Starting phenix.real_space_refine on Sun Sep 29 00:01:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/09_2024/6kff_9971.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/09_2024/6kff_9971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/09_2024/6kff_9971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/09_2024/6kff_9971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/09_2024/6kff_9971.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/09_2024/6kff_9971.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14072 2.51 5 N 3432 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21192 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 6.57, per 1000 atoms: 0.31 Number of scatterers: 21192 At special positions: 0 Unit cell: (121.968, 121.968, 108.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3592 8.00 N 3432 7.00 C 14072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 248 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.75 Conformation dependent library (CDL) restraints added in 2.7 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 71.7% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix removed outlier: 3.830A pdb=" N GLY A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 212 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix removed outlier: 3.829A pdb=" N GLY B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 212 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 350 Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.537A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix removed outlier: 3.829A pdb=" N GLY C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 212 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 276 through 305 removed outlier: 4.070A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 305 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 350 Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.537A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN C 363 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 53 removed outlier: 4.057A pdb=" N ARG D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix removed outlier: 3.830A pdb=" N GLY D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 168 Processing helix chain 'D' and resid 168 through 182 removed outlier: 3.915A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 212 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 305 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 350 Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN D 363 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 364 " --> pdb=" O SER D 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix removed outlier: 3.829A pdb=" N GLY E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 removed outlier: 4.146A pdb=" N LYS E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 212 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 305 " --> pdb=" O TYR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE E 330 " --> pdb=" O SER E 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 350 Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN E 363 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE E 364 " --> pdb=" O SER E 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 134 removed outlier: 4.479A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix removed outlier: 3.830A pdb=" N GLY F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 168 through 182 removed outlier: 3.917A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 212 Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS F 305 " --> pdb=" O TYR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 350 Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN F 363 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 364 " --> pdb=" O SER F 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 134 removed outlier: 4.479A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix removed outlier: 3.829A pdb=" N GLY G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 4.146A pdb=" N LYS G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 168 Processing helix chain 'G' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 212 Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 276 through 305 removed outlier: 4.070A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 305 " --> pdb=" O TYR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 308 No H-bonds generated for 'chain 'G' and resid 306 through 308' Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 326 through 335 removed outlier: 3.548A pdb=" N PHE G 330 " --> pdb=" O SER G 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G 331 " --> pdb=" O ASP G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 350 Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG G 362 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN G 363 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 364 " --> pdb=" O SER G 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 53 removed outlier: 4.057A pdb=" N ARG H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix removed outlier: 3.829A pdb=" N GLY H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 212 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS H 305 " --> pdb=" O TYR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 308 No H-bonds generated for 'chain 'H' and resid 306 through 308' Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE H 330 " --> pdb=" O SER H 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE H 331 " --> pdb=" O ASP H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 350 Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG H 362 " --> pdb=" O THR H 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN H 363 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE H 364 " --> pdb=" O SER H 360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA4, first strand: chain 'D' and resid 56 through 57 Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 57 Processing sheet with id=AA6, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AA7, first strand: chain 'G' and resid 56 through 57 Processing sheet with id=AA8, first strand: chain 'H' and resid 56 through 57 1240 hydrogen bonds defined for protein. 3624 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: 7.10 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6312 1.34 - 1.46: 5601 1.46 - 1.58: 9791 1.58 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 21832 Sorted by residual: bond pdb=" C ARG G 168 " pdb=" N PRO G 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.17e-01 bond pdb=" C ARG H 168 " pdb=" N PRO H 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.07e-01 bond pdb=" C ARG D 168 " pdb=" N PRO D 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.06e-01 bond pdb=" C ARG E 168 " pdb=" N PRO E 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.74e-01 bond pdb=" C ARG A 168 " pdb=" N PRO A 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.66e-01 ... (remaining 21827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 28985 1.49 - 2.98: 591 2.98 - 4.46: 79 4.46 - 5.95: 65 5.95 - 7.44: 24 Bond angle restraints: 29744 Sorted by residual: angle pdb=" C TRP G 107 " pdb=" N VAL G 108 " pdb=" CA VAL G 108 " ideal model delta sigma weight residual 120.33 122.46 -2.13 8.00e-01 1.56e+00 7.06e+00 angle pdb=" C TRP B 107 " pdb=" N VAL B 108 " pdb=" CA VAL B 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 7.00e+00 angle pdb=" C TRP C 107 " pdb=" N VAL C 108 " pdb=" CA VAL C 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 6.99e+00 angle pdb=" C TRP F 107 " pdb=" N VAL F 108 " pdb=" CA VAL F 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 6.99e+00 angle pdb=" C TRP E 107 " pdb=" N VAL E 108 " pdb=" CA VAL E 108 " ideal model delta sigma weight residual 120.33 122.44 -2.11 8.00e-01 1.56e+00 6.93e+00 ... (remaining 29739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 10928 17.32 - 34.64: 1244 34.64 - 51.96: 210 51.96 - 69.28: 16 69.28 - 86.60: 40 Dihedral angle restraints: 12438 sinusoidal: 4798 harmonic: 7640 Sorted by residual: dihedral pdb=" CB CYS A 76 " pdb=" SG CYS A 76 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 137.00 -44.00 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CA GLU C 274 " pdb=" C GLU C 274 " pdb=" N LYS C 275 " pdb=" CA LYS C 275 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLU H 274 " pdb=" C GLU H 274 " pdb=" N LYS H 275 " pdb=" CA LYS H 275 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 12435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1859 0.026 - 0.051: 855 0.051 - 0.077: 412 0.077 - 0.103: 108 0.103 - 0.129: 54 Chirality restraints: 3288 Sorted by residual: chirality pdb=" CA TRP B 236 " pdb=" N TRP B 236 " pdb=" C TRP B 236 " pdb=" CB TRP B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA TRP G 236 " pdb=" N TRP G 236 " pdb=" C TRP G 236 " pdb=" CB TRP G 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA TRP F 236 " pdb=" N TRP F 236 " pdb=" C TRP F 236 " pdb=" CB TRP F 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 3285 not shown) Planarity restraints: 3632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 119 " -0.010 2.00e-02 2.50e+03 9.91e-03 1.72e+00 pdb=" CG PHE D 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE D 119 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 119 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE D 119 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 119 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 119 " -0.010 2.00e-02 2.50e+03 9.75e-03 1.66e+00 pdb=" CG PHE F 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE F 119 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE F 119 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 119 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 119 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 119 " -0.009 2.00e-02 2.50e+03 9.75e-03 1.66e+00 pdb=" CG PHE C 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 119 