653 (tp30) cc_final: 0.7428 (mm-30) REVERT: B 84 LYS cc_start: 0.8332 (mttt) cc_final: 0.7932 (tttt) REVERT: B 121 GLU cc_start: 0.6923 (pm20) cc_final: 0.6709 (pm20) REVERT: B 139 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8000 (mmm-85) REVERT: B 268 MET cc_start: 0.7950 (tpp) cc_final: 0.7538 (mtm) REVERT: B 378 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7275 (mt-10) REVERT: C 84 LYS cc_start: 0.8461 (mttt) cc_final: 0.8134 (tttt) REVERT: C 94 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8149 (tm-30) REVERT: C 160 ARG cc_start: 0.7358 (mmm-85) cc_final: 0.7021 (mtp85) REVERT: C 399 GLU cc_start: 0.6504 (tp30) cc_final: 0.6121 (tp30) REVERT: D 84 LYS cc_start: 0.8343 (mttt) cc_final: 0.7965 (tttt) REVERT: D 189 MET cc_start: 0.8517 (mmm) cc_final: 0.8267 (mmm) REVERT: E 84 LYS cc_start: 0.8338 (mttt) cc_final: 0.7933 (tttt) REVERT: E 121 GLU cc_start: 0.6840 (pm20) cc_final: 0.6614 (pm20) REVERT: E 160 ARG cc_start: 0.7269 (mmm-85) cc_final: 0.6811 (mmm-85) REVERT: E 268 MET cc_start: 0.7945 (tpp) cc_final: 0.7516 (mtm) REVERT: E 369 GLU cc_start: 0.5867 (mt-10) cc_final: 0.5520 (tt0) REVERT: E 378 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7288 (mt-10) REVERT: F 39 ARG cc_start: 0.7506 (ttm170) cc_final: 0.7305 (ttt180) REVERT: F 84 LYS cc_start: 0.8386 (mttt) cc_final: 0.8065 (tttt) REVERT: F 315 MET cc_start: 0.1408 (ttp) cc_final: 0.1194 (ttm) REVERT: F 399 GLU cc_start: 0.6510 (tp30) cc_final: 0.6117 (tp30) REVERT: G 84 LYS cc_start: 0.8336 (mttt) cc_final: 0.7968 (tttt) REVERT: H 84 LYS cc_start: 0.8337 (mttt) cc_final: 0.7934 (tttt) REVERT: H 160 ARG cc_start: 0.7430 (mmm-85) cc_final: 0.6862 (mmm-85) REVERT: H 268 MET cc_start: 0.7928 (tpp) cc_final: 0.7527 (mtm) REVERT: H 378 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7280 (mt-10) REVERT: H 397 MET cc_start: 0.7401 (mmm) cc_final: 0.7140 (mmm) REVERT: I 84 LYS cc_start: 0.8385 (mttt) cc_final: 0.8056 (tttt) REVERT: I 94 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8169 (tm-30) REVERT: I 171 PHE cc_start: 0.6907 (m-10) cc_final: 0.6666 (m-10) REVERT: I 315 MET cc_start: 0.1407 (ttp) cc_final: 0.1182 (ttm) REVERT: I 399 GLU cc_start: 0.6504 (tp30) cc_final: 0.6118 (tp30) REVERT: J 84 LYS cc_start: 0.8334 (mttt) cc_final: 0.7924 (tttt) REVERT: J 154 PHE cc_start: 0.8048 (p90) cc_final: 0.7844 (p90) REVERT: K 84 LYS cc_start: 0.8326 (mttt) cc_final: 0.7918 (tttt) REVERT: K 121 GLU cc_start: 0.6944 (pm20) cc_final: 0.6719 (pm20) REVERT: K 139 ARG cc_start: 0.8298 (mtp85) cc_final: 0.7928 (mmm-85) REVERT: K 160 ARG cc_start: 0.7263 (mmm-85) cc_final: 0.6817 (mmm-85) REVERT: K 378 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7264 (mt-10) REVERT: K 420 ASP cc_start: 0.7275 (p0) cc_final: 0.7056 (p0) REVERT: L 39 ARG cc_start: 0.7520 (ttm170) cc_final: 0.7287 (ttt180) REVERT: L 84 LYS cc_start: 0.8381 (mttt) cc_final: 0.8069 (tttt) REVERT: L 160 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.7031 (mtp85) REVERT: L 162 GLN cc_start: 0.7731 (tt0) cc_final: 0.7490 (tt0) REVERT: L 315 MET cc_start: 0.1367 (ttp) cc_final: 0.1151 (ttm) REVERT: L 399 GLU cc_start: 0.6529 (tp30) cc_final: 0.6139 (tp30) REVERT: b 62 TYR cc_start: 0.5139 (m-80) cc_final: 0.4921 (m-80) REVERT: c 16 GLU cc_start: 0.8168 (mp0) cc_final: 0.7589 (mp0) REVERT: f 65 ARG cc_start: 0.6743 (tmt170) cc_final: 0.6436 (ttp80) REVERT: g 65 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6442 (mmm-85) REVERT: h 62 TYR cc_start: 0.5175 (m-80) cc_final: 0.4950 (m-10) REVERT: i 16 GLU cc_start: 0.8150 (mp0) cc_final: 0.7570 (mp0) REVERT: k 35 MET cc_start: 0.8271 (mmm) cc_final: 0.8064 (mmm) REVERT: k 62 TYR cc_start: 0.5126 (m-80) cc_final: 0.4900 (m-80) outliers start: 219 outliers final: 162 residues processed: 1346 average time/residue: 0.6587 time to fit residues: 1454.0556 Evaluate side-chains 1334 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1171 time to evaluate : 5.