Starting phenix.real_space_refine on Thu Sep 18 22:34:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kff_9971/09_2025/6kff_9971.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kff_9971/09_2025/6kff_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 { model { file = "/net/cci-nas-00/data/ceres_data/6kff_9971/09_2025/6kff_9971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kff_9971/09_2025/6kff_9971.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kff_9971/09_2025/6kff_9971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kff_9971/09_2025/6kff_9971.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F, G, H Time building chain proxies: 2.15, per 1000 atoms: 0.10 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=16, 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 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 76 " - pdb=" SG CYS H 248 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 647.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.63 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: 2.89 Time building geometry restraints manager: 2.47 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: 10949 17.32 - 34.64: 1251 34.64 - 51.96: 224 51.96 - 69.28: 16 69.28 - 86.60: 40 Dihedral angle restraints: 12480 sinusoidal: 4840 harmonic: 7640 Sorted by residual: dihedral pdb=" CB CYS F 76 " pdb=" SG CYS F 76 " pdb=" SG CYS F 248 " pdb=" CB CYS F 248 " ideal model delta sinusoidal sigma weight residual 93.00 137.02 -44.02 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS G 76 " pdb=" SG CYS G 76 " pdb=" SG CYS G 248 " pdb=" CB CYS G 248 " ideal model delta sinusoidal sigma weight residual 93.00 137.01 -44.01 1 1.00e+01 1.00e-02 2.70e+01 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 ... (remaining 12477 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: 2.18 - 2.73: 1164 2.73 - 3.27: 22887 3.27 - 3.81: 35035 3.81 - 4.36: 38025 4.36 - 4.90: 66422 Nonbonded interactions: 163533 Sorted by model distance: nonbonded pdb=" O ASN D 31 " pdb=" OG1 THR D 35 " model vdw 2.182 3.040 nonbonded pdb=" O ASN A 31 " pdb=" OG1 THR A 35 " model vdw 2.183 3.040 nonbonded pdb=" O ASN B 31 " pdb=" OG1 THR B 35 " model vdw 2.183 3.040 nonbonded pdb=" O ASN G 31 " pdb=" OG1 THR G 35 " model vdw 2.183 3.040 nonbonded pdb=" O ASN F 31 " pdb=" OG1 THR F 35 " model vdw 2.183 3.040 ... (remaining 163528 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 15.100 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.360 ------------------------------------------------------------------------------- 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 21848 Z= 0.160 Angle : 0.604 7.440 29776 Z= 0.321 Chirality : 0.038 0.129 3288 Planarity : 0.003 0.021 3632 Dihedral : 15.084 86.599 7472 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.18 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG H 362 TYR 0.009 0.001 TYR B 110 PHE 0.023 0.001 PHE D 119 TRP 0.011 0.001 TRP A 68 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00356 (21832) covalent geometry : angle 0.60385 (29744) SS BOND : bond 0.00094 ( 16) SS BOND : angle 0.56640 ( 32) hydrogen bonds : bond 0.11147 ( 1240) hydrogen bonds : angle 5.43526 ( 3624) *********************** 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 to be fit. rotamer outliers: 8 poor density : 926 time to evaluate : 0.770 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: 0.1589 time to fit residues: 219.9935 Evaluate side-chains 753 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 747 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0040 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- 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 234 ASN B 247 HIS B 329 GLN C 206 GLN C 234 ASN C 247 HIS C 329 GLN D 21 GLN D 234 ASN D 247 HIS D 329 GLN E 50 HIS E 234 ASN E 247 HIS E 329 GLN F 21 GLN F 50 HIS 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 234 ASN H 247 HIS H 329 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.103880 restraints weight = 32243.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107712 restraints weight = 17076.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.110318 restraints weight = 11262.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.112112 restraints weight = 8488.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.113403 restraints weight = 6896.800| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 21848 Z= 0.128 Angle : 0.614 10.102 29776 Z= 0.300 Chirality : 0.040 0.178 3288 Planarity : 0.004 0.035 3632 Dihedral : 4.749 22.916 2798 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.75 % Allowed : 20.30 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.17), residues: 2496 helix: 0.63 (0.13), residues: 1688 sheet: -4.21 (0.36), residues: 80 loop : -3.50 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 29 TYR 0.017 0.001 TYR G 301 PHE 0.021 0.001 PHE H 124 TRP 0.031 0.001 TRP A 59 HIS 0.010 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00272 (21832) covalent geometry : angle 0.61203 (29744) SS BOND : bond 0.00202 ( 16) SS BOND : angle 1.44304 ( 32) hydrogen bonds : bond 0.04153 ( 1240) hydrogen bonds : angle 4.37988 ( 3624) *********************** 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 871 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 809 time to evaluate : 0.759 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 58 CYS cc_start: 0.7194 (m) cc_final: 0.6878 (m) REVERT: A 65 ASN cc_start: 0.6712 (p0) cc_final: 0.6446 (p0) REVERT: A 70 ASN cc_start: 0.8781 (t0) cc_final: 0.8427 (t0) REVERT: A 123 ARG cc_start: 0.8335 (ttm170) cc_final: 0.7943 (ttp-170) REVERT: A 137 LEU cc_start: 0.9230 (tt) cc_final: 0.9013 (tt) REVERT: A 153 ASP cc_start: 0.8599 (m-30) cc_final: 0.8293 (m-30) REVERT: A 157 LYS cc_start: 0.8176 (tptt) cc_final: 0.7575 (ttmm) REVERT: A 175 ASP cc_start: 0.8028 (m-30) cc_final: 0.7544 (m-30) REVERT: A 208 TYR cc_start: 0.8335 (t80) cc_final: 0.7858 (t80) REVERT: A 310 LYS cc_start: 0.7046 (ttpt) cc_final: 0.6415 (tptm) REVERT: B 65 ASN cc_start: 0.7644 (p0) cc_final: 0.7240 (p0) REVERT: B 146 ARG cc_start: 0.8932 (ttp80) cc_final: 0.8374 (mtm110) REVERT: B 153 ASP cc_start: 0.8789 (m-30) cc_final: 0.8442 (m-30) REVERT: B 158 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7966 (t80) REVERT: B 170 SER cc_start: 0.9387 (t) cc_final: 0.9167 (m) REVERT: B 208 TYR cc_start: 0.8461 (t80) cc_final: 0.8154 (t80) REVERT: B 305 LYS cc_start: 0.8565 (tttm) cc_final: 0.8351 (tmtt) REVERT: B 310 LYS cc_start: 0.7275 (ttpt) cc_final: 0.6563 (tptt) REVERT: B 315 TYR cc_start: 0.8320 (m-10) cc_final: 0.7559 (m-10) REVERT: B 322 LYS cc_start: 