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 119 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 119 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 119 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 119 " -0.002 2.00e-02 2.50e+03 ... (remaining 3629 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 133 2.60 - 3.18: 19389 3.18 - 3.75: 32896 3.75 - 4.33: 41863 4.33 - 4.90: 69294 Nonbonded interactions: 163575 Sorted by model distance: nonbonded pdb=" SG CYS G 76 " pdb=" SG CYS G 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 76 " pdb=" SG CYS D 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS E 76 " pdb=" SG CYS E 248 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS H 76 " pdb=" SG CYS H 248 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 76 " pdb=" SG CYS B 248 " model vdw 2.030 3.760 ... (remaining 163570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.190 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 42.660 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.004 0.026 21832 Z= 0.226 Angle : 0.604 7.440 29744 Z= 0.321 Chirality : 0.038 0.129 3288 Planarity : 0.003 0.021 3632 Dihedral : 15.084 86.599 7472 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 0.35 % Allowed : 6.96 % Favored : 92.69 % 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: -2.57 (0.15), residues: 2496 helix: -0.50 (0.11), residues: 1672 sheet: -4.64 (0.29), residues: 80 loop : -4.12 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 68 HIS 0.004 0.001 HIS A 50 PHE 0.023 0.001 PHE D 119 TYR 0.009 0.001 TYR B 110 ARG 0.002 0.000 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 926 time to evaluate : 2.358 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: A 137 LEU cc_start: 0.9301 (tt) cc_final: 0.9094 (tt) REVERT: A 153 ASP cc_start: 0.8634 (m-30) cc_final: 0.8271 (m-30) REVERT: A 166 GLU cc_start: 0.7628 (pt0) cc_final: 0.7270 (pt0) REVERT: A 175 ASP cc_start: 0.8000 (m-30) cc_final: 0.7429 (m-30) REVERT: A 194 LEU cc_start: 0.9418 (mt) cc_final: 0.9043 (mt) REVERT: A 208 TYR cc_start: 0.8326 (t80) cc_final: 0.7846 (t80) REVERT: A 304 ASN cc_start: 0.8695 (t0) cc_final: 0.8389 (t0) REVERT: A 310 LYS cc_start: 0.6931 (ttpt) cc_final: 0.6552 (tptt) REVERT: A 339 LEU cc_start: 0.9254 (tp) cc_final: 0.9036 (tp) REVERT: A 353 PRO cc_start: 0.9486 (Cg_endo) cc_final: 0.9219 (Cg_exo) REVERT: B 58 CYS cc_start: 0.6717 (m) cc_final: 0.6494 (m) REVERT: B 146 ARG cc_start: 0.8918 (ttp80) cc_final: 0.8343 (mtm110) REVERT: B 153 ASP cc_start: 0.8678 (m-30) cc_final: 0.8243 (m-30) REVERT: B 172 TYR cc_start: 0.9068 (t80) cc_final: 0.8817 (t80) REVERT: B 270 ASN cc_start: 0.9167 (t0) cc_final: 0.8855 (t0) REVERT: B 304 ASN cc_start: 0.8321 (t0) cc_final: 0.7817 (t0) REVERT: B 310 LYS cc_start: 0.7220 (ttpt) cc_final: 0.6514 (tptt) REVERT: B 332 SER cc_start: 0.9205 (t) cc_final: 0.8999 (t) REVERT: B 353 PRO cc_start: 0.9576 (Cg_endo) cc_final: 0.9325 (Cg_exo) REVERT: B 359 ILE cc_start: 0.9395 (tp) cc_final: 0.9132 (tp) REVERT: C 154 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8066 (mtmt) REVERT: C 157 LYS cc_start: 0.8268 (tptt) cc_final: 0.7688 (ttpp) REVERT: C 198 TRP cc_start: 0.8737 (t-100) cc_final: 0.8528 (t-100) REVERT: C 208 TYR cc_start: 0.8275 (t80) cc_final: 0.7811 (t80) REVERT: C 310 LYS cc_start: 0.6681 (ttpt) cc_final: 0.6165 (tptt) REVERT: C 339 LEU cc_start: 0.9253 (tp) cc_final: 0.9039 (tp) REVERT: C 353 PRO cc_start: 0.9551 (Cg_endo) cc_final: 0.9235 (Cg_exo) REVERT: C 359 ILE cc_start: 0.9411 (tp) cc_final: 0.9207 (tp) REVERT: D 58 CYS cc_start: 0.7177 (m) cc_final: 0.6803 (m) REVERT: D 146 ARG cc_start: 0.8910 (ttp80) cc_final: 0.8286 (mtp-110) REVERT: D 192 TYR cc_start: 0.9016 (t80) cc_final: 0.8656 (t80) REVERT: D 270 ASN cc_start: 0.9148 (t0) cc_final: 0.8821 (t0) REVERT: D 304 ASN cc_start: 0.8353 (t0) cc_final: 0.8030 (t0) REVERT: D 310 LYS cc_start: 0.6960 (ttpt) cc_final: 0.6510 (tptt) REVERT: D 325 ILE cc_start: 0.8840 (mp) cc_final: 0.8622 (mp) REVERT: D 353 PRO cc_start: 0.9527 (Cg_endo) cc_final: 0.9307 (Cg_exo) REVERT: D 359 ILE cc_start: 0.9389 (tp) cc_final: 0.9184 (tp) REVERT: E 65 ASN cc_start: 0.7162 (p0) cc_final: 0.6726 (p0) REVERT: E 68 TRP cc_start: 0.7866 (t-100) cc_final: 0.7656 (t-100) REVERT: E 157 LYS cc_start: 0.8300 (tptt) cc_final: 0.7881 (ttpp) REVERT: E 166 GLU cc_start: 0.7558 (pt0) cc_final: 0.7223 (pt0) REVERT: E 178 ARG cc_start: 0.8938 (ttm-80) cc_final: 0.8667 (ttp-110) REVERT: E 208 TYR cc_start: 0.8103 (t80) cc_final: 0.7539 (t80) REVERT: E 310 LYS cc_start: 0.7104 (ttpt) cc_final: 0.6594 (tptt) REVERT: E 339 LEU cc_start: 0.9204 (tp) cc_final: 0.9002 (tp) REVERT: F 58 CYS cc_start: 0.7240 (m) cc_final: 0.6896 (m) REVERT: F 157 LYS cc_start: 0.8360 (tptt) cc_final: 0.7717 (ttmm) REVERT: F 194 LEU cc_start: 0.9221 (mt) cc_final: 0.8908 (mt) REVERT: F 310 LYS cc_start: 0.7153 (ttpt) cc_final: 0.6762 (tptt) REVERT: F 353 PRO cc_start: 0.9581 (Cg_endo) cc_final: 0.9301 (Cg_exo) REVERT: G 154 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8243 (mtpt) REVERT: G 157 LYS cc_start: 0.8301 (tptt) cc_final: 0.7725 (ttpp) REVERT: G 208 TYR cc_start: 0.8240 (t80) cc_final: 0.7752 (t80) REVERT: G 310 LYS cc_start: 0.6964 (ttpt) cc_final: 0.6236 (tptt) REVERT: G 322 LYS cc_start: 0.7669 (pttm) cc_final: 0.6898 (mptt) REVERT: G 339 LEU cc_start: 0.9308 (tp) cc_final: 0.9078 (tp) REVERT: G 353 PRO cc_start: 0.9542 (Cg_endo) cc_final: 0.9273 (Cg_exo) REVERT: G 359 ILE cc_start: 0.9350 (tp) cc_final: 0.9144 (tp) REVERT: H 58 CYS cc_start: 0.7131 (m) cc_final: 0.6644 (m) REVERT: H 192 TYR cc_start: 0.8960 (t80) cc_final: 0.8760 (t80) REVERT: H 310 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6603 (tptt) REVERT: H 313 LYS cc_start: 0.9300 (ttmt) cc_final: 0.9082 (ttmm) outliers start: 8 outliers final: 6 residues processed: 928 average time/residue: 0.3653 time to fit residues: 502.9499 Evaluate side-chains 753 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 747 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain H residue 171 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 67 GLN A 234 ASN A 247 HIS A 329 GLN B 21 GLN B 73 ASN B 234 ASN B 247 HIS B 329 GLN C 206 GLN C 234 ASN C 247 HIS C 329 GLN D 21 GLN D 73 ASN D 234 ASN D 247 HIS D 329 GLN E 50 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN E 247 HIS E 329 GLN F 21 GLN F 50 HIS F 73 ASN F 234 ASN F 247 HIS F 329 GLN G 234 ASN G 247 HIS G 329 GLN H 21 GLN H 50 HIS H 73 ASN H 234 ASN H 247 HIS H 329 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21832 Z= 0.307 Angle : 0.669 10.610 29744 Z= 0.326 Chirality : 0.043 0.188 3288 Planarity : 0.004 0.029 3632 Dihedral : 4.978 23.608 2798 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.77 % Allowed : 21.19 % Favored : 75.04 % 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: -1.18 (0.17), residues: 2496 helix: 0.53 (0.12), residues: 1688 sheet: -3.99 (0.47), residues: 80 loop : -3.59 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 59 HIS 0.010 0.002 HIS F 50 PHE 0.022 0.002 PHE D 242 TYR 0.017 0.002 TYR G 301 ARG 0.005 0.000 ARG E 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 780 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.6529 (p0) cc_final: 0.6322 (p0) REVERT: A 123 ARG cc_start: 0.8329 (ttm170) cc_final: 0.8044 (ttp-170) REVERT: A 153 ASP cc_start: 0.8512 (m-30) cc_final: 0.7998 (m-30) REVERT: A 157 LYS cc_start: 0.8219 (tptt) cc_final: 0.7629 (ttmm) REVERT: A 206 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8683 (mm110) REVERT: A 208 TYR cc_start: 0.8230 (t80) cc_final: 0.7793 (t80) REVERT: A 310 LYS cc_start: 0.6957 (ttpt) cc_final: 0.6565 (tptt) REVERT: A 353 PRO cc_start: 0.9464 (Cg_endo) cc_final: 0.9211 (Cg_exo) REVERT: B 146 ARG cc_start: 0.8970 (ttp80) cc_final: 0.8384 (mtm110) REVERT: B 153 ASP cc_start: 0.8716 (m-30) cc_final: 0.8358 (m-30) REVERT: B 158 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8005 (t80) REVERT: B 208 TYR cc_start: 0.8364 (t80) cc_final: 0.8105 (t80) REVERT: B 310 LYS cc_start: 0.7125 (ttpt) cc_final: 0.6524 (tptt) REVERT: B 332 SER cc_start: 0.9041 (t) cc_final: 0.8824 (t) REVERT: B 353 PRO cc_start: 0.9590 (Cg_endo) cc_final: 0.9369 (Cg_exo) REVERT: B 359 ILE cc_start: 0.9474 (tp) cc_final: 0.9170 (tp) REVERT: C 58 CYS cc_start: 0.8845 (m) cc_final: 0.8410 (m) REVERT: C 65 ASN cc_start: 0.7252 (p0) cc_final: 0.6732 (p0) REVERT: C 153 ASP cc_start: 0.8801 (m-30) cc_final: 0.8156 (m-30) REVERT: C 154 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8177 (mtpt) REVERT: C 157 LYS cc_start: 0.8217 (tptt) cc_final: 0.7791 (ttpp) REVERT: C 198 TRP cc_start: 0.8789 (t-100) cc_final: 0.8536 (t-100) REVERT: C 208 TYR cc_start: 0.8249 (t80) cc_final: 0.7812 (t80) REVERT: C 310 LYS cc_start: 0.6788 (ttpt) cc_final: 0.6181 (tptt) REVERT: C 353 PRO cc_start: 0.9488 (Cg_endo) cc_final: 0.9236 (Cg_exo) REVERT: C 359 ILE cc_start: 0.9403 (tp) cc_final: 0.9194 (tp) REVERT: D 146 ARG cc_start: 0.8976 (ttp80) cc_final: 0.8304 (mtp-110) REVERT: D 153 ASP cc_start: 0.8824 (m-30) cc_final: 0.8412 (m-30) REVERT: D 192 TYR cc_start: 0.9050 (t80) cc_final: 0.8737 (t80) REVERT: D 267 LEU cc_start: 0.9300 (mp) cc_final: 0.9062 (mt) REVERT: D 310 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6759 (tptt) REVERT: D 332 SER cc_start: 0.9078 (m) cc_final: 0.8818 (t) REVERT: D 353 PRO cc_start: 0.9533 (Cg_endo) cc_final: 0.9332 (Cg_exo) REVERT: D 359 ILE cc_start: 0.9479 (tp) cc_final: 0.9236 (tp) REVERT: E 58 CYS cc_start: 0.8792 (m) cc_final: 0.8242 (m) REVERT: E 157 LYS cc_start: 0.8378 (tptt) cc_final: 0.7882 (ttmm) REVERT: E 178 ARG cc_start: 0.8978 (ttm-80) cc_final: 0.8776 (ttp-110) REVERT: E 206 GLN cc_start: 0.9246 (mm-40) cc_final: 0.8579 (mm-40) REVERT: E 208 TYR cc_start: 0.8095 (t80) cc_final: 0.7463 (t80) REVERT: E 310 LYS cc_start: 0.7242 (ttpt) cc_final: 0.6729 (tptt) REVERT: F 137 LEU cc_start: 0.9271 (tt) cc_final: 0.9068 (tt) REVERT: F 157 LYS cc_start: 0.8244 (tptt) cc_final: 0.7733 (ttmm) REVERT: F 310 LYS cc_start: 0.7126 (ttpt) cc_final: 0.6723 (tptt) REVERT: G 58 CYS cc_start: 0.8863 (m) cc_final: 0.8435 (m) REVERT: G 65 ASN cc_start: 0.7257 (p0) cc_final: 0.6956 (p0) REVERT: G 67 GLN cc_start: 0.7738 (mt0) cc_final: 0.7458 (mt0) REVERT: G 68 TRP cc_start: 0.7938 (t-100) cc_final: 0.7729 (t-100) REVERT: G 153 ASP cc_start: 0.8802 (m-30) cc_final: 0.8458 (m-30) REVERT: G 154 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8174 (mtpt) REVERT: G 157 LYS cc_start: 0.8269 (tptt) cc_final: 0.7763 (ttpp) REVERT: G 208 TYR cc_start: 0.8209 (t80) cc_final: 0.7770 (t80) REVERT: G 310 LYS cc_start: 0.6913 (ttpt) cc_final: 0.6320 (tptt) REVERT: G 322 LYS cc_start: 0.7788 (pttm) cc_final: 0.6737 (mptt) REVERT: H 137 LEU cc_start: 0.9355 (tt) cc_final: 0.9147 (tt) REVERT: H 146 ARG cc_start: 0.8951 (ttp80) cc_final: 0.8496 (mtp-110) REVERT: H 192 TYR cc_start: 0.9130 (t80) cc_final: 0.8839 (t80) REVERT: H 263 VAL cc_start: 0.8912 (t) cc_final: 0.8697 (p) REVERT: H 310 LYS cc_start: 0.7141 (ttpt) cc_final: 0.6610 (tptt) REVERT: H 313 LYS cc_start: 0.9313 (ttmt) cc_final: 0.9047 (ttmm) outliers start: 85 outliers final: 55 residues processed: 822 average time/residue: 0.3360 time to fit residues: 413.0036 Evaluate side-chains 783 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 727 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 232 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 230 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 363 ASN D 50 HIS D 73 ASN E 73 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN F 206 GLN F 329 GLN G 50 HIS G 73 ASN G 363 ASN H 73 ASN H 115 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21832 Z= 0.247 Angle : 0.624 8.375 29744 Z= 0.306 Chirality : 0.041 0.155 3288 Planarity : 0.003 0.028 3632 Dihedral : 4.813 22.485 2792 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.72 % Allowed : 24.47 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.17), residues: 2496 helix: 0.79 (0.13), residues: 1688 sheet: -3.57 (0.55), residues: 80 loop : -3.31 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 59 HIS 0.012 0.002 HIS B 50 PHE 0.022 0.001 PHE G 64 TYR 0.014 0.001 TYR F 301 ARG 0.009 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 770 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.6312 (p0) cc_final: 0.5415 (p0) REVERT: A 67 GLN cc_start: 0.8171 (mp10) cc_final: 0.7242 (mp-120) REVERT: A 123 ARG cc_start: 0.8317 (ttm170) cc_final: 0.8041 (ttp-170) REVERT: A 153 ASP cc_start: 0.8598 (m-30) cc_final: 0.7993 (m-30) REVERT: A 157 LYS cc_start: 0.8277 (tptt) cc_final: 0.7657 (ttmm) REVERT: A 206 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8678 (mm110) REVERT: A 208 TYR cc_start: 0.8193 (t80) cc_final: 0.7548 (t80) REVERT: A 310 LYS cc_start: 0.6941 (ttpt) cc_final: 0.6415 (tptm) REVERT: A 353 PRO cc_start: 0.9442 (Cg_endo) cc_final: 0.9192 (Cg_exo) REVERT: B 146 ARG cc_start: 0.8947 (ttp80) cc_final: 0.8392 (mtm110) REVERT: B 153 ASP cc_start: 0.8712 (m-30) cc_final: 0.8303 (m-30) REVERT: B 208 TYR cc_start: 0.8380 (t80) cc_final: 0.8077 (t80) REVERT: B 310 LYS cc_start: 0.7215 (ttpt) cc_final: 0.6469 (tptt) REVERT: B 332 SER cc_start: 0.9009 (t) cc_final: 0.8800 (t) REVERT: B 353 PRO cc_start: 0.9575 (Cg_endo) cc_final: 0.9363 (Cg_exo) REVERT: B 359 ILE cc_start: 0.9498 (tp) cc_final: 0.9194 (tp) REVERT: C 153 ASP cc_start: 0.8779 (m-30) cc_final: 0.8133 (m-30) REVERT: C 154 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8202 (mtpt) REVERT: C 157 LYS cc_start: 0.8282 (tptt) cc_final: 0.7727 (ttpp) REVERT: C 158 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8034 (t80) REVERT: C 208 TYR cc_start: 0.8216 (t80) cc_final: 0.7483 (t80) REVERT: C 305 LYS cc_start: 0.8367 (tttm) cc_final: 0.8050 (tmtt) REVERT: C 310 LYS cc_start: 0.6755 (ttpt) cc_final: 0.6064 (tptm) REVERT: C 322 LYS cc_start: 0.7625 (pttm) cc_final: 0.6599 (mptt) REVERT: C 353 PRO cc_start: 0.9459 (Cg_endo) cc_final: 0.9196 (Cg_exo) REVERT: C 359 ILE cc_start: 0.9413 (tp) cc_final: 0.9211 (tp) REVERT: D 67 GLN cc_start: 0.8468 (mt0) cc_final: 0.8234 (mt0) REVERT: D 105 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6979 (m-10) REVERT: D 146 ARG cc_start: 0.8952 (ttp80) cc_final: 0.8363 (mtp-110) REVERT: D 153 ASP cc_start: 0.8805 (m-30) cc_final: 0.8366 (m-30) REVERT: D 158 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7745 (t80) REVERT: D 183 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8764 (ttpp) REVERT: D 192 TYR cc_start: 0.8982 (t80) cc_final: 0.8674 (t80) REVERT: D 310 LYS cc_start: 0.7139 (ttpt) cc_final: 0.6750 (tptt) REVERT: D 332 SER cc_start: 0.9110 (m) cc_final: 0.8852 (t) REVERT: D 353 PRO cc_start: 0.9526 (Cg_endo) cc_final: 0.9315 (Cg_exo) REVERT: D 359 ILE cc_start: 0.9467 (tp) cc_final: 0.9188 (tp) REVERT: E 65 ASN cc_start: 0.6932 (p0) cc_final: 0.6566 (p0) REVERT: E 67 GLN cc_start: 0.8359 (mp10) cc_final: 0.8086 (mp10) REVERT: E 68 TRP cc_start: 0.7928 (t-100) cc_final: 0.7691 (t-100) REVERT: E 157 LYS cc_start: 0.8400 (tptt) cc_final: 0.7913 (ttmm) REVERT: E 158 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7925 (t80) REVERT: E 178 ARG cc_start: 0.8945 (ttm-80) cc_final: 0.8730 (ttp-110) REVERT: E 206 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8592 (mm-40) REVERT: E 208 TYR cc_start: 0.8091 (t80) cc_final: 0.7471 (t80) REVERT: E 310 LYS cc_start: 0.7208 (ttpt) cc_final: 0.6704 (tptt) REVERT: E 353 PRO cc_start: 0.9444 (Cg_endo) cc_final: 0.9161 (Cg_exo) REVERT: F 73 ASN cc_start: 0.9196 (m-40) cc_final: 0.8977 (m-40) REVERT: F 105 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.7089 (m-10) REVERT: F 157 LYS cc_start: 0.8276 (tptt) cc_final: 0.7736 (ttmm) REVERT: F 158 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7866 (t80) REVERT: F 304 ASN cc_start: 0.8631 (t0) cc_final: 0.8051 (t0) REVERT: F 310 LYS cc_start: 0.7260 (ttpt) cc_final: 0.6859 (tptt) REVERT: F 353 PRO cc_start: 0.9575 (Cg_endo) cc_final: 0.9348 (Cg_exo) REVERT: G 65 ASN cc_start: 0.6888 (p0) cc_final: 0.6464 (p0) REVERT: G 68 TRP cc_start: 0.7939 (t-100) cc_final: 0.7619 (t-100) REVERT: G 70 ASN cc_start: 0.8489 (t0) cc_final: 0.8115 (t0) REVERT: G 123 ARG cc_start: 0.8405 (ttm170) cc_final: 0.8127 (ttp-170) REVERT: G 153 ASP cc_start: 0.8764 (m-30) cc_final: 0.8443 (m-30) REVERT: G 154 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8156 (mtpt) REVERT: G 157 LYS cc_start: 0.8319 (tptt) cc_final: 0.7734 (ttpp) REVERT: G 158 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7951 (t80) REVERT: G 192 TYR cc_start: 0.9102 (t80) cc_final: 0.8775 (t80) REVERT: G 208 TYR cc_start: 0.8176 (t80) cc_final: 0.7499 (t80) REVERT: G 305 LYS cc_start: 0.8581 (tttm) cc_final: 0.8196 (tmtt) REVERT: G 310 LYS cc_start: 0.7081 (ttpt) cc_final: 0.6489 (tptt) REVERT: G 322 LYS cc_start: 0.7598 (pttm) cc_final: 0.6500 (mptt) REVERT: G 353 PRO cc_start: 0.9458 (Cg_endo) cc_final: 0.9199 (Cg_exo) REVERT: H 65 ASN cc_start: 0.6943 (p0) cc_final: 0.6677 (p0) REVERT: H 105 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.7004 (m-10) REVERT: H 137 LEU cc_start: 0.9342 (tt) cc_final: 0.9122 (tt) REVERT: H 146 ARG cc_start: 0.8937 (ttp80) cc_final: 0.8491 (mtp-110) REVERT: H 153 ASP cc_start: 0.8630 (m-30) cc_final: 0.8202 (m-30) REVERT: H 157 LYS cc_start: 0.8292 (tptt) cc_final: 0.7945 (ttmm) REVERT: H 158 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7863 (t80) REVERT: H 161 ARG cc_start: 0.8336 (ttp-110) cc_final: 0.8070 (ttp-110) REVERT: H 192 TYR cc_start: 0.9144 (t80) cc_final: 0.8884 (t80) REVERT: H 310 LYS cc_start: 0.7166 (ttpt) cc_final: 0.6515 (tptt) REVERT: H 313 LYS cc_start: 0.9299 (ttmt) cc_final: 0.9063 (ttmm) outliers start: 84 outliers final: 63 residues processed: 803 average time/residue: 0.3406 time to fit residues: 416.4561 Evaluate side-chains 815 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 743 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 233 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 270 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 115 GLN C 50 HIS C 206 GLN D 73 ASN D 115 GLN E 50 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS F 73 ASN F 206 GLN G 206 GLN H 50 HIS H 73 ASN H 115 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21832 Z= 0.271 Angle : 0.621 7.920 29744 Z= 0.305 Chirality : 0.041 0.139 3288 Planarity : 0.004 0.034 3632 Dihedral : 4.769 21.902 2792 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.41 % Allowed : 24.60 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.17), residues: 2496 helix: 0.87 (0.13), residues: 1688 sheet: -3.66 (0.52), residues: 80 loop : -3.17 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 68 HIS 0.017 0.003 HIS G 50 PHE 0.020 0.001 PHE H 64 TYR 0.014 0.001 TYR F 301 ARG 0.008 0.000 ARG H 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 768 time to evaluate : 2.398 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: A 123 ARG cc_start: 0.8344 (ttm170) cc_final: 0.8062 (ttp-170) REVERT: A 153 ASP cc_start: 0.8583 (m-30) cc_final: 0.7868 (m-30) REVERT: A 154 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8376 (mtpt) REVERT: A 157 LYS cc_start: 0.8211 (tptt) cc_final: 0.7423 (ttpp) REVERT: A 158 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7526 (t80) REVERT: A 208 TYR cc_start: 0.8169 (t80) cc_final: 0.7501 (t80) REVERT: A 274 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: A 305 LYS cc_start: 0.8495 (tttm) cc_final: 0.8217 (tmtt) REVERT: A 310 LYS cc_start: 0.7081 (ttpt) cc_final: 0.6419 (tptm) REVERT: A 353 PRO cc_start: 0.9497 (Cg_endo) cc_final: 0.9258 (Cg_exo) REVERT: B 146 ARG cc_start: 0.8928 (ttp80) cc_final: 0.8386 (mtm110) REVERT: B 153 ASP cc_start: 0.8700 (m-30) cc_final: 0.8259 (m-30) REVERT: B 158 PHE cc_start: 0.7669 (t80) cc_final: 0.7374 (t80) REVERT: B 208 TYR cc_start: 0.8391 (t80) cc_final: 0.8086 (t80) REVERT: B 274 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: B 310 LYS cc_start: 0.7219 (ttpt) cc_final: 0.6527 (tptt) REVERT: B 353 PRO cc_start: 0.9576 (Cg_endo) cc_final: 0.9371 (Cg_exo) REVERT: B 359 ILE cc_start: 0.9471 (tp) cc_final: 0.9144 (tp) REVERT: C 70 ASN cc_start: 0.8477 (t0) cc_final: 0.8105 (t0) REVERT: C 123 ARG cc_start: 0.8420 (ttm170) cc_final: 0.8162 (ttp-170) REVERT: C 153 ASP cc_start: 0.8757 (m-30) cc_final: 0.8140 (m-30) REVERT: C 154 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8219 (mtpt) REVERT: C 157 LYS cc_start: 0.8233 (tptt) cc_final: 0.7701 (ttpp) REVERT: C 158 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7982 (t80) REVERT: C 208 TYR cc_start: 0.8218 (t80) cc_final: 0.7483 (t80) REVERT: C 267 LEU cc_start: 0.9178 (mt) cc_final: 0.8903 (mt) REVERT: C 274 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: C 305 LYS cc_start: 0.8377 (tttm) cc_final: 0.8107 (tmtt) REVERT: C 310 LYS cc_start: 0.7045 (ttpt) cc_final: 0.6304 (tptm) REVERT: C 322 LYS cc_start: 0.7669 (pttm) cc_final: 0.6590 (mptt) REVERT: C 353 PRO cc_start: 0.9459 (Cg_endo) cc_final: 0.9196 (Cg_exo) REVERT: C 359 ILE cc_start: 0.9432 (tp) cc_final: 0.9207 (tp) REVERT: D 105 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6856 (m-10) REVERT: D 146 ARG cc_start: 0.8965 (ttp80) cc_final: 0.8360 (mtp-110) REVERT: D 153 ASP cc_start: 0.8787 (m-30) cc_final: 0.8272 (m-30) REVERT: D 158 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7530 (t80) REVERT: D 192 TYR cc_start: 0.8967 (t80) cc_final: 0.8652 (t80) REVERT: D 274 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: D 304 ASN cc_start: 0.8454 (t0) cc_final: 0.8084 (t0) REVERT: D 310 LYS cc_start: 0.7097 (ttpt) cc_final: 0.6745 (tptt) REVERT: D 359 ILE cc_start: 0.9472 (tp) cc_final: 0.9163 (tp) REVERT: E 65 ASN cc_start: 0.6962 (p0) cc_final: 0.6690 (p0) REVERT: E 68 TRP cc_start: 0.7938 (t-100) cc_final: 0.7737 (t-100) REVERT: E 157 LYS cc_start: 0.8401 (tptt) cc_final: 0.7808 (ttmm) REVERT: E 158 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7900 (t80) REVERT: E 178 ARG cc_start: 0.8952 (ttm-80) cc_final: 0.8719 (ttp-110) REVERT: E 206 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8506 (mm-40) REVERT: E 208 TYR cc_start: 0.8117 (t80) cc_final: 0.7491 (t80) REVERT: E 274 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.6518 (mp0) REVERT: E 310 LYS cc_start: 0.7215 (ttpt) cc_final: 0.6734 (tptt) REVERT: E 353 PRO cc_start: 0.9449 (Cg_endo) cc_final: 0.9185 (Cg_exo) REVERT: F 105 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.7000 (m-10) REVERT: F 157 LYS cc_start: 0.8259 (tptt) cc_final: 0.7924 (ttmm) REVERT: F 158 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7787 (t80) REVERT: F 274 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: F 304 ASN cc_start: 0.8629 (t0) cc_final: 0.8060 (t0) REVERT: F 310 LYS cc_start: 0.7275 (ttpt) cc_final: 0.6890 (tptt) REVERT: F 353 PRO cc_start: 0.9581 (Cg_endo) cc_final: 0.9355 (Cg_exo) REVERT: G 67 GLN cc_start: 0.8350 (mp10) cc_final: 0.7900 (mp10) REVERT: G 68 TRP cc_start: 0.7943 (t-100) cc_final: 0.7676 (t-100) REVERT: G 70 ASN cc_start: 0.8514 (t0) cc_final: 0.8141 (t0) REVERT: G 123 ARG cc_start: 0.8391 (ttm170) cc_final: 0.8143 (ttp-170) REVERT: G 153 ASP cc_start: 0.8746 (m-30) cc_final: 0.8432 (m-30) REVERT: G 154 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8211 (mtpt) REVERT: G 157 LYS cc_start: 0.8323 (tptt) cc_final: 0.7721 (ttpp) REVERT: G 158 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7962 (t80) REVERT: G 208 TYR cc_start: 0.8205 (t80) cc_final: 0.7512 (t80) REVERT: G 267 LEU cc_start: 0.9180 (mt) cc_final: 0.8900 (mt) REVERT: G 274 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: G 305 LYS cc_start: 0.8796 (tttm) cc_final: 0.8368 (tmtt) REVERT: G 310 LYS cc_start: 0.7092 (ttpt) cc_final: 0.6549 (tptt) REVERT: G 322 LYS cc_start: 0.7589 (pttm) cc_final: 0.6498 (mptt) REVERT: G 353 PRO cc_start: 0.9449 (Cg_endo) cc_final: 0.9193 (Cg_exo) REVERT: H 65 ASN cc_start: 0.7054 (p0) cc_final: 0.6809 (p0) REVERT: H 105 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.7024 (m-10) REVERT: H 137 LEU cc_start: 0.9381 (tt) cc_final: 0.9175 (tt) REVERT: H 146 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8343 (mtp-110) REVERT: H 153 ASP cc_start: 0.8625 (m-30) cc_final: 0.8206 (m-30) REVERT: H 157 LYS cc_start: 0.8293 (tptt) cc_final: 0.7909 (ttmm) REVERT: H 158 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7932 (t80) REVERT: H 177 ILE cc_start: 0.9574 (mm) cc_final: 0.9370 (mt) REVERT: H 192 TYR cc_start: 0.9146 (t80) cc_final: 0.8901 (t80) REVERT: H 274 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: H 310 LYS cc_start: 0.7203 (ttpt) cc_final: 0.6544 (tptt) REVERT: H 313 LYS cc_start: 0.9298 (ttmt) cc_final: 0.9072 (ttmm) outliers start: 122 outliers final: 81 residues processed: 827 average time/residue: 0.3309 time to fit residues: 415.8249 Evaluate side-chains 844 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 745 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 0.0030 chunk 222 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS B 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 115 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN F 206 GLN G 50 HIS H 50 HIS H 73 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21832 Z= 0.245 Angle : 0.612 11.557 29744 Z= 0.298 Chirality : 0.041 0.208 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.674 22.219 2792 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 6.03 % Allowed : 24.96 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2496 helix: 0.95 (0.13), residues: 1712 sheet: -3.72 (0.51), residues: 80 loop : -2.95 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 68 HIS 0.012 0.003 HIS G 50 PHE 0.015 0.001 PHE G 64 TYR 0.015 0.001 TYR F 301 ARG 0.005 0.000 ARG H 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 771 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8397 (ttm170) cc_final: 0.8110 (ttp-170) REVERT: A 153 ASP cc_start: 0.8564 (m-30) cc_final: 0.7889 (m-30) REVERT: A 154 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8369 (mtpt) REVERT: A 157 LYS cc_start: 0.8209 (tptt) cc_final: 0.7398 (ttpp) REVERT: A 158 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7444 (t80) REVERT: A 208 TYR cc_start: 0.8176 (t80) cc_final: 0.7493 (t80) REVERT: A 221 LEU cc_start: 0.5887 (OUTLIER) cc_final: 0.5675 (pp) REVERT: A 274 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: A 305 LYS cc_start: 0.8532 (tttm) cc_final: 0.8200 (tmtt) REVERT: A 310 LYS cc_start: 0.7085 (ttpt) cc_final: 0.6429 (tptm) REVERT: A 353 PRO cc_start: 0.9485 (Cg_endo) cc_final: 0.9267 (Cg_exo) REVERT: B 146 ARG cc_start: 0.8914 (ttp80) cc_final: 0.8390 (mtm110) REVERT: B 153 ASP cc_start: 0.8670 (m-30) cc_final: 0.8238 (m-30) REVERT: B 158 PHE cc_start: 0.7737 (t80) cc_final: 0.7341 (t80) REVERT: B 208 TYR cc_start: 0.8359 (t80) cc_final: 0.8052 (t80) REVERT: B 274 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: B 310 LYS cc_start: 0.7220 (ttpt) cc_final: 0.6548 (tptt) REVERT: B 322 LYS cc_start: 0.7834 (pttm) cc_final: 0.7121 (mptt) REVERT: B 359 ILE cc_start: 0.9471 (tp) cc_final: 0.9165 (tp) REVERT: C 70 ASN cc_start: 0.8447 (t0) cc_final: 0.8092 (t0) REVERT: C 123 ARG cc_start: 0.8429 (ttm170) cc_final: 0.8154 (ttp-170) REVERT: C 153 ASP cc_start: 0.8712 (m-30) cc_final: 0.8119 (m-30) REVERT: C 154 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8286 (mtpt) REVERT: C 157 LYS cc_start: 0.8305 (tptt) cc_final: 0.7588 (ttpp) REVERT: C 158 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7989 (t80) REVERT: C 208 TYR cc_start: 0.8239 (t80) cc_final: 0.7511 (t80) REVERT: C 221 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5911 (pp) REVERT: C 274 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: C 305 LYS cc_start: 0.8505 (tttm) cc_final: 0.8159 (tmtt) REVERT: C 310 LYS cc_start: 0.7036 (ttpt) cc_final: 0.6322 (tptm) REVERT: C 322 LYS cc_start: 0.7647 (pttm) cc_final: 0.6584 (mptt) REVERT: C 353 PRO cc_start: 0.9410 (Cg_endo) cc_final: 0.9145 (Cg_exo) REVERT: C 359 ILE cc_start: 0.9433 (tp) cc_final: 0.9208 (tp) REVERT: D 105 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.7048 (m-10) REVERT: D 146 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8356 (mtp-110) REVERT: D 153 ASP cc_start: 0.8777 (m-30) cc_final: 0.8313 (m-30) REVERT: D 158 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7557 (t80) REVERT: D 192 TYR cc_start: 0.8927 (t80) cc_final: 0.8607 (t80) REVERT: D 274 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: D 304 ASN cc_start: 0.8458 (t0) cc_final: 0.8084 (t0) REVERT: D 310 LYS cc_start: 0.7129 (ttpt) cc_final: 0.6725 (tptt) REVERT: D 332 SER cc_start: 0.9194 (m) cc_final: 0.8912 (t) REVERT: D 359 ILE cc_start: 0.9471 (tp) cc_final: 0.9165 (tp) REVERT: E 28 ASP cc_start: 0.6863 (m-30) cc_final: 0.6536 (m-30) REVERT: E 68 TRP cc_start: 0.7862 (t-100) cc_final: 0.7582 (t-100) REVERT: E 129 MET cc_start: 0.7431 (tpp) cc_final: 0.7094 (tpp) REVERT: E 153 ASP cc_start: 0.8752 (m-30) cc_final: 0.8157 (m-30) REVERT: E 157 LYS cc_start: 0.8435 (tptt) cc_final: 0.7916 (ttmm) REVERT: E 158 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7948 (t80) REVERT: E 178 ARG cc_start: 0.8949 (ttm-80) cc_final: 0.8696 (ttp-110) REVERT: E 206 GLN cc_start: 0.9285 (mm-40) cc_final: 0.8528 (mm-40) REVERT: E 208 TYR cc_start: 0.8125 (t80) cc_final: 0.7679 (t80) REVERT: E 274 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: E 305 LYS cc_start: 0.8425 (tttm) cc_final: 0.8073 (tmtt) REVERT: E 310 LYS cc_start: 0.7134 (ttpt) cc_final: 0.6678 (tptt) REVERT: E 345 MET cc_start: 0.9200 (tpp) cc_final: 0.8939 (mpp) REVERT: E 353 PRO cc_start: 0.9434 (Cg_endo) cc_final: 0.9185 (Cg_exo) REVERT: F 59 TRP cc_start: 0.7839 (t-100) cc_final: 0.7087 (t-100) REVERT: F 153 ASP cc_start: 0.8723 (m-30) cc_final: 0.8293 (m-30) REVERT: F 157 LYS cc_start: 0.8220 (tptt) cc_final: 0.7892 (ttmm) REVERT: F 158 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7712 (t80) REVERT: F 274 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: F 304 ASN cc_start: 0.8468 (t0) cc_final: 0.8016 (t0) REVERT: F 310 LYS cc_start: 0.7291 (ttpt) cc_final: 0.6887 (tptt) REVERT: F 353 PRO cc_start: 0.9573 (Cg_endo) cc_final: 