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 424 GLN Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 120 PHE Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain J residue 424 GLN Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 116 MET Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 65 ARG Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 222 optimal weight: 7.9990 chunk 595 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 388 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 661 optimal weight: 0.7980 chunk 549 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 347 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 26 ASN C 185 HIS ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 GLN F 26 ASN ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 GLN ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 54576 Z= 0.348 Angle : 0.705 7.416 74028 Z= 0.366 Chirality : 0.046 0.140 8196 Planarity : 0.005 0.067 9804 Dihedral : 5.632 28.293 7465 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 4.43 % Allowed : 16.53 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.09), residues: 6816 helix: -1.13 (0.10), residues: 2448 sheet: -2.54 (0.20), residues: 588 loop : -3.02 (0.08), residues: 3780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 66 HIS 0.009 0.002 HIS C 185 PHE 0.042 0.003 PHE G 30 TYR 0.020 0.001 TYR C 132 ARG 0.009 0.001 ARG i 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1415 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 1162 time to evaluate : 6.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7589 (ttt180) REVERT: A 84 LYS cc_start: 0.8335 (mttt) cc_final: 0.8001 (tttt) REVERT: A 378 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7143 (mt-10) REVERT: B 23 ARG cc_start: 0.8081 (tpt90) cc_final: 0.7338 (tpt-90) REVERT: B 84 LYS cc_start: 0.8299 (mttt) cc_final: 0.7969 (tttt) REVERT: B 121 GLU cc_start: 0.7170 (pm20) cc_final: 0.6958 (pm20) REVERT: B 305 THR cc_start: 0.7389 (p) cc_final: 0.7127 (p) REVERT: B 378 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7341 (mt-10) REVERT: C 84 LYS cc_start: 0.8388 (mttt) cc_final: 0.8092 (tttt) REVERT: C 129 ASP cc_start: 0.8082 (p0) cc_final: 0.7199 (p0) REVERT: C 160 ARG cc_start: 0.7508 (mmm-85) cc_final: 0.7214 (tpt-90) REVERT: C 162 GLN cc_start: 0.7994 (tt0) cc_final: 0.7737 (tt0) REVERT: C 351 ARG cc_start: 0.8686 (tpp-160) cc_final: 0.8452 (ttm-80) REVERT: C 375 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7672 (mt-10) REVERT: C 399 GLU cc_start: 0.6644 (tp30) cc_final: 0.6197 (tp30) REVERT: D 84 LYS cc_start: 0.8338 (mttt) cc_final: 0.7985 (tttt) REVERT: D 160 ARG cc_start: 0.7868 (mmm-85) cc_final: 0.7632 (mmm-85) REVERT: E 23 ARG cc_start: 0.8073 (tpt90) cc_final: 0.7342 (tpt-90) REVERT: E 84 LYS cc_start: 0.8292 (mttt) cc_final: 0.7950 (tttt) REVERT: E 121 GLU cc_start: 0.6949 (pm20) cc_final: 0.6745 (pm20) REVERT: E 160 ARG cc_start: 0.7517 (mmm-85) cc_final: 0.6928 (mmm-85) REVERT: E 305 THR cc_start: 0.7483 (p) cc_final: 0.7227 (p) REVERT: E 369 GLU cc_start: 0.5931 (mt-10) cc_final: 0.5729 (tt0) REVERT: E 378 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7327 (mt-10) REVERT: F 84 LYS cc_start: 0.8384 (mttt) cc_final: 0.8094 (tttt) REVERT: F 136 MET cc_start: 0.8615 (mtm) cc_final: 0.8355 (ptp) REVERT: F 399 GLU cc_start: 0.6657 (tp30) cc_final: 0.6200 (tp30) REVERT: G 39 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7584 (ttt180) REVERT: G 84 LYS cc_start: 0.8334 (mttt) cc_final: 0.7987 (tttt) REVERT: G 378 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7156 (mt-10) REVERT: H 84 LYS cc_start: 0.8293 (mttt) cc_final: 0.7952 (tttt) REVERT: H 305 THR cc_start: 0.7495 (p) cc_final: 0.7232 (p) REVERT: H 378 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7319 (mt-10) REVERT: I 84 LYS cc_start: 0.8375 (mttt) cc_final: 0.8096 (tttt) REVERT: I 399 GLU cc_start: 0.6640 (tp30) cc_final: 0.6204 (tp30) REVERT: J 39 ARG cc_start: 0.7793 (ttm170) cc_final: 0.7584 (ttt180) REVERT: J 84 LYS cc_start: 0.8358 (mttt) cc_final: 0.8016 (tttt) REVERT: J 160 ARG cc_start: 0.7878 (mmm-85) cc_final: 0.7653 (mmm-85) REVERT: K 23 ARG cc_start: 0.8077 (tpt90) cc_final: 0.7346 (tpt-90) REVERT: K 84 LYS cc_start: 0.8294 (mttt) cc_final: 0.7953 (tttt) REVERT: K 305 THR cc_start: 0.7401 (p) cc_final: 0.7147 (p) REVERT: K 378 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7354 (mt-10) REVERT: K 420 ASP cc_start: 0.7466 (p0) cc_final: 0.7257 (p0) REVERT: L 84 LYS cc_start: 0.8383 (mttt) cc_final: 0.8099 (tttt) REVERT: L 136 MET cc_start: 0.8763 (mtm) cc_final: 0.8537 (mtm) REVERT: L 399 GLU cc_start: 0.6630 (tp30) cc_final: 0.6185 (tp30) REVERT: a 62 TYR cc_start: 0.6339 (m-80) cc_final: 0.6109 (m-80) REVERT: a 65 ARG cc_start: 0.6329 (mtp180) cc_final: 0.4991 (mtp180) REVERT: c 16 GLU cc_start: 0.8098 (mp0) cc_final: 0.7794 (mp0) REVERT: d 65 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7187 (mtp180) REVERT: e 16 GLU cc_start: 0.8194 (pm20) cc_final: 0.7839 (pm20) REVERT: g 62 TYR cc_start: 0.6328 (m-80) cc_final: 0.5911 (m-10) REVERT: i 16 GLU cc_start: 0.8095 (mp0) cc_final: 0.7792 (mp0) REVERT: i 65 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.6968 (tmm160) REVERT: j 65 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.7194 (mtp180) REVERT: l 16 GLU cc_start: 0.7807 (mp0) cc_final: 0.7243 (mp0) outliers start: 253 outliers final: 188 residues processed: 1283 average time/residue: 0.6959 time to fit residues: 1443.2643 Evaluate side-chains 1301 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 1113 time to evaluate : 5.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 424 GLN Chi-restraints excluded: chain H residue 26 ASN Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 390 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 424 GLN Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 424 GLN Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 42 VAL Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 110 SER Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 42 VAL Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 638 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 377 optimal weight: 0.9980 chunk 483 optimal weight: 6.9990 chunk 374 optimal weight: 4.9990 chunk 557 optimal weight: 6.9990 chunk 369 optimal weight: 0.6980 chunk 659 optimal weight: 10.0000 chunk 412 optimal weight: 4.9990 chunk 401 optimal weight: 5.9990 chunk 304 optimal weight: 0.0670 overall best weight: 2.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 ASN ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 54576 Z= 0.215 Angle : 0.631 9.167 74028 Z= 0.325 Chirality : 0.042 0.147 8196 Planarity : 0.005 0.057 9804 Dihedral : 5.322 27.387 7465 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.18 % Allowed : 17.02 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.09), residues: 6816 helix: -0.82 (0.10), residues: 2448 sheet: -2.44 (0.20), residues: 588 loop : -2.95 (0.09), residues: 3780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 32 HIS 0.009 0.001 HIS C 185 PHE 0.040 0.002 PHE F 30 TYR 0.013 0.001 TYR d 62 ARG 0.012 0.001 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 1186 time to evaluate : 6.