0.7863 (pttm) cc_final: 0.7113 (mptt) REVERT: B 332 SER cc_start: 0.9024 (t) cc_final: 0.8796 (t) REVERT: B 359 ILE cc_start: 0.9388 (tp) cc_final: 0.9096 (tp) REVERT: C 65 ASN cc_start: 0.7448 (p0) cc_final: 0.6971 (p0) REVERT: C 123 ARG cc_start: 0.8451 (ttm170) cc_final: 0.8072 (ttp-170) REVERT: C 153 ASP cc_start: 0.8829 (m-30) cc_final: 0.8182 (m-30) REVERT: C 154 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8232 (mtpt) REVERT: C 157 LYS cc_start: 0.8190 (tptt) cc_final: 0.7725 (ttpp) REVERT: C 178 ARG cc_start: 0.9014 (ttm-80) cc_final: 0.8813 (ttp-110) REVERT: C 198 TRP cc_start: 0.8673 (t-100) cc_final: 0.8360 (t-100) REVERT: C 208 TYR cc_start: 0.8347 (t80) cc_final: 0.7880 (t80) REVERT: C 310 LYS cc_start: 0.6808 (ttpt) cc_final: 0.5951 (tptm) REVERT: C 322 LYS cc_start: 0.7623 (pttm) cc_final: 0.6583 (mptt) REVERT: C 353 PRO cc_start: 0.9400 (Cg_endo) cc_final: 0.9190 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7623 (p0) cc_final: 0.7134 (p0) REVERT: D 146 ARG cc_start: 0.8952 (ttp80) cc_final: 0.8219 (mtp-110) REVERT: D 153 ASP cc_start: 0.8817 (m-30) cc_final: 0.8374 (m-30) REVERT: D 158 PHE cc_start: 0.8303 (t80) cc_final: 0.7971 (t80) REVERT: D 192 TYR cc_start: 0.9149 (t80) cc_final: 0.8866 (t80) REVERT: D 206 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8460 (mm-40) REVERT: D 310 LYS cc_start: 0.7176 (ttpt) cc_final: 0.6717 (tptt) REVERT: D 332 SER cc_start: 0.9017 (m) cc_final: 0.8779 (t) REVERT: D 359 ILE cc_start: 0.9407 (tp) cc_final: 0.9184 (tp) REVERT: E 65 ASN cc_start: 0.7209 (p0) cc_final: 0.6770 (p0) REVERT: E 68 TRP cc_start: 0.8062 (t-100) cc_final: 0.7840 (t-100) REVERT: E 154 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8371 (mtpt) REVERT: E 157 LYS cc_start: 0.8323 (tptt) cc_final: 0.7812 (ttpp) REVERT: E 206 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8481 (mm-40) REVERT: E 208 TYR cc_start: 0.8275 (t80) cc_final: 0.7796 (t80) REVERT: E 310 LYS cc_start: 0.7169 (ttpt) cc_final: 0.6622 (tptt) REVERT: E 322 LYS cc_start: 0.7550 (pttm) cc_final: 0.6455 (mptt) REVERT: F 157 LYS cc_start: 0.8174 (tptt) cc_final: 0.7663 (ttmm) REVERT: F 194 LEU cc_start: 0.9151 (mt) cc_final: 0.8852 (mt) REVERT: F 310 LYS cc_start: 0.7315 (ttpt) cc_final: 0.6889 (tptt) REVERT: G 64 PHE cc_start: 0.8154 (m-80) cc_final: 0.7862 (m-10) REVERT: G 65 ASN cc_start: 0.7481 (p0) cc_final: 0.7037 (p0) REVERT: G 67 GLN cc_start: 0.8055 (mt0) cc_final: 0.7775 (mt0) REVERT: G 123 ARG cc_start: 0.8420 (ttm170) cc_final: 0.8064 (ttp-170) REVERT: G 153 ASP cc_start: 0.8846 (m-30) cc_final: 0.8470 (m-30) REVERT: G 154 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8192 (mtpt) REVERT: G 157 LYS cc_start: 0.8240 (tptt) cc_final: 0.7729 (ttpp) REVERT: G 208 TYR cc_start: 0.8289 (t80) cc_final: 0.7836 (t80) REVERT: G 304 ASN cc_start: 0.8718 (t0) cc_final: 0.8404 (t0) REVERT: G 310 LYS cc_start: 0.6959 (ttpt) cc_final: 0.6239 (tptt) REVERT: G 322 LYS cc_start: 0.7606 (pttm) cc_final: 0.6789 (mptt) REVERT: G 353 PRO cc_start: 0.9410 (Cg_endo) cc_final: 0.9192 (Cg_exo) REVERT: H 157 LYS cc_start: 0.8189 (tptt) cc_final: 0.7700 (ttmm) REVERT: H 158 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7827 (t80) REVERT: H 178 ARG cc_start: 0.8982 (ttm-80) cc_final: 0.8759 (ttm-80) REVERT: H 192 TYR cc_start: 0.9224 (t80) cc_final: 0.8978 (t80) REVERT: H 206 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8526 (mm-40) REVERT: H 229 ASP cc_start: 0.8588 (m-30) cc_final: 0.8313 (m-30) REVERT: H 310 LYS cc_start: 0.7247 (ttpt) cc_final: 0.6643 (tptt) REVERT: H 313 LYS cc_start: 0.9317 (ttmt) cc_final: 0.9068 (ttmm) outliers start: 62 outliers final: 34 residues processed: 843 average time/residue: 0.1505 time to fit residues: 191.0443 Evaluate side-chains 756 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 720 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 360 SER 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 299 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 360 SER 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 299 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER 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 125 ILE Chi-restraints excluded: chain H residue 158 PHE 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 90 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 172 optimal weight: 0.3980 chunk 161 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** D 50 HIS D 329 GLN G 50 HIS G 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.105257 restraints weight = 32213.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.109098 restraints weight = 17044.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111658 restraints weight = 11236.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.113495 restraints weight = 8460.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.114680 restraints weight = 6863.856| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21848 Z= 0.150 Angle : 0.607 7.994 29776 Z= 0.298 Chirality : 0.040 0.149 3288 Planarity : 0.004 0.029 3632 Dihedral : 4.606 22.227 2792 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.81 % Allowed : 23.40 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.17), residues: 2496 helix: 0.88 (0.13), residues: 1688 sheet: -3.95 (0.39), residues: 80 loop : -3.29 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 161 TYR 0.015 0.001 TYR F 301 PHE 0.015 0.001 PHE B 147 TRP 0.037 0.001 TRP C 59 HIS 0.012 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00345 (21832) covalent geometry : angle 0.60368 (29744) SS BOND : bond 0.00172 ( 16) SS BOND : angle 2.04118 ( 32) hydrogen bonds : bond 0.04020 ( 1240) hydrogen bonds : angle 4.26167 ( 3624) *********************** 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 834 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 748 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.6734 (p0) cc_final: 0.6251 (p0) REVERT: A 68 TRP cc_start: 0.8002 (t-100) cc_final: 0.7799 (t-100) REVERT: A 123 ARG cc_start: 0.8360 (ttm170) cc_final: 0.7967 (ttp-170) REVERT: A 137 LEU cc_start: 0.9250 (tt) cc_final: 0.9037 (tt) REVERT: A 153 ASP cc_start: 0.8632 (m-30) cc_final: 0.8259 (m-30) REVERT: A 157 LYS cc_start: 0.8277 (tptt) cc_final: 0.7598 (ttmm) REVERT: A 158 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7106 (t80) REVERT: A 170 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9084 (m) REVERT: A 208 TYR cc_start: 0.8343 (t80) cc_final: 0.7656 (t80) REVERT: A 305 LYS cc_start: 0.8558 (tttm) cc_final: 0.8123 (tmtt) REVERT: A 310 LYS cc_start: 0.7143 (ttpt) cc_final: 0.6404 (tptm) REVERT: B 65 ASN cc_start: 0.7635 (p0) cc_final: 