0.9356 (Cg_exo) REVERT: G 68 TRP cc_start: 0.7900 (t-100) cc_final: 0.7682 (t-100) REVERT: G 123 ARG cc_start: 0.8399 (ttm170) cc_final: 0.8146 (ttp-170) REVERT: G 153 ASP cc_start: 0.8741 (m-30) cc_final: 0.8448 (m-30) REVERT: G 154 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8178 (mtpt) REVERT: G 157 LYS cc_start: 0.8337 (tptt) cc_final: 0.7616 (ttpp) REVERT: G 158 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7963 (t80) REVERT: G 208 TYR cc_start: 0.8192 (t80) cc_final: 0.7490 (t80) REVERT: G 221 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5866 (pp) REVERT: G 274 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: G 305 LYS cc_start: 0.8834 (tttm) cc_final: 0.8404 (tmtt) REVERT: G 310 LYS cc_start: 0.7073 (ttpt) cc_final: 0.6555 (tptt) REVERT: G 322 LYS cc_start: 0.7575 (pttm) cc_final: 0.6580 (mptt) REVERT: G 353 PRO cc_start: 0.9442 (Cg_endo) cc_final: 0.9189 (Cg_exo) REVERT: H 65 ASN cc_start: 0.7220 (p0) cc_final: 0.6925 (p0) REVERT: H 137 LEU cc_start: 0.9382 (tt) cc_final: 0.9163 (tt) REVERT: H 146 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8356 (mtp-110) REVERT: H 153 ASP cc_start: 0.8611 (m-30) cc_final: 0.8203 (m-30) REVERT: H 157 LYS cc_start: 0.8220 (tptt) cc_final: 0.7835 (ttmm) REVERT: H 158 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7666 (t80) REVERT: H 177 ILE cc_start: 0.9571 (mm) cc_final: 0.9370 (mt) REVERT: H 192 TYR cc_start: 0.9139 (t80) cc_final: 0.8910 (t80) REVERT: H 208 TYR cc_start: 0.8433 (t80) cc_final: 0.8111 (t80) REVERT: H 274 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: H 305 LYS cc_start: 0.8544 (tttm) cc_final: 0.8321 (tmtt) REVERT: H 310 LYS cc_start: 0.7208 (ttpt) cc_final: 0.6557 (tptt) REVERT: H 313 LYS cc_start: 0.9297 (ttmt) cc_final: 0.9050 (ttmm) outliers start: 136 outliers final: 99 residues processed: 841 average time/residue: 0.3336 time to fit residues: 425.6313 Evaluate side-chains 862 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 744 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 205 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 270 ASN B 50 HIS B 67 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN G 73 ASN G 206 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21832 Z= 0.164 Angle : 0.587 12.682 29744 Z= 0.285 Chirality : 0.039 0.202 3288 Planarity : 0.003 0.031 3632 Dihedral : 4.462 21.607 2792 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.08 % Allowed : 27.44 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2496 helix: 1.12 (0.13), residues: 1712 sheet: -3.60 (0.53), residues: 80 loop : -2.97 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 59 HIS 0.023 0.002 HIS G 50 PHE 0.020 0.001 PHE B 64 TYR 0.021 0.001 TYR H 300 ARG 0.014 0.000 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 787 time to evaluate : 2.255 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: A 123 ARG cc_start: 0.8369 (ttm170) cc_final: 0.8090 (ttp-170) REVERT: A 153 ASP cc_start: 0.8541 (m-30) cc_final: 0.7272 (m-30) REVERT: A 154 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8446 (mtpt) REVERT: A 157 LYS cc_start: 0.8204 (tptt) cc_final: 0.7370 (ttpp) REVERT: A 158 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7401 (t80) REVERT: A 208 TYR cc_start: 0.8198 (t80) cc_final: 0.7739 (t80) REVERT: A 221 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.6026 (pp) REVERT: A 274 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: A 305 LYS cc_start: 0.8521 (tttm) cc_final: 0.8195 (tmtt) REVERT: A 310 LYS cc_start: 0.7099 (ttpt) cc_final: 0.6476 (tptm) REVERT: A 353 PRO cc_start: 0.9377 (Cg_endo) cc_final: 0.9155 (Cg_exo) REVERT: B 146 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8217 (mtp-110) REVERT: B 153 ASP cc_start: 0.8634 (m-30) cc_final: 0.8212 (m-30) REVERT: B 158 PHE cc_start: 0.7664 (t80) cc_final: 0.7242 (t80) REVERT: B 170 SER cc_start: 0.9471 (t) cc_final: 0.9238 (m) REVERT: B 208 TYR cc_start: 0.8426 (t80) cc_final: 0.8085 (t80) REVERT: B 274 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: B 310 LYS cc_start: 0.7201 (ttpt) cc_final: 0.6568 (tptt) REVERT: B 315 TYR cc_start: 0.8270 (m-10) cc_final: 0.7496 (m-10) REVERT: B 322 LYS cc_start: 0.7809 (pttm) cc_final: 0.7131 (mptt) REVERT: B 359 ILE cc_start: 0.9463 (tp) cc_final: 0.9166 (tp) REVERT: C 70 ASN cc_start: 0.8396 (t0) cc_final: 0.8049 (t0) REVERT: C 123 ARG cc_start: 0.8400 (ttm170) cc_final: 0.8146 (ttp-170) REVERT: C 153 ASP cc_start: 0.8658 (m-30) cc_final: 0.7432 (m-30) REVERT: C 154 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8292 (mtpt) REVERT: C 157 LYS cc_start: 0.8300 (tptt) cc_final: 0.7608 (ttpp) REVERT: C 158 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7909 (t80) REVERT: C 208 TYR cc_start: 0.8213 (t80) cc_final: 0.7737 (t80) REVERT: C 274 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: C 305 LYS cc_start: 0.8528 (tttm) cc_final: 0.8184 (tmtt) REVERT: C 310 LYS cc_start: 0.7051 (ttpt) cc_final: 0.6313 (tptm) REVERT: C 322 LYS cc_start: 0.7502 (pttm) cc_final: 0.6786 (mptt) REVERT: C 353 PRO cc_start: 0.9338 (Cg_endo) cc_final: 0.9070 (Cg_exo) REVERT: C 359 ILE cc_start: 0.9408 (tp) cc_final: 0.9156 (tp) REVERT: D 105 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6855 (m-10) REVERT: D 153 ASP cc_start: 0.8679 (m-30) cc_final: 0.8224 (m-30) REVERT: D 158 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7579 (t80) REVERT: D 192 TYR cc_start: 0.8894 (t80) cc_final: 0.8627 (t80) REVERT: D 274 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: D 304 ASN cc_start: 0.8408 (t0) cc_final: 0.8085 (t0) REVERT: D 310 LYS cc_start: 0.7185 (ttpt) cc_final: 0.6809 (tptt) REVERT: D 315 TYR cc_start: 0.8342 (m-10) cc_final: 0.7597 (m-10) REVERT: D 322 LYS cc_start: 0.7584 (pttm) cc_final: 0.6935 (mptt) REVERT: D 332 SER cc_start: 0.9167 (m) cc_final: 0.8904 (t) REVERT: D 359 ILE cc_start: 0.9460 (tp) cc_final: 0.9169 (tp) REVERT: E 29 ARG cc_start: 0.7575 (tpp-160) cc_final: 0.6896 (tpp-160) REVERT: E 68 TRP cc_start: 0.7823 (t-100) cc_final: 0.7551 (t-100) REVERT: E 129 MET cc_start: 0.7410 (tpp) cc_final: 0.7085 (tpp) REVERT: E 153 ASP cc_start: 0.8745 (m-30) cc_final: 0.8436 (m-30) REVERT: E 157 LYS cc_start: 0.8408 (tptt) cc_final: 0.7862 (ttmm) REVERT: E 158 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7963 (t80) REVERT: E 199 GLN cc_start: 0.7838 (tp40) cc_final: 0.7476 (tp40) REVERT: E 206 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8507 (mm-40) REVERT: E 208 TYR cc_start: 0.8149 (t80) cc_final: 0.7698 (t80) REVERT: E 274 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: E 305 LYS cc_start: 0.8402 (tttm) cc_final: 0.8065 (tmtt) REVERT: E 310 LYS cc_start: 0.7091 (ttpt) cc_final: 0.6571 (tptt) REVERT: E 322 LYS cc_start: 0.7418 (pttm) cc_final: 0.6615 (tttm) REVERT: E 353 PRO cc_start: 0.9295 (Cg_endo) cc_final: 0.9059 (Cg_exo) REVERT: F 59 TRP cc_start: 0.7913 (t-100) cc_final: 0.7122 (t-100) REVERT: F 153 ASP cc_start: 0.8658 (m-30) cc_final: 0.8194 (m-30) REVERT: F 157 LYS cc_start: 0.8210 (tptt) cc_final: 0.7902 (ttmm) REVERT: F 158 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7537 (t80) REVERT: F 274 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: F 304 ASN cc_start: 0.8463 (t0) cc_final: 0.8107 (t0) REVERT: F 310 LYS cc_start: 0.7245 (ttpt) cc_final: 0.6852 (tptt) REVERT: F 315 TYR cc_start: 0.8331 (m-10) cc_final: 0.7538 (m-10) REVERT: F 322 LYS cc_start: 0.7737 (pttm) cc_final: 0.7135 (mptt) REVERT: F 332 SER cc_start: 0.9172 (m) cc_final: 0.8864 (t) REVERT: G 70 ASN cc_start: 0.8457 (t0) cc_final: 0.8091 (t0) REVERT: G 73 ASN cc_start: 0.9222 (m-40) cc_final: 0.8926 (m-40) REVERT: G 123 ARG cc_start: 0.8384 (ttm170) cc_final: 0.8111 (ttp-170) REVERT: G 153 ASP cc_start: 0.8665 (m-30) cc_final: 0.8377 (m-30) REVERT: G 154 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8228 (mtpt) REVERT: G 157 LYS cc_start: 0.8358 (tptt) cc_final: 0.7629 (ttpp) REVERT: G 158 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7824 (t80) REVERT: G 208 TYR cc_start: 0.8187 (t80) cc_final: 0.7737 (t80) REVERT: G 221 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5897 (pp) REVERT: G 274 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: G 305 LYS cc_start: 0.8671 (tttm) cc_final: 0.8431 (tmtt) REVERT: G 310 LYS cc_start: 0.7043 (ttpt) cc_final: 0.6444 (tptm) REVERT: G 322 LYS cc_start: 0.7351 (pttm) cc_final: 0.6477 (tttm) REVERT: G 353 PRO cc_start: 0.9356 (Cg_endo) cc_final: 0.9115 (Cg_exo) REVERT: H 65 ASN cc_start: 0.7093 (p0) cc_final: 0.6727 (p0) REVERT: H 137 LEU cc_start: 0.9338 (tt) cc_final: 0.9121 (tt) REVERT: H 146 ARG cc_start: 0.8936 (ttp80) cc_final: 0.8292 (mtp-110) REVERT: H 153 ASP cc_start: 0.8585 (m-30) cc_final: 0.8200 (m-30) REVERT: H 157 LYS cc_start: 0.8270 (tptt) cc_final: 0.7682 (ttmm) REVERT: H 158 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7617 (t80) REVERT: H 206 GLN cc_start: 0.8833 (tp40) cc_final: 0.8629 (tp40) REVERT: H 208 TYR cc_start: 0.8410 (t80) cc_final: 0.8060 (t80) REVERT: H 274 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: H 310 LYS cc_start: 0.7212 (ttpt) cc_final: 0.6631 (tptt) REVERT: H 313 LYS cc_start: 0.9280 (ttmt) cc_final: 0.8997 (ttmm) REVERT: H 315 TYR cc_start: 0.8319 (m-10) cc_final: 0.7574 (m-10) REVERT: H 322 LYS cc_start: 0.7758 (pttm) cc_final: 0.7117 (mptt) REVERT: H 359 ILE cc_start: 0.9459 (tp) cc_final: 0.9125 (tp) outliers start: 92 outliers final: 53 residues processed: 843 average time/residue: 0.2914 time to fit residues: 373.8008 Evaluate side-chains 807 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 736 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS D 50 HIS D 63 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN G 50 HIS G 73 ASN G 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21832 Z= 0.204 Angle : 0.597 13.919 29744 Z= 0.291 Chirality : 0.039 0.183 3288 Planarity : 0.003 0.036 3632 Dihedral : 4.398 22.109 2792 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.27 % Allowed : 27.26 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2496 