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8319 (mttt) cc_final: 0.7986 (tttt) REVERT: A 238 MET cc_start: 0.8476 (ttm) cc_final: 0.8213 (ttp) REVERT: A 373 GLU cc_start: 0.7787 (tp30) cc_final: 0.7451 (mm-30) REVERT: B 23 ARG cc_start: 0.7927 (tpt90) cc_final: 0.7178 (tpt-90) REVERT: B 84 LYS cc_start: 0.8286 (mttt) cc_final: 0.7981 (tttt) REVERT: B 305 THR cc_start: 0.7239 (p) cc_final: 0.6985 (p) REVERT: B 378 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7276 (mt-10) REVERT: C 75 ASP cc_start: 0.8208 (p0) cc_final: 0.7961 (p0) REVERT: C 84 LYS cc_start: 0.8348 (mttt) cc_final: 0.8057 (tttt) REVERT: C 160 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.7077 (tpt-90) REVERT: C 162 GLN cc_start: 0.7883 (tt0) cc_final: 0.7615 (tt0) REVERT: C 375 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7658 (mt-10) REVERT: C 399 GLU cc_start: 0.6643 (tp30) cc_final: 0.6260 (tp30) REVERT: D 84 LYS cc_start: 0.8316 (mttt) cc_final: 0.7972 (tttt) REVERT: D 189 MET cc_start: 0.8525 (mmm) cc_final: 0.8281 (mmm) REVERT: E 84 LYS cc_start: 0.8281 (mttt) cc_final: 0.7971 (tttt) REVERT: E 305 THR cc_start: 0.7338 (p) cc_final: 0.7076 (p) REVERT: E 378 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7290 (mt-10) REVERT: F 84 LYS cc_start: 0.8346 (mttt) cc_final: 0.8077 (tttt) REVERT: F 399 GLU cc_start: 0.6707 (tp30) cc_final: 0.6310 (tp30) REVERT: G 84 LYS cc_start: 0.8315 (mttt) cc_final: 0.7972 (tttt) REVERT: G 189 MET cc_start: 0.8540 (mmm) cc_final: 0.8292 (mmm) REVERT: G 373 GLU cc_start: 0.7795 (tp30) cc_final: 0.7448 (mm-30) REVERT: G 378 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7095 (mt-10) REVERT: H 84 LYS cc_start: 0.8280 (mttt) cc_final: 0.7975 (tttt) REVERT: H 305 THR cc_start: 0.7346 (p) cc_final: 0.7077 (p) REVERT: H 378 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7277 (mt-10) REVERT: H 420 ASP cc_start: 0.7332 (p0) cc_final: 0.7106 (p0) REVERT: I 84 LYS cc_start: 0.8334 (mttt) cc_final: 0.8064 (tttt) REVERT: I 399 GLU cc_start: 0.6644 (tp30) cc_final: 0.6263 (tp30) REVERT: J 84 LYS cc_start: 0.8318 (mttt) cc_final: 0.7983 (tttt) REVERT: K 84 LYS cc_start: 0.8278 (mttt) cc_final: 0.7963 (tttt) REVERT: K 305 THR cc_start: 0.7244 (p) cc_final: 0.6990 (p) REVERT: K 378 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7271 (mt-10) REVERT: K 420 ASP cc_start: 0.7388 (p0) cc_final: 0.7153 (p0) REVERT: L 84 LYS cc_start: 0.8345 (mttt) cc_final: 0.8077 (tttt) REVERT: L 399 GLU cc_start: 0.6652 (tp30) cc_final: 0.6260 (tp30) REVERT: a 65 ARG cc_start: 0.6326 (mtp180) cc_final: 0.5409 (mtp180) REVERT: b 46 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8096 (tptm) REVERT: d 62 TYR cc_start: 0.6354 (m-80) cc_final: 0.5888 (m-10) REVERT: f 59 ARG cc_start: 0.7529 (mmp-170) cc_final: 0.7295 (mmp-170) REVERT: g 62 TYR cc_start: 0.6127 (m-80) cc_final: 0.5789 (m-10) REVERT: j 62 TYR cc_start: 0.6362 (m-80) cc_final: 0.5900 (m-10) outliers start: 239 outliers final: 184 residues processed: 1298 average time/residue: 0.6670 time to fit residues: 1415.9255 Evaluate side-chains 1337 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1152 time to evaluate : 6.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 424 GLN Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 42 VAL Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 46 LYS Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 42 VAL Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 407 optimal weight: 7.9990 chunk 263 optimal weight: 0.0060 chunk 393 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 419 optimal weight: 2.9990 chunk 449 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 518 optimal weight: 0.0980 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 215 ASN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 54576 Z= 0.230 Angle : 0.641 7.940 74028 Z= 0.330 Chirality : 0.043 0.208 8196 Planarity : 0.005 0.048 9804 Dihedral : 5.255 26.391 7465 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 4.38 % Allowed : 17.16 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.09), residues: 6816 helix: -0.70 (0.10), residues: 2460 sheet: -2.39 (0.21), residues: 588 loop : -2.89 (0.09), residues: 3768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 49 HIS 0.006 0.001 HIS C 185 PHE 0.041 0.002 PHE F 30 TYR 0.015 0.001 TYR C 132 ARG 0.014 0.001 ARG I 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 1153 time to evaluate : 5.