0.7077 (p0) REVERT: B 105 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6890 (m-10) REVERT: B 146 ARG cc_start: 0.8921 (ttp80) cc_final: 0.8402 (mtm110) REVERT: B 153 ASP cc_start: 0.8805 (m-30) cc_final: 0.8388 (m-30) REVERT: B 170 SER cc_start: 0.9413 (t) cc_final: 0.9206 (m) REVERT: B 206 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8181 (mm-40) REVERT: B 208 TYR cc_start: 0.8459 (t80) cc_final: 0.8123 (t80) REVERT: B 305 LYS cc_start: 0.8658 (tttm) cc_final: 0.8344 (tmtt) REVERT: B 310 LYS cc_start: 0.7249 (ttpt) cc_final: 0.6463 (tptt) REVERT: B 322 LYS cc_start: 0.7861 (pttm) cc_final: 0.7087 (mptt) REVERT: B 332 SER cc_start: 0.9034 (t) cc_final: 0.8815 (t) REVERT: B 359 ILE cc_start: 0.9425 (tp) cc_final: 0.9145 (tp) REVERT: C 68 TRP cc_start: 0.8131 (t-100) cc_final: 0.7921 (t-100) REVERT: C 105 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.7085 (m-10) REVERT: C 123 ARG cc_start: 0.8428 (ttm170) cc_final: 0.8053 (ttp-170) REVERT: C 153 ASP cc_start: 0.8754 (m-30) cc_final: 0.8103 (m-30) REVERT: C 154 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8210 (mtpt) REVERT: C 157 LYS cc_start: 0.8215 (tptt) cc_final: 0.7723 (ttpp) REVERT: C 198 TRP cc_start: 0.8673 (t-100) cc_final: 0.8281 (t-100) REVERT: C 208 TYR cc_start: 0.8397 (t80) cc_final: 0.7894 (t80) REVERT: C 236 TRP cc_start: 0.8852 (p-90) cc_final: 0.8635 (p-90) REVERT: C 267 LEU cc_start: 0.9153 (mp) cc_final: 0.8733 (mp) REVERT: C 305 LYS cc_start: 0.8416 (tttm) cc_final: 0.8028 (tmtt) REVERT: C 310 LYS cc_start: 0.6854 (ttpt) cc_final: 0.6061 (tptm) REVERT: C 322 LYS cc_start: 0.7546 (pttm) cc_final: 0.6474 (mptt) REVERT: C 353 PRO cc_start: 0.9395 (Cg_endo) cc_final: 0.9186 (Cg_exo) REVERT: D 64 PHE cc_start: 0.8432 (m-10) cc_final: 0.8230 (m-10) REVERT: D 65 ASN cc_start: 0.7446 (p0) cc_final: 0.6990 (p0) REVERT: D 67 GLN cc_start: 0.8654 (mt0) cc_final: 0.8443 (mt0) REVERT: D 146 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8439 (mtm110) REVERT: D 153 ASP cc_start: 0.8842 (m-30) cc_final: 0.8372 (m-30) REVERT: D 192 TYR cc_start: 0.9102 (t80) cc_final: 0.8822 (t80) REVERT: D 206 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8455 (mm-40) REVERT: D 208 TYR cc_start: 0.8516 (t80) cc_final: 0.8193 (t80) REVERT: D 275 LYS cc_start: 0.8714 (mptt) cc_final: 0.8493 (mmtt) REVERT: D 310 LYS cc_start: 0.7233 (ttpt) cc_final: 0.6756 (tptt) REVERT: D 332 SER cc_start: 0.9146 (m) cc_final: 0.8927 (t) REVERT: D 359 ILE cc_start: 0.9400 (tp) cc_final: 0.9107 (tp) REVERT: E 28 ASP cc_start: 0.6756 (m-30) cc_final: 0.6518 (m-30) REVERT: E 65 ASN cc_start: 0.7173 (p0) cc_final: 0.6366 (p0) REVERT: E 68 TRP cc_start: 0.8084 (t-100) cc_final: 0.7859 (t-100) REVERT: E 129 MET cc_start: 0.8118 (tpp) cc_final: 0.7882 (tpp) REVERT: E 157 LYS cc_start: 0.8359 (tptt) cc_final: 0.7779 (ttmm) REVERT: E 158 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7836 (t80) REVERT: E 175 ASP cc_start: 0.8120 (m-30) cc_final: 0.7422 (m-30) REVERT: E 206 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8360 (mm-40) REVERT: E 208 TYR cc_start: 0.8247 (t80) cc_final: 0.7761 (t80) REVERT: E 310 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6647 (tptt) REVERT: E 322 LYS cc_start: 0.7533 (pttm) cc_final: 0.6504 (mptt) REVERT: E 353 PRO cc_start: 0.9392 (Cg_endo) cc_final: 0.9178 (Cg_exo) REVERT: F 157 LYS cc_start: 0.8149 (tptt) cc_final: 0.7671 (ttmm) REVERT: F 158 PHE cc_start: 0.8115 (t80) cc_final: 0.7709 (t80) REVERT: F 304 ASN cc_start: 0.8614 (t0) cc_final: 0.7962 (t0) REVERT: F 310 LYS cc_start: 0.7347 (ttpt) cc_final: 0.6892 (tptt) REVERT: G 65 ASN cc_start: 0.7384 (p0) cc_final: 0.6855 (p0) REVERT: G 68 TRP cc_start: 0.8162 (t-100) cc_final: 0.7937 (t-100) REVERT: G 105 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.7006 (m-10) REVERT: G 123 ARG cc_start: 0.8429 (ttm170) cc_final: 0.8066 (ttp-170) REVERT: G 153 ASP cc_start: 0.8847 (m-30) cc_final: 0.8459 (m-30) REVERT: G 154 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8271 (mtpt) REVERT: G 157 LYS cc_start: 0.8302 (tptt) cc_final: 0.7682 (ttpp) REVERT: G 158 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7669 (t80) REVERT: G 192 TYR cc_start: 0.9082 (t80) cc_final: 0.8786 (t80) REVERT: G 198 TRP cc_start: 0.8838 (t-100) cc_final: 0.8503 (t-100) REVERT: G 208 TYR cc_start: 0.8304 (t80) cc_final: 0.7606 (t80) REVERT: G 236 TRP cc_start: 0.8846 (p-90) cc_final: 0.8590 (p-90) REVERT: G 267 LEU cc_start: 0.9177 (mp) cc_final: 0.8680 (mp) REVERT: G 305 LYS cc_start: 0.8388 (tttm) cc_final: 0.7975 (tmtt) REVERT: G 310 LYS cc_start: 0.6885 (ttpt) cc_final: 0.6263 (tptt) REVERT: G 322 LYS cc_start: 0.7524 (pttm) cc_final: 0.6682 (mptt) REVERT: G 353 PRO cc_start: 0.9405 (Cg_endo) cc_final: 0.9200 (Cg_exo) REVERT: H 47 LEU cc_start: 0.9457 (mm) cc_final: 0.9223 (mm) REVERT: H 65 ASN cc_start: 0.7339 (p0) cc_final: 0.6783 (p0) REVERT: H 157 LYS cc_start: 0.8222 (tptt) cc_final: 0.7884 (ttmm) REVERT: H 158 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7497 (t80) REVERT: H 206 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8513 (mm-40) REVERT: H 208 TYR cc_start: 0.8554 (t80) cc_final: 0.8233 (t80) REVERT: H 229 ASP cc_start: 0.8602 (m-30) cc_final: 0.8342 (m-30) REVERT: H 310 LYS cc_start: 0.7299 (ttpt) cc_final: 0.6689 (tptt) REVERT: H 313 LYS cc_start: 0.9340 (ttmt) cc_final: 0.9097 (ttmm) REVERT: H 322 LYS cc_start: 0.7827 (pttm) cc_final: 0.7048 (mptt) REVERT: H 359 ILE cc_start: 0.9458 (tp) cc_final: 0.9116 (tp) outliers start: 86 outliers final: 66 residues processed: 784 average time/residue: 0.1481 time to fit residues: 177.3359 Evaluate side-chains 799 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 725 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 170 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 50 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 105 TYR 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 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 60 THR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 263 VAL 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 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 ILE 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 264 LEU Chi-restraints excluded: chain E residue 299 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 162 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE 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 60 THR Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 37 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 170 SER Chi-restraints excluded: chain H residue 193 THR 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 190 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 206 GLN E 50 HIS E 67 GLN F 50 HIS G 270 ASN H 50 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.125826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.103368 restraints weight = 32468.