helix: 1.16 (0.13), residues: 1728 sheet: -3.71 (0.53), residues: 80 loop : -2.92 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 236 HIS 0.012 0.001 HIS C 50 PHE 0.022 0.001 PHE A 330 TYR 0.020 0.001 TYR H 300 ARG 0.013 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 758 time to evaluate : 2.558 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: A 123 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8086 (ttp-170) REVERT: A 153 ASP cc_start: 0.8601 (m-30) cc_final: 0.8000 (m-30) REVERT: A 157 LYS cc_start: 0.8209 (tptt) cc_final: 0.7390 (ttpp) REVERT: A 208 TYR cc_start: 0.8153 (t80) cc_final: 0.7483 (t80) REVERT: A 221 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5993 (pp) REVERT: A 236 TRP cc_start: 0.8445 (p-90) cc_final: 0.8138 (p-90) REVERT: A 274 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: A 310 LYS cc_start: 0.7103 (ttpt) cc_final: 0.6481 (tptm) REVERT: A 345 MET cc_start: 0.9272 (tpp) cc_final: 0.8866 (tpp) REVERT: A 353 PRO cc_start: 0.9356 (Cg_endo) cc_final: 0.9139 (Cg_exo) REVERT: B 130 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8909 (tp) REVERT: B 146 ARG cc_start: 0.8881 (ttp80) cc_final: 0.8418 (mtp-110) REVERT: B 153 ASP cc_start: 0.8615 (m-30) cc_final: 0.8206 (m-30) REVERT: B 158 PHE cc_start: 0.7671 (t80) cc_final: 0.7330 (t80) REVERT: B 170 SER cc_start: 0.9472 (t) cc_final: 0.9245 (m) REVERT: B 208 TYR cc_start: 0.8426 (t80) cc_final: 0.8096 (t80) REVERT: B 248 CYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8491 (p) REVERT: B 274 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: B 304 ASN cc_start: 0.8450 (t0) cc_final: 0.8066 (t0) REVERT: B 310 LYS cc_start: 0.7301 (ttpt) cc_final: 0.6689 (tptt) REVERT: B 322 LYS cc_start: 0.7804 (pttm) cc_final: 0.7134 (mptt) REVERT: B 359 ILE cc_start: 0.9480 (tp) cc_final: 0.9175 (tp) REVERT: C 123 ARG cc_start: 0.8428 (ttm170) cc_final: 0.8141 (ttp-170) REVERT: C 153 ASP cc_start: 0.8639 (m-30) cc_final: 0.8086 (m-30) REVERT: C 154 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8279 (mtpt) REVERT: C 157 LYS cc_start: 0.8322 (tptt) cc_final: 0.7583 (ttpp) REVERT: C 158 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7928 (t80) REVERT: C 208 TYR cc_start: 0.8225 (t80) cc_final: 0.7748 (t80) REVERT: C 274 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: C 310 LYS cc_start: 0.7081 (ttpt) cc_final: 0.6369 (tptm) REVERT: C 322 LYS cc_start: 0.7413 (pttm) cc_final: 0.6694 (mptt) REVERT: C 353 PRO cc_start: 0.9374 (Cg_endo) cc_final: 0.9133 (Cg_exo) REVERT: C 359 ILE cc_start: 0.9421 (tp) cc_final: 0.9164 (tp) REVERT: D 28 ASP cc_start: 0.7260 (m-30) cc_final: 0.7033 (m-30) REVERT: D 153 ASP cc_start: 0.8741 (m-30) cc_final: 0.8342 (m-30) REVERT: D 158 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7697 (t80) REVERT: D 192 TYR cc_start: 0.8935 (t80) cc_final: 0.8681 (t80) REVERT: D 208 TYR cc_start: 0.8320 (t80) cc_final: 0.8065 (t80) REVERT: D 274 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: D 304 ASN cc_start: 0.8490 (t0) cc_final: 0.8146 (t0) REVERT: D 310 LYS cc_start: 0.7234 (ttpt) cc_final: 0.6829 (tptt) REVERT: D 315 TYR cc_start: 0.8363 (m-10) cc_final: 0.7587 (m-10) REVERT: D 322 LYS cc_start: 0.7568 (pttm) cc_final: 0.6933 (mptt) REVERT: D 332 SER cc_start: 0.9174 (m) cc_final: 0.8927 (t) REVERT: D 359 ILE cc_start: 0.9419 (tp) cc_final: 0.9106 (tp) REVERT: E 68 TRP cc_start: 0.7813 (t-100) cc_final: 0.7502 (t-100) REVERT: E 129 MET cc_start: 0.7426 (tpp) cc_final: 0.7087 (tpp) REVERT: E 142 LYS cc_start: 0.9161 (ttmm) cc_final: 0.8881 (mtpp) REVERT: E 153 ASP cc_start: 0.8737 (m-30) cc_final: 0.8473 (m-30) REVERT: E 157 LYS cc_start: 0.8306 (tptt) cc_final: 0.7775 (ttmm) REVERT: E 158 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7968 (t80) REVERT: E 175 ASP cc_start: 0.8099 (m-30) cc_final: 0.7544 (m-30) REVERT: E 206 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8522 (mm-40) REVERT: E 208 TYR cc_start: 0.8168 (t80) cc_final: 0.7730 (t80) REVERT: E 274 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: E 305 LYS cc_start: 0.8376 (tttm) cc_final: 0.8113 (tmtt) REVERT: E 310 LYS cc_start: 0.7129 (ttpt) cc_final: 0.6598 (tptt) REVERT: E 322 LYS cc_start: 0.7348 (pttm) cc_final: 0.6474 (tttm) REVERT: E 353 PRO cc_start: 0.9357 (Cg_endo) cc_final: 0.9114 (Cg_exo) REVERT: F 59 TRP cc_start: 0.7935 (t-100) cc_final: 0.7098 (t-100) REVERT: F 65 ASN cc_start: 0.7186 (p0) cc_final: 0.6976 (p0) REVERT: F 153 ASP cc_start: 0.8636 (m-30) cc_final: 0.8224 (m-30) REVERT: F 157 LYS cc_start: 0.8210 (tptt) cc_final: 0.7763 (ttmm) REVERT: F 158 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7664 (t80) REVERT: F 183 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8788 (ttpt) REVERT: F 274 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: F 310 LYS cc_start: 0.7277 (ttpt) cc_final: 0.6904 (tptt) REVERT: F 322 LYS cc_start: 0.7709 (pttm) cc_final: 0.7112 (mptt) REVERT: F 332 SER cc_start: 0.9178 (m) cc_final: 0.8894 (t) REVERT: G 70 ASN cc_start: 0.8475 (t0) cc_final: 0.8128 (t0) REVERT: G 123 ARG cc_start: 0.8386 (ttm170) cc_final: 0.8115 (ttp-170) REVERT: G 153 ASP cc_start: 0.8661 (m-30) cc_final: 0.8389 (m-30) REVERT: G 154 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8255 (mtpt) REVERT: G 157 LYS cc_start: 0.8344 (tptt) cc_final: 0.7587 (ttpp) REVERT: G 158 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7814 (t80) REVERT: G 208 TYR cc_start: 0.8199 (t80) cc_final: 0.7765 (t80) REVERT: G 221 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5861 (pp) REVERT: G 274 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: G 310 LYS cc_start: 0.7043 (ttpt) cc_final: 0.6444 (tptm) REVERT: G 322 LYS cc_start: 0.7333 (pttm) cc_final: 0.6634 (mptt) REVERT: G 353 PRO cc_start: 0.9356 (Cg_endo) cc_final: 0.9118 (Cg_exo) REVERT: H 28 ASP cc_start: 0.7134 (m-30) cc_final: 0.6844 (m-30) REVERT: H 65 ASN cc_start: 0.7088 (p0) cc_final: 0.6762 (p0) REVERT: H 130 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8816 (tp) REVERT: H 137 LEU cc_start: 0.9373 (tt) cc_final: 0.9147 (tt) REVERT: H 146 ARG cc_start: 0.8940 (ttp80) cc_final: 0.8374 (mtp-110) REVERT: H 153 ASP cc_start: 0.8569 (m-30) cc_final: 0.8176 (m-30) REVERT: H 158 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7590 (t80) REVERT: H 208 TYR cc_start: 0.8405 (t80) cc_final: 0.8038 (t80) REVERT: H 274 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: H 310 LYS cc_start: 0.7260 (ttpt) cc_final: 0.6671 (tptt) REVERT: H 313 LYS cc_start: 0.9301 (ttmt) cc_final: 0.9047 (ttmm) REVERT: H 315 TYR cc_start: 0.8361 (m-10) cc_final: 0.7603 (m-10) REVERT: H 322 LYS cc_start: 0.7815 (pttm) cc_final: 0.7152 (mptt) REVERT: H 359 ILE cc_start: 0.9478 (tp) cc_final: 0.9144 (tp) outliers start: 119 outliers final: 79 residues processed: 828 average time/residue: 0.3499 time to fit residues: 447.7490 Evaluate side-chains 835 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 737 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 0.0370 chunk 22 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 67 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 73 ASN C 115 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN F 206 GLN G 115 GLN H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21832 Z= 0.168 Angle : 0.607 13.255 29744 Z= 0.294 Chirality : 0.039 0.201 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.260 20.064 2792 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.65 % Allowed : 28.59 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2496 helix: 1.24 (0.13), residues: 1720 sheet: -3.64 (0.54), residues: 80 loop : -2.84 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 236 HIS 0.018 0.002 HIS C 50 PHE 0.020 0.001 PHE B 64 TYR 0.018 0.001 TYR H 300 ARG 0.009 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 758 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8357 (ttm170) cc_final: 0.8085 (ttp-170) REVERT: A 153 ASP cc_start: 0.8522 (m-30) cc_final: 0.7326 (m-30) REVERT: A 158 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7353 (t80) REVERT: A 208 TYR cc_start: 0.8133 (t80) cc_final: 0.7676 (t80) REVERT: A 221 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5900 (pp) REVERT: A 236 TRP cc_start: 0.8421 (p-90) cc_final: 0.8097 (p-90) REVERT: A 274 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: A 305 LYS cc_start: 0.8404 (tmtt) cc_final: 0.8020 (tttm) REVERT: A 310 LYS cc_start: 0.7019 (ttpt) cc_final: 0.6476 (tptm) REVERT: A 345 MET cc_start: 0.9224 (tpp) cc_final: 0.8798 (tpp) REVERT: B 146 ARG cc_start: 0.8819 (ttp80) cc_final: 0.8235 (mtp-110) REVERT: B 153 ASP cc_start: 0.8582 (m-30) cc_final: 0.8217 (m-30) REVERT: B 158 PHE cc_start: 0.7779 (t80) cc_final: 0.7407 (t80) REVERT: B 170 SER cc_start: 0.9371 (t) cc_final: 0.9150 (m) REVERT: B 208 TYR cc_start: 0.8403 (t80) cc_final: 0.8083 (t80) REVERT: B 274 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.6320 (mp0) REVERT: B 310 LYS cc_start: 0.7269 (ttpt) cc_final: 0.6633 (tptm) REVERT: B 315 TYR cc_start: 0.8253 (m-10) cc_final: 0.7516 (m-10) REVERT: B 322 LYS cc_start: 0.7762 (pttm) cc_final: 0.7125 (mptt) REVERT: B 359 ILE cc_start: 0.9452 (tp) cc_final: 0.9171 (tp) REVERT: C 73 ASN cc_start: 0.9237 (m-40) cc_final: 0.8997 (m-40) REVERT: C 123 ARG cc_start: 0.8371 (ttm170) cc_final: 0.8161 (ttp-170) REVERT: C 153 ASP cc_start: 0.8588 (m-30) cc_final: 0.7370 (m-30) REVERT: C 157 LYS cc_start: 0.8308 (tptt) cc_final: 0.7692 (ttmm) REVERT: C 158 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7798 (t80) REVERT: C 208 TYR cc_start: 0.8183 (t80) cc_final: 0.7681 (t80) REVERT: C 274 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: C 310 LYS cc_start: 0.7088 (ttpt) cc_final: 0.6413 (tptm) REVERT: C 322 LYS cc_start: 0.7357 (pttm) cc_final: 0.6634 (tmtt) REVERT: C 359 ILE cc_start: 0.9403 (tp) cc_final: 0.9143 (tp) REVERT: D 28 ASP cc_start: 0.7133 (m-30) cc_final: 0.6897 (m-30) REVERT: D 47 LEU cc_start: 0.9410 (mm) cc_final: 0.9204 (mm) REVERT: D 153 ASP cc_start: 0.8650 (m-30) cc_final: 0.8218 (m-30) REVERT: D 158 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7487 (t80) REVERT: D 192 TYR cc_start: 0.8890 (t80) cc_final: 0.8663 (t80) REVERT: D 208 TYR cc_start: 0.8287 (t80) cc_final: 0.7994 (t80) REVERT: D 274 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.6369 (mp0) REVERT: D 304 ASN cc_start: 0.8458 (t0) cc_final: 0.8084 (t0) REVERT: D 310 LYS cc_start: 0.7254 (ttpt) cc_final: 0.6861 (tptt) REVERT: D 315 TYR cc_start: 0.8308 (m-10) cc_final: 0.7614 (m-10) REVERT: D 322 LYS cc_start: 0.7535 (pttm) cc_final: 0.6935 (mptt) REVERT: D 332 SER cc_start: 0.9164 (m) cc_final: 0.8925 (t) REVERT: D 359 ILE cc_start: 0.9420 (tp) cc_final: 0.9093 (tp) REVERT: E 68 TRP cc_start: 0.7783 (t-100) cc_final: 0.7536 (t-100) REVERT: E 70 ASN cc_start: 0.8391 (t0) cc_final: 0.8024 (t0) REVERT: E 142 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8863 (mtpp) REVERT: E 153 ASP cc_start: 0.8648 (m-30) cc_final: 0.8385 (m-30) REVERT: E 157 LYS cc_start: 0.8313 (tptt) cc_final: 0.7769 (ttmm) REVERT: E 158 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7871 (t80) REVERT: E 175 ASP cc_start: 0.8069 (m-30) cc_final: 0.7578 (m-30) REVERT: E 206 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8557 (mm-40) REVERT: E 208 TYR cc_start: 0.8191 (t80) cc_final: 0.7703 (t80) REVERT: E 274 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: E 310 LYS cc_start: 0.7052 (ttpt) cc_final: 0.6554 (tptt) REVERT: E 322 LYS cc_start: 0.7275 (pttm) cc_final: 0.6453 (tttm) REVERT: E 345 MET cc_start: 0.9203 (tpp) cc_final: 0.8836 (tpp) REVERT: E 353 PRO cc_start: 0.9318 (Cg_endo) cc_final: 0.9086 (Cg_exo) REVERT: F 59 TRP cc_start: 0.7906 (t-100) cc_final: 0.7173 (t-100) REVERT: F 65 ASN cc_start: 0.7099 (p0) cc_final: 0.6874 (p0) REVERT: F 153 ASP cc_start: 0.8623 (m-30) cc_final: 0.8236 (m-30) REVERT: F 157 LYS cc_start: 0.8153 (tptt) cc_final: 0.7731 (ttmm) REVERT: F 158 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7556 (t80) REVERT: F 274 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: F 310 LYS cc_start: 0.7323 (ttpt) cc_final: 0.6927 (tptt) REVERT: F 315 TYR cc_start: 0.8311 (m-10) cc_final: 0.7568 (m-10) REVERT: F 322 LYS cc_start: 0.7558 (pttm) cc_final: 0.6992 (mptt) REVERT: F 332 SER cc_start: 0.9164 (m) cc_final: 0.8893 (t) REVERT: G 32 SER cc_start: 0.5495 (OUTLIER) cc_final: 0.5112 (p) REVERT: G 123 ARG cc_start: 0.8354 (ttm170) cc_final: 0.8153 (ttp-170) REVERT: G 153 ASP cc_start: 0.8636 (m-30) cc_final: 0.8355 (m-30) REVERT: G 154 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8237 (mtpt) REVERT: G 157 LYS cc_start: 0.8327 (tptt) cc_final: 0.7543 (ttpp) REVERT: G 158 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7634 (t80) REVERT: G 208 TYR cc_start: 0.8190 (t80) cc_final: 0.7688 (t80) REVERT: G 221 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5835 (pp) REVERT: G 274 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.6445 (mp0) REVERT: G 310 LYS cc_start: 0.7070 (ttpt) cc_final: 0.6491 (tptm) REVERT: G 322 LYS cc_start: 0.7264 (pttm) cc_final: 0.6479 (tttm) REVERT: G 353 PRO cc_start: 0.9300 (Cg_endo) cc_final: 0.9062 (Cg_exo) REVERT: H 65 ASN cc_start: 0.7070 (p0) cc_final: 0.6759 (p0) REVERT: H 130 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8779 (tp) REVERT: H 137 LEU cc_start: 0.9320 (tt) cc_final: 0.9108 (tt) REVERT: H 146 ARG cc_start: 0.8908 (ttp80) cc_final: 0.8319 (mtp-110) REVERT: H 153 ASP cc_start: 0.8574 (m-30) cc_final: 0.8240 (m-30) REVERT: H 158 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7396 (t80) REVERT: H 208 TYR cc_start: 0.8382 (t80) cc_final: 0.8023 (t80) REVERT: H 274 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: H 310 LYS cc_start: 0.7298 (ttpt) cc_final: 0.6727 (tptt) REVERT: H 313 LYS cc_start: 0.9285 (ttmt) cc_final: 0.8952 (ttmm) REVERT: H 315 TYR cc_start: 0.8326 (m-10) cc_final: 0.7595 (m-10) REVERT: H 316 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8440 (mm) REVERT: H 322 LYS cc_start: 0.7744 (pttm) cc_final: 0.6990 (tttm) REVERT: H 359 ILE cc_start: 0.9458 (tp) cc_final: 0.9130 (tp) outliers start: 105 outliers final: 68 residues processed: 825 average time/residue: 0.3143 time to fit residues: 397.6256 Evaluate side-chains 818 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 730 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 73 ASN D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN G 50 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21832 Z= 0.208 Angle : 0.626 12.975 29744 Z= 0.302 Chirality : 0.039 0.171 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.265 21.208 2792 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.79 % Allowed : 28.50 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2496 helix: 1.22 (0.13), residues: 1736 sheet: -3.79 (0.52), residues: 80 loop : -2.83 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 236 HIS 0.021 0.001 HIS C 50 PHE 0.038 0.001 PHE B 64 TYR 0.018 0.001 TYR H 300 ARG 0.009 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 739 time to evaluate : 2.240 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: A 123 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8158 (ttp-170) REVERT: A 153 ASP cc_start: 0.8558 (m-30) cc_final: 0.8304 (m-30) REVERT: A 208 TYR cc_start: 0.8154 (t80) cc_final: 0.7683 (t80) REVERT: A 221 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5999 (pp) REVERT: A 236 TRP cc_start: 0.8399 (p-90) cc_final: 0.8151 (p-90) REVERT: A 274 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: A 305 LYS cc_start: 0.8487 (tmtt) cc_final: 0.8224 (tttm) REVERT: A 310 LYS cc_start: 0.7090 (ttpt) cc_final: 0.6434 (tptm) REVERT: A 345 MET cc_start: 0.9214 (tpp) cc_final: 0.8797 (tpp) REVERT: B 130 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.8888 (tp) REVERT: B 146 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8416 (mtp-110) REVERT: B 153 ASP cc_start: 0.8593 (m-30) cc_final: 0.8242 (m-30) REVERT: B 158 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7499 (t80) REVERT: B 170 SER cc_start: 0.9401 (t) cc_final: 0.9181 (m) REVERT: B 208 TYR cc_start: 0.8414 (t80) cc_final: 0.8100 (t80) REVERT: B 274 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: B 310 LYS cc_start: 0.7306 (ttpt) cc_final: 0.6666 (tptm) REVERT: B 315 TYR cc_start: 0.8267 (m-10) cc_final: 0.7567 (m-10) REVERT: B 322 LYS cc_start: 0.7745 (pttm) cc_final: 0.7143 (mptt) REVERT: B 359 ILE cc_start: 0.9467 (tp) cc_final: 0.9182 (tp) REVERT: C 123 ARG cc_start: 0.8402 (ttm170) cc_final: 0.8197 (ttp-170) REVERT: C 153 ASP cc_start: 0.8579 (m-30) cc_final: 0.8045 (m-30) REVERT: C 157 LYS cc_start: 0.8213 (tptt) cc_final: 0.7508 (ttpp) REVERT: C 158 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7805 (t80) REVERT: C 208 TYR cc_start: 0.8194 (t80) cc_final: 0.7703 (t80) REVERT: C 236 TRP cc_start: 0.8422 (p-90) cc_final: 0.8212 (p-90) REVERT: C 274 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: C 310 LYS cc_start: 0.7097 (ttpt) cc_final: 0.6442 (tptm) REVERT: C 322 LYS cc_start: 0.7397 (pttm) cc_final: 0.6709 (mptt) REVERT: C 359 ILE cc_start: 0.9421 (tp) cc_final: 0.9171 (tp) REVERT: D 28 ASP cc_start: 0.7214 (m-30) cc_final: 0.6997 (m-30) REVERT: D 130 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8866 (tp) REVERT: D 153 ASP cc_start: 0.8634 (m-30) cc_final: 0.8249 (m-30) REVERT: D 158 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7571 (t80) REVERT: D 192 TYR cc_start: 0.8905 (t80) cc_final: 0.8655 (t80) REVERT: D 208 TYR cc_start: 0.8283 (t80) cc_final: 0.7979 (t80) REVERT: D 274 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: D 304 ASN cc_start: 0.8469 (t0) cc_final: 0.8091 (t0) REVERT: D 310 LYS cc_start: 0.7280 (ttpt) cc_final: 0.6879 (tptt) REVERT: D 315 TYR cc_start: 0.8304 (m-10) cc_final: 0.7551 (m-10) REVERT: D 322 LYS cc_start: 0.7554 (pttm) cc_final: 0.6956 (mptt) REVERT: D 332 SER cc_start: 0.9181 (m) cc_final: 0.8821 (p) REVERT: D 359 ILE cc_start: 0.9442 (tp) cc_final: 0.9093 (tp) REVERT: E 68 TRP cc_start: 0.7804 (t-100) cc_final: 0.7552 (t-100) REVERT: E 153 ASP cc_start: 0.8646 (m-30) cc_final: 0.8386 (m-30) REVERT: E 157 LYS cc_start: 0.8319 (tptt) cc_final: 0.7763 (ttmm) REVERT: E 158 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7929 (t80) REVERT: E 170 SER cc_start: 0.9533 (m) cc_final: 0.9140 (m) REVERT: E 175 ASP cc_start: 0.8101 (m-30) cc_final: 0.7609 (m-30) REVERT: E 206 GLN cc_start: 0.9283 (mm-40) cc_final: 0.8724 (mm110) REVERT: E 208 TYR cc_start: 0.8172 (t80) cc_final: 0.7655 (t80) REVERT: E 274 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: E 310 LYS cc_start: 0.7076 (ttpt) cc_final: 0.6580 (tptt) REVERT: E 322 LYS cc_start: 0.7289 (pttm) cc_final: 0.6459 (tttm) REVERT: E 353 PRO cc_start: 0.9303 (Cg_endo) cc_final: 0.9070 (Cg_exo) REVERT: F 59 TRP cc_start: 0.7892 (t-100) cc_final: 0.7142 (t-100) REVERT: F 65 ASN cc_start: 0.7135 (p0) cc_final: 0.6888 (p0) REVERT: F 130 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8785 (tp) REVERT: F 153 ASP cc_start: 0.8606 (m-30) cc_final: 0.8230 (m-30) REVERT: F 157 LYS cc_start: 0.8213 (tptt) cc_final: 0.7796 (ttmm) REVERT: F 158 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7607 (t80) REVERT: F 274 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: F 310 LYS cc_start: 0.7368 (ttpt) cc_final: 0.6955 (tptt) REVERT: F 315 TYR cc_start: 0.8284 (m-10) cc_final: 0.7538 (m-10) REVERT: F 322 LYS cc_start: 0.7564 (pttm) cc_final: 0.6993 (mptt) REVERT: F 332 SER cc_start: 0.9174 (m) cc_final: 0.8910 (t) REVERT: G 68 TRP cc_start: 0.7790 (t-100) cc_final: 0.7560 (t-100) REVERT: G 107 TRP cc_start: 0.8182 (m100) cc_final: 0.7610 (m-10) REVERT: G 123 ARG cc_start: 0.8383 (ttm170) cc_final: 0.8165 (ttp-170) REVERT: G 153 ASP cc_start: 0.8626 (m-30) cc_final: 0.8373 (m-30) REVERT: G 154 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8243 (mtpt) REVERT: G 157 LYS cc_start: 0.8327 (tptt) cc_final: 0.7536 (ttpp) REVERT: G 158 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7640 (t80) REVERT: G 208 TYR cc_start: 0.8194 (t80) cc_final: 0.7722 (t80) REVERT: G 221 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5829 (pp) REVERT: G 236 TRP cc_start: 0.8444 (p-90) cc_final: 0.8217 (p-90) REVERT: G 274 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: G 310 LYS cc_start: 0.7137 (ttpt) cc_final: 0.6548 (tptm) REVERT: G 322 LYS cc_start: 0.7301 (pttm) cc_final: 0.6630 (mptt) REVERT: G 353 PRO cc_start: 0.9313 (Cg_endo) cc_final: 0.9089 (Cg_exo) REVERT: H 65 ASN cc_start: 0.7098 (p0) cc_final: 0.6753 (p0) REVERT: H 130 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8815 (tp) REVERT: H 137 LEU cc_start: 0.9366 (tt) cc_final: 0.9142 (tt) REVERT: H 153 ASP cc_start: 0.8560 (m-30) cc_final: 0.8229 (m-30) REVERT: H 158 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7455 (t80) REVERT: H 208 TYR cc_start: 0.8396 (t80) cc_final: 0.8037 (t80) REVERT: H 274 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: H 310 LYS cc_start: 0.7326 (ttpt) cc_final: 0.6742 (tptt) REVERT: H 313 LYS cc_start: 0.9285 (ttmt) cc_final: 0.8965 (ttmm) REVERT: H 315 TYR cc_start: 0.8341 (m-10) cc_final: 0.7594 (m-10) REVERT: H 316 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8457 (mm) REVERT: H 322 LYS cc_start: 0.7769 (pttm) cc_final: 0.7145 (mptt) REVERT: H 359 ILE cc_start: 0.9473 (tp) cc_final: 0.9144 (tp) outliers start: 108 outliers final: 76 residues processed: 806 average time/residue: 0.3130 time to fit residues: 387.2474 Evaluate side-chains 823 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 725 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 255 optimal weight: 0.4980 chunk 234 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 161 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 115 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 73 ASN F 79 HIS G 50 HIS G 115 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21832 Z= 0.165 Angle : 0.619 12.957 29744 Z= 0.299 Chirality : 0.039 0.168 3288 Planarity : 0.003 0.030 3632 Dihedral : 4.174 20.964 2792 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.03 % Allowed : 29.79 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2496 helix: 1.26 (0.13), residues: 1736 sheet: -3.75 (0.52), residues: 80 loop : -2.77 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 236 HIS 0.024 0.002 HIS C 50 PHE 0.019 0.001 PHE D 330 TYR 0.017 0.001 TYR H 300 ARG 0.009 0.000 ARG E 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 752 time to evaluate : 2.380 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: A 123 ARG cc_start: 0.8350 (ttm170) cc_final: 0.8134 (ttp-170) REVERT: A 153 ASP cc_start: 0.8510 (m-30) cc_final: 0.8287 (m-30) REVERT: A 208 TYR cc_start: 0.8115 (t80) cc_final: 0.7607 (t80) REVERT: A 221 LEU cc_start: 0.6130 (OUTLIER) cc_final: 0.5854 (pp) REVERT: A 236 TRP cc_start: 0.8352 (p-90) cc_final: 0.8131 (p-90) REVERT: A 274 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.6369 (mp0) REVERT: A 305 LYS cc_start: 0.8535 (tmtt) cc_final: 0.8256 (tttp) REVERT: A 310 LYS cc_start: 0.7065 (ttpt) cc_final: 0.6429 (tptm) REVERT: B 146 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8236 (mtp-110) REVERT: B 153 ASP cc_start: 0.8562 (m-30) cc_final: 0.8217 (m-30) REVERT: B 158 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7468 (t80) REVERT: B 208 TYR cc_start: 0.8390 (t80) cc_final: 0.8084 (t80) REVERT: B 274 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: B 304 ASN cc_start: 0.8430 (t0) cc_final: 0.8067 (t0) REVERT: B 310 LYS cc_start: 0.7292 (ttpt) cc_final: 0.6697 (tptm) REVERT: B 315 TYR cc_start: 0.8218 (m-10) cc_final: 0.7532 (m-10) REVERT: B 322 LYS cc_start: 0.7702 (pttm) cc_final: 0.6925 (tttm) REVERT: B 359 ILE cc_start: 0.9431 (tp) cc_final: 0.9116 (tp) REVERT: C 123 ARG cc_start: 0.8353 (ttm170) cc_final: 0.8132 (ttp-170) REVERT: C 153 ASP cc_start: 0.8566 (m-30) cc_final: 0.7369 (m-30) REVERT: C 157 LYS cc_start: 0.8213 (tptt) cc_final: 0.7471 (ttpp) REVERT: C 158 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7722 (t80) REVERT: C 175 ASP cc_start: 0.8058 (m-30) cc_final: 0.7549 (m-30) REVERT: C 208 TYR cc_start: 0.8166 (t80) cc_final: 0.7634 (t80) REVERT: C 236 TRP cc_start: 0.8343 (p-90) cc_final: 0.8046 (p-90) REVERT: C 274 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.6323 (mp0) REVERT: C 310 LYS cc_start: 0.7052 (ttpt) cc_final: 0.6417 (tptm) REVERT: C 322 LYS cc_start: 0.7293 (pttm) cc_final: 0.6634 (mptt) REVERT: C 359 ILE cc_start: 0.9409 (tp) cc_final: 0.9160 (tp) REVERT: D 130 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.8840 (tp) REVERT: D 153 ASP cc_start: 0.8631 (m-30) cc_final: 0.8282 (m-30) REVERT: D 158 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7386 (t80) REVERT: D 192 TYR cc_start: 0.8876 (t80) cc_final: 0.8648 (t80) REVERT: D 208 TYR cc_start: 0.8234 (t80) cc_final: 0.7908 (t80) REVERT: D 274 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.6324 (mp0) REVERT: D 304 ASN cc_start: 0.8448 (t0) cc_final: 0.8095 (t0) REVERT: D 310 LYS cc_start: 0.7333 (ttpt) cc_final: 0.6913 (tptt) REVERT: D 315 TYR cc_start: 0.8295 (m-10) cc_final: 0.7620 (m-10) REVERT: D 322 LYS cc_start: 0.7427 (pttm) cc_final: 0.6869 (mptt) REVERT: D 332 SER cc_start: 0.9142 (m) cc_final: 0.8784 (p) REVERT: D 359 ILE cc_start: 0.9431 (tp) cc_final: 0.9086 (tp) REVERT: E 68 TRP cc_start: 0.7762 (t-100) cc_final: 0.7520 (t-100) REVERT: E 70 ASN cc_start: 0.8432 (t0) cc_final: 0.8127 (t0) REVERT: E 142 LYS cc_start: 0.9175 (ttmm) cc_final: 0.8886 (mtpp) REVERT: E 153 ASP cc_start: 0.8630 (m-30) cc_final: 0.8356 (m-30) REVERT: E 157 LYS cc_start: 0.8311 (tptt) cc_final: 0.7745 (ttmm) REVERT: E 158 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7831 (t80) REVERT: E 175 ASP cc_start: 0.8071 (m-30) cc_final: 0.7579 (m-30) REVERT: E 206 GLN cc_start: 0.9262 (mm-40) cc_final: 0.8563 (mm-40) REVERT: E 208 TYR cc_start: 0.8200 (t80) cc_final: 0.7708 (t80) REVERT: E 274 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.6468 (mp0) REVERT: E 310 LYS cc_start: 0.7080 (ttpt) cc_final: 0.6587 (tptt) REVERT: E 322 LYS cc_start: 0.7186 (pttm) cc_final: 0.6448 (tttm) REVERT: E 353 PRO cc_start: 0.9260 (Cg_endo) cc_final: 0.9026 (Cg_exo) REVERT: F 59 TRP cc_start: 0.7901 (t-100) cc_final: 0.7162 (t-100) REVERT: F 65 ASN cc_start: 0.7040 (p0) cc_final: 0.6792 (p0) REVERT: F 130 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8785 (tp) REVERT: F 153 ASP cc_start: 0.8641 (m-30) cc_final: 0.8282 (m-30) REVERT: F 158 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7650 (t80) REVERT: F 208 TYR cc_start: 0.8290 (t80) cc_final: 0.8068 (t80) REVERT: F 274 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: F 304 ASN cc_start: 0.8459 (t0) cc_final: 0.8113 (t0) REVERT: F 310 LYS cc_start: 0.7388 (ttpt) cc_final: 0.6914 (tptt) REVERT: F 315 TYR cc_start: 0.8294 (m-10) cc_final: 0.7570 (m-10) REVERT: F 322 LYS cc_start: 0.7401 (pttm) cc_final: 0.6813 (mptt) REVERT: F 332 SER cc_start: 0.9157 (m) cc_final: 0.8897 (t) REVERT: G 59 TRP cc_start: 0.8180 (t-100) cc_final: 0.7762 (t-100) REVERT: G 68 TRP cc_start: 0.7785 (t-100) cc_final: 0.7562 (t-100) REVERT: G 123 ARG cc_start: 0.8354 (ttm170) cc_final: 0.8140 (ttp-170) REVERT: G 153 ASP cc_start: 0.8613 (m-30) cc_final: 0.8362 (m-30) REVERT: G 154 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8175 (mtpt) REVERT: G 157 LYS cc_start: 0.8248 (tptt) cc_final: 0.7452 (ttpp) REVERT: G 158 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7690 (t80) REVERT: G 208 TYR cc_start: 0.8199 (t80) cc_final: 0.7693 (t80) REVERT: G 221 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5784 (pp) REVERT: G 236 TRP cc_start: 0.8359 (p-90) cc_final: 0.8062 (p-90) REVERT: G 274 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: G 310 LYS cc_start: 0.7090 (ttpt) cc_final: 0.6511 (tptm) REVERT: G 322 LYS cc_start: 0.7237 (pttm) cc_final: 0.6455 (tttm) REVERT: G 353 PRO cc_start: 0.9284 (Cg_endo) cc_final: 0.9073 (Cg_exo) REVERT: H 65 ASN cc_start: 0.7014 (p0) cc_final: 0.6694 (p0) REVERT: H 130 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8793 (tp) REVERT: H 137 LEU cc_start: 0.9322 (tt) cc_final: 0.9102 (tt) REVERT: H 153 ASP cc_start: 0.8567 (m-30) cc_final: 0.8253 (m-30) REVERT: H 158 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7530 (t80) REVERT: H 208 TYR cc_start: 0.8369 (t80) cc_final: 0.8006 (t80) REVERT: H 274 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: H 310 LYS cc_start: 0.7295 (ttpt) cc_final: 0.6693 (tptm) REVERT: H 313 LYS cc_start: 0.9263 (ttmt) cc_final: 0.8926 (ttmm) REVERT: H 315 TYR cc_start: 0.8313 (m-10) cc_final: 0.7619 (m-10) REVERT: H 316 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8417 (mm) REVERT: H 322 LYS cc_start: 0.7668 (pttm) cc_final: 0.6940 (tttm) REVERT: H 359 ILE cc_start: 0.9445 (tp) cc_final: 0.9121 (tp) outliers start: 91 outliers final: 66 residues processed: 812 average time/residue: 0.3343 time to fit residues: 422.3563 Evaluate side-chains 808 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 721 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 332 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.130984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.108512 restraints weight = 32033.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.112320 restraints weight = 17332.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.114938 restraints weight = 11523.172| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21832 Z= 0.191 Angle : 0.612 11.980 29744 Z= 0.298 Chirality : 0.038 0.145 3288 Planarity : 0.004 0.030 3632 Dihedral : 4.213 21.485 2792 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.17 % Allowed : 29.48 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2496 helix: 1.31 (0.13), residues: 1720 sheet: -3.54 (0.89), residues: 40 loop : -2.80 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP E 236 HIS 0.018 0.002 HIS C 50 PHE 0.027 0.001 PHE F 330 TYR 0.018 0.001 TYR H 300 ARG 0.008 0.000 ARG E 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6230.71 seconds wall clock time: 110 minutes 18.74 seconds (6618.74 seconds total)