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8318 (mttt) cc_final: 0.7964 (tttt) REVERT: A 378 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7080 (mt-10) REVERT: B 23 ARG cc_start: 0.7954 (tpt90) cc_final: 0.7168 (tpt-90) REVERT: B 84 LYS cc_start: 0.8280 (mttt) cc_final: 0.7980 (tttt) REVERT: B 305 THR cc_start: 0.7254 (p) cc_final: 0.7000 (p) REVERT: B 378 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7287 (mt-10) REVERT: C 84 LYS cc_start: 0.8335 (mttt) cc_final: 0.8067 (tttt) REVERT: C 160 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7108 (tpt-90) REVERT: C 399 GLU cc_start: 0.6732 (tp30) cc_final: 0.6327 (tp30) REVERT: D 84 LYS cc_start: 0.8313 (mttt) cc_final: 0.7950 (tttt) REVERT: D 378 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7102 (mt-10) REVERT: E 23 ARG cc_start: 0.7964 (tpt90) cc_final: 0.7252 (tpt-90) REVERT: E 84 LYS cc_start: 0.8274 (mttt) cc_final: 0.7970 (tttt) REVERT: E 305 THR cc_start: 0.7377 (p) cc_final: 0.7101 (p) REVERT: E 378 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7297 (mt-10) REVERT: F 84 LYS cc_start: 0.8326 (mttt) cc_final: 0.8063 (tttt) REVERT: F 142 SER cc_start: 0.8979 (m) cc_final: 0.8699 (p) REVERT: F 399 GLU cc_start: 0.6761 (tp30) cc_final: 0.6393 (tp30) REVERT: G 84 LYS cc_start: 0.8311 (mttt) cc_final: 0.7952 (tttt) REVERT: G 378 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7088 (mt-10) REVERT: H 84 LYS cc_start: 0.8269 (mttt) cc_final: 0.7966 (tttt) REVERT: H 160 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.7089 (mtp85) REVERT: H 305 THR cc_start: 0.7371 (p) cc_final: 0.7110 (p) REVERT: H 378 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7290 (mt-10) REVERT: I 84 LYS cc_start: 0.8322 (mttt) cc_final: 0.8074 (tttt) REVERT: I 399 GLU cc_start: 0.6725 (tp30) cc_final: 0.6327 (tp30) REVERT: J 84 LYS cc_start: 0.8316 (mttt) cc_final: 0.7963 (tttt) REVERT: K 23 ARG cc_start: 0.7975 (tpt90) cc_final: 0.7245 (tpt-90) REVERT: K 84 LYS cc_start: 0.8285 (mttt) cc_final: 0.7985 (tttt) REVERT: K 305 THR cc_start: 0.7269 (p) cc_final: 0.7017 (p) REVERT: K 378 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7283 (mt-10) REVERT: K 420 ASP cc_start: 0.7519 (p0) cc_final: 0.7259 (p0) REVERT: L 84 LYS cc_start: 0.8328 (mttt) cc_final: 0.8064 (tttt) REVERT: L 160 ARG cc_start: 0.7434 (mmm-85) cc_final: 0.7180 (mtp85) REVERT: L 399 GLU cc_start: 0.6762 (tp30) cc_final: 0.6359 (tp30) REVERT: a 62 TYR cc_start: 0.6186 (m-80) cc_final: 0.5802 (m-10) REVERT: d 62 TYR cc_start: 0.6221 (m-80) cc_final: 0.5820 (m-10) REVERT: d 65 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7117 (ttp80) REVERT: f 16 GLU cc_start: 0.7874 (mp0) cc_final: 0.7635 (mp0) REVERT: g 62 TYR cc_start: 0.5906 (m-80) cc_final: 0.5501 (m-10) REVERT: j 62 TYR cc_start: 0.6233 (m-80) cc_final: 0.5819 (m-10) outliers start: 250 outliers final: 195 residues processed: 1268 average time/residue: 0.6981 time to fit residues: 1449.6215 Evaluate side-chains 1327 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 1131 time to evaluate : 5.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 424 GLN Chi-restraints excluded: chain H residue 26 ASN Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain a residue 8 SER Chi-restraints excluded: chain a residue 12 THR Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 12 THR Chi-restraints excluded: chain e residue 46 LYS Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 46 LYS Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 84 VAL Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 46 LYS Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 12 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 599 optimal weight: 0.8980 chunk 631 optimal weight: 0.7980 chunk 576 optimal weight: 30.0000 chunk 614 optimal weight: 0.0770 chunk 369 optimal weight: 9.9990 chunk 267 optimal weight: 4.9990 chunk 482 optimal weight: 0.0000 chunk 188 optimal weight: 8.9990 chunk 555 optimal weight: 8.9990 chunk 581 optimal weight: 10.0000 chunk 612 optimal weight: 8.