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107130 restraints weight = 17264.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109705 restraints weight = 11423.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.111358 restraints weight = 8605.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.112679 restraints weight = 7058.265| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21848 Z= 0.187 Angle : 0.618 7.790 29776 Z= 0.305 Chirality : 0.041 0.142 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.630 22.355 2792 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.19 % Allowed : 23.98 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.17), residues: 2496 helix: 0.95 (0.13), residues: 1688 sheet: -3.87 (0.39), residues: 80 loop : -3.21 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 362 TYR 0.015 0.001 TYR F 301 PHE 0.016 0.001 PHE B 242 TRP 0.021 0.001 TRP G 59 HIS 0.017 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00436 (21832) covalent geometry : angle 0.61567 (29744) SS BOND : bond 0.00229 ( 16) SS BOND : angle 1.86718 ( 32) hydrogen bonds : bond 0.04078 ( 1240) hydrogen bonds : angle 4.24252 ( 3624) *********************** 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 862 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 745 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.6812 (p0) cc_final: 0.6304 (p0) REVERT: A 68 TRP cc_start: 0.8129 (t-100) cc_final: 0.7896 (t-100) REVERT: A 123 ARG cc_start: 0.8386 (ttm170) cc_final: 0.7978 (ttp-170) REVERT: A 153 ASP cc_start: 0.8691 (m-30) cc_final: 0.7947 (m-30) REVERT: A 157 LYS cc_start: 0.8201 (tptt) cc_final: 0.7492 (ttmm) REVERT: A 158 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7104 (t80) REVERT: A 170 SER cc_start: 0.9457 (OUTLIER) cc_final: 0.9088 (m) REVERT: A 199 GLN cc_start: 0.8083 (tp40) cc_final: 0.7827 (tp40) REVERT: A 206 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8403 (mm110) REVERT: A 208 TYR cc_start: 0.8325 (t80) cc_final: 0.7668 (t80) REVERT: A 274 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: A 305 LYS cc_start: 0.8603 (tttm) cc_final: 0.8200 (tmtt) REVERT: A 310 LYS cc_start: 0.7186 (ttpt) cc_final: 0.6458 (tptm) REVERT: B 65 ASN cc_start: 0.7565 (p0) cc_final: 0.7136 (p0) REVERT: B 105 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6963 (m-10) REVERT: B 146 ARG cc_start: 0.8952 (ttp80) cc_final: 0.8412 (mtm110) REVERT: B 153 ASP cc_start: 0.8792 (m-30) cc_final: 0.8329 (m-30) REVERT: B 158 PHE cc_start: 0.7475 (t80) cc_final: 0.7193 (t80) REVERT: B 208 TYR cc_start: 0.8491 (t80) cc_final: 0.8186 (t80) REVERT: B 274 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: B 305 LYS cc_start: 0.8667 (tttm) cc_final: 0.8378 (tmtt) REVERT: B 310 LYS cc_start: 0.7276 (ttpt) cc_final: 0.6520 (tptt) REVERT: B 322 LYS cc_start: 0.7878 (pttm) cc_final: 0.7103 (mptt) REVERT: B 359 ILE cc_start: 0.9483 (tp) cc_final: 0.9202 (tp) REVERT: C 64 PHE cc_start: 0.8352 (m-80) cc_final: 0.7928 (m-10) REVERT: C 68 TRP cc_start: 0.8175 (t-100) cc_final: 0.7955 (t-100) REVERT: C 105 