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 54576 Z= 0.174 Angle : 0.612 9.402 74028 Z= 0.313 Chirality : 0.041 0.188 8196 Planarity : 0.005 0.048 9804 Dihedral : 5.000 25.398 7465 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.22 % Allowed : 18.61 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.10), residues: 6816 helix: -0.40 (0.11), residues: 2460 sheet: -2.27 (0.21), residues: 588 loop : -2.78 (0.09), residues: 3768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 49 HIS 0.005 0.001 HIS C 185 PHE 0.035 0.002 PHE L 30 TYR 0.014 0.001 TYR l 113 ARG 0.009 0.001 ARG j 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 1219 time to evaluate : 6.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8298 (mttt) cc_final: 0.7949 (tttt) REVERT: A 160 ARG cc_start: 0.7517 (mmm-85) cc_final: 0.6732 (mmm160) REVERT: B 84 LYS cc_start: 0.8267 (mttt) cc_final: 0.7953 (tttt) REVERT: B 378 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7241 (mt-10) REVERT: C 94 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8037 (tm-30) REVERT: C 142 SER cc_start: 0.8853 (m) cc_final: 0.8636 (p) REVERT: C 399 GLU cc_start: 0.6756 (tp30) cc_final: 0.6426 (tp30) REVERT: D 84 LYS cc_start: 0.8296 (mttt) cc_final: 0.7929 (tttt) REVERT: E 84 LYS cc_start: 0.8257 (mttt) cc_final: 0.7935 (tttt) REVERT: E 378 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7248 (mt-10) REVERT: F 84 LYS cc_start: 0.8325 (mttt) cc_final: 0.8052 (tttt) REVERT: F 142 SER cc_start: 0.8920 (m) cc_final: 0.8702 (p) REVERT: F 399 GLU cc_start: 0.6701 (tp30) cc_final: 0.6374 (tp30) REVERT: G 84 LYS cc_start: 0.8298 (mttt) cc_final: 0.7928 (tttt) REVERT: G 157 ARG cc_start: 0.7525 (mtp180) cc_final: 0.7315 (mtp180) REVERT: G 189 MET cc_start: 0.8537 (mmm) cc_final: 0.8303 (mmm) REVERT: G 378 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7075 (mt-10) REVERT: H 84 LYS cc_start: 0.8253 (mttt) cc_final: 0.7938 (tttt) REVERT: H 378 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7231 (mt-10) REVERT: I 84 LYS cc_start: 0.8312 (mttt) cc_final: 0.8057 (tttt) REVERT: I 94 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8133 (tm-30) REVERT: I 160 ARG cc_start: 0.7342 (mmm-85) cc_final: 0.6993 (tpt-90) REVERT: I 399 GLU cc_start: 0.6721 (tp30) cc_final: 0.6390 (tp30) REVERT: J 84 LYS cc_start: 0.8376 (mttt) cc_final: 0.8017 (tttt) REVERT: K 84 LYS cc_start: 0.8335 (mttt) cc_final: 0.7906 (tttt) REVERT: K 369 GLU cc_start: 0.7374 (tt0) cc_final: 0.7077 (pt0) REVERT: K 378 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7225 (mt-10) REVERT: K 420 ASP cc_start: 0.7455 (p0) cc_final: 0.7211 (p0) REVERT: L 84 LYS cc_start: 0.8322 (mttt) cc_final: 0.8058 (tttt) REVERT: L 160 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.7176 (mtp85) REVERT: L 399 GLU cc_start: 0.6744 (tp30) cc_final: 0.6383 (tp30) REVERT: a 62 TYR cc_start: 0.6139 (m-80) cc_final: 0.5811 (m-10) REVERT: a 65 ARG cc_start: 0.6287 (mtp180) cc_final: 0.6029 (mtm180) REVERT: d 62 TYR cc_start: 0.5983 (m-80) cc_final: 0.5498 (m-10) REVERT: d 65 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7223 (ttm-80) REVERT: f 59 ARG cc_start: 0.8819 (tpp-160) cc_final: 0.8374 (tpm170) REVERT: g 62 TYR cc_start: 0.5906 (m-80) cc_final: 0.5590 (m-10) REVERT: i 16 GLU cc_start: 0.7896 (pm20) cc_final: 0.7645 (pm20) REVERT: j 62 TYR cc_start: 0.6002 (m-80) cc_final: 0.5523 (m-10) REVERT: l 16 GLU cc_start: 0.8193 (mp0) cc_final: 0.7947 (mp0) outliers start: 184 outliers final: 158 residues processed: 1300 average time/residue: 0.6685 time to fit residues: 1425.0228 Evaluate side-chains 1317 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1159 time to evaluate : 6.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 424 GLN Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 46 LYS Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain h residue 46 LYS Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 46 LYS Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 403 optimal weight: 10.0000 chunk 649 optimal weight: 0.8980 chunk 396 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 chunk 451 optimal weight: 10.0000 chunk 681 optimal weight: 0.9980 chunk 627 optimal weight: 10.0000 chunk 542 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 419 optimal weight: 3.9990 chunk 332 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 ASN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 215 ASN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 54576 Z= 0.262 Angle : 0.666 9.681 74028 Z= 0.341 Chirality : 0.043 0.153 8196 Planarity : 0.005 0.059 9804 Dihedral : 5.213 26.840 7465 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.38 % Allowed : 18.86 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.09), residues: 6816 helix: -0.53 (0.11), residues: 2460 sheet: -2.31 (0.21), residues: 588 loop : -2.77 (0.09), residues: 3768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 66 HIS 0.005 0.002 HIS L 179 PHE 0.041 0.002 PHE C 30 TYR 0.013 0.001 TYR l 113 ARG 0.010 0.001 ARG g 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 1147 time to evaluate : 6.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8320 (mttt) cc_final: 0.7966 (tttt) REVERT: A 373 GLU cc_start: 0.7869 (tp30) cc_final: 0.7491 (mm-30) REVERT: A 378 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7160 (mt-10) REVERT: B 23 ARG cc_start: 0.8057 (tpt90) cc_final: 0.7258 (tpt-90) REVERT: B 84 LYS cc_start: 0.8277 (mttt) cc_final: 0.7999 (tttt) REVERT: B 305 THR cc_start: 0.7256 (p) cc_final: 0.7001 (p) REVERT: B 378 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7280 (mt-10) REVERT: C 160 ARG cc_start: 0.7344 (mmm-85) cc_final: 0.7096 (mtp85) REVERT: D 84 LYS cc_start: 0.8296 (mttt) cc_final: 0.7951 (tttt) REVERT: E 23 ARG cc_start: 0.8011 (tpt90) cc_final: 0.7258 (tpt-90) REVERT: E 84 LYS cc_start: 0.8277 (mttt) cc_final: 0.7986 (tttt) REVERT: E 160 ARG cc_start: 0.7335 (mmm-85) cc_final: 0.7008 (mtp85) REVERT: E 305 THR cc_start: 0.7343 (p) cc_final: 0.7080 (p) REVERT: E 378 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7291 (mt-10) REVERT: F 84 LYS cc_start: 0.8333 (mttt) cc_final: 0.8072 (tttt) REVERT: F 142 SER cc_start: 0.8985 (m) cc_final: 0.8696 (p) REVERT: F 399 GLU cc_start: 0.6881 (tp30) cc_final: 0.6520 (tp30) REVERT: F 420 ASP cc_start: 0.7653 (p0) cc_final: 0.7400 (p0) REVERT: G 84 LYS cc_start: 0.8305 (mttt) cc_final: 0.7947 (tttt) REVERT: G 189 MET cc_start: 0.8542 (mmm) cc_final: 0.8280 (mmm) REVERT: G 378 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7134 (mt-10) REVERT: H 84 LYS cc_start: 0.8267 (mttt) cc_final: 0.7984 (tttt) REVERT: H 160 ARG cc_start: 0.7568 (mmm-85) cc_final: 0.7185 (mtp85) REVERT: H 305 THR cc_start: 0.7340 (p) cc_final: 0.7085 (p) REVERT: H 378 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7273 (mt-10) REVERT: I 84 LYS cc_start: 0.8324 (mttt) cc_final: 0.8077 (tttt) REVERT: I 159 LYS cc_start: 0.7578 (pptt) cc_final: 0.7126 (mttm) REVERT: I 160 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.6973 (mtp85) REVERT: I 399 GLU cc_start: 0.6844 (tp30) cc_final: 0.6478 (tp30) REVERT: J 75 ASP cc_start: 0.7936 (p0) cc_final: 0.7631 (p0) REVERT: J 84 LYS cc_start: 0.8311 (mttt) cc_final: 0.7957 (tttt) REVERT: J 160 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.6798 (mmm160) REVERT: K 23 ARG cc_start: 0.8058 (tpt90) cc_final: 0.7284 (tpt-90) REVERT: K 84 LYS cc_start: 0.8382 (mttt) cc_final: 0.7977 (tttt) REVERT: K 305 THR cc_start: 0.7315 (p) cc_final: 0.7075 (p) REVERT: K 378 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7273 (mt-10) REVERT: K 420 ASP cc_start: 0.7534 (p0) cc_final: 0.7266 (p0) REVERT: L 84 LYS cc_start: 0.8341 (mttt) cc_final: 0.8079 (tttt) REVERT: L 160 ARG cc_start: 0.7544 (mmm-85) cc_final: 0.7153 (mtp-110) REVERT: a 65 ARG cc_start: 0.6344 (mtp180) cc_final: 0.6124 (mtm180) REVERT: d 62 TYR cc_start: 0.5960 (m-80) cc_final: 0.5479 (m-10) REVERT: f 65 ARG cc_start: 0.7452 (tpp80) cc_final: 0.6284 (tpp80) REVERT: g 62 TYR cc_start: 0.5966 (m-80) cc_final: 0.5687 (m-10) REVERT: g 65 ARG cc_start: 0.6170 (mtm180) cc_final: 0.5827 (mtt180) REVERT: j 62 TYR cc_start: 0.6146 (m-80) cc_final: 0.5638 (m-10) REVERT: j 65 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.6811 (ttp80) REVERT: l 16 GLU cc_start: 0.8049 (mp0) cc_final: 0.7777 (mp0) outliers start: 193 outliers final: 168 residues processed: 1232 average time/residue: 0.6764 time to fit residues: 1365.8534 Evaluate side-chains 1299 residues out of total 5712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 1131 time to evaluate : 5.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 364 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 210 MET Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 364 ILE Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 424 GLN Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 256 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 364 ILE Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 364 ILE Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 431 GLU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 VAL Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 424 GLN Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 177 ILE Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain b residue 89 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 79 ILE Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 46 LYS Chi-restraints excluded: chain h residue 79 ILE Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 89 THR Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 84 VAL Chi-restraints excluded: chain i residue 89 THR Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 88 SER Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain l residue 84 VAL Chi-restraints excluded: chain l residue 89 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 431 optimal weight: 4.9990 chunk 578 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 500 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 543 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 558 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 228 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 = 0.3764 r_free = 0.3764 target = 0.162426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.137076 restraints weight = 77596.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.140610 restraints weight = 44071.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.142873 restraints weight = 30386.224| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 54576 Z= 0.231 Angle : 0.654 9.600 74028 Z= 0.334 Chirality : 0.043 0.191 8196 Planarity : 0.005 0.045 9804 Dihedral : 5.171 27.288 7465 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.19 % Allowed : 18.87 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.10), residues: 6816 helix: -0.37 (0.11), residues: 2460 sheet: -2.31 (0.21), residues: 588 loop : -2.78 (0.09), residues: 3768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 49 HIS 0.004 0.001 HIS L 179 PHE 0.038 0.002 PHE F 30 TYR 0.013 0.001 TYR l 113 ARG 0.009 0.001 ARG g 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20028.99 seconds wall clock time: 391 minutes 54.43 seconds (23514.43 seconds total)