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: C 123 ARG cc_start: 0.8449 (ttm170) cc_final: 0.8071 (ttp-170) REVERT: C 153 ASP cc_start: 0.8752 (m-30) cc_final: 0.8129 (m-30) REVERT: C 154 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8249 (mtpt) REVERT: C 157 LYS cc_start: 0.8265 (tptt) cc_final: 0.7680 (ttpp) REVERT: C 192 TYR cc_start: 0.9242 (t80) cc_final: 0.8992 (t80) REVERT: C 208 TYR cc_start: 0.8367 (t80) cc_final: 0.7610 (t80) REVERT: C 236 TRP cc_start: 0.8899 (p-90) cc_final: 0.8684 (p-90) REVERT: C 274 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.6232 (mp0) REVERT: C 305 LYS cc_start: 0.8452 (tttm) cc_final: 0.8094 (tmtt) REVERT: C 310 LYS cc_start: 0.6807 (ttpt) cc_final: 0.6091 (tptm) REVERT: C 322 LYS cc_start: 0.7572 (pttm) cc_final: 0.6489 (mptt) REVERT: C 353 PRO cc_start: 0.9422 (Cg_endo) cc_final: 0.9213 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7613 (p0) cc_final: 0.7225 (p0) REVERT: D 105 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.7235 (m-10) REVERT: D 146 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8448 (mtm110) REVERT: D 153 ASP cc_start: 0.8839 (m-30) cc_final: 0.8348 (m-30) REVERT: D 192 TYR cc_start: 0.9102 (t80) cc_final: 0.8817 (t80) REVERT: D 208 TYR cc_start: 0.8470 (t80) cc_final: 0.8128 (t80) REVERT: D 274 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: D 310 LYS cc_start: 0.7268 (ttpt) cc_final: 0.6788 (tptt) REVERT: D 332 SER cc_start: 0.9184 (m) cc_final: 0.8932 (t) REVERT: D 359 ILE cc_start: 0.9439 (tp) cc_final: 0.9158 (tp) REVERT: E 28 ASP cc_start: 0.6792 (m-30) cc_final: 0.6469 (m-30) REVERT: E 65 ASN cc_start: 0.7082 (p0) cc_final: 0.6473 (p0) REVERT: E 67 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: E 68 TRP cc_start: 0.8121 (t-100) cc_final: 0.7907 (t-100) REVERT: E 129 MET cc_start: 0.8141 (tpp) cc_final: 0.7896 (tpp) REVERT: E 157 LYS cc_start: 0.8398 (tptt) cc_final: 0.7814 (ttmm) REVERT: E 158 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7847 (t80) REVERT: E 206 GLN cc_start: 0.9246 (mm-40) cc_final: 0.8323 (mm-40) REVERT: E 208 TYR cc_start: 0.8191 (t80) cc_final: 0.7725 (t80) REVERT: E 274 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: E 310 LYS cc_start: 0.7211 (ttpt) cc_final: 0.6678 (tptt) REVERT: E 322 LYS cc_start: 0.7556 (pttm) cc_final: 0.6465 (mptt) REVERT: E 353 PRO cc_start: 0.9449 (Cg_endo) cc_final: 0.9236 (Cg_exo) REVERT: F 157 LYS cc_start: 0.8172 (tptt) cc_final: 0.7657 (ttmm) REVERT: F 158 PHE cc_start: 0.8172 (t80) cc_final: 0.7752 (t80) REVERT: F 310 LYS cc_start: 0.7343 (ttpt) cc_final: 0.6869 (tptt) REVERT: G 68 TRP cc_start: 0.8153 (t-100) cc_final: 0.7892 (t-100) REVERT: G 105 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.7084 (m-10) REVERT: G 123 ARG cc_start: 0.8446 (ttm170) cc_final: 0.8091 (ttp-170) REVERT: G 153 ASP cc_start: 0.8805 (m-30) cc_final: 0.8471 (m-30) REVERT: G 154 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8248 (mtpt) REVERT: G 157 LYS cc_start: 0.8304 (tptt) cc_final: 0.7675 (ttpp) REVERT: G 158 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7704 (t80) REVERT: G 208 TYR cc_start: 0.8284 (t80) cc_final: 0.7568 (t80) REVERT: G 236 TRP cc_start: 0.8831 (p-90) cc_final: 0.8621 (p-90) REVERT: G 305 LYS cc_start: 0.8593 (tttm) cc_final: 0.8112 (tmtt) REVERT: G 310 LYS cc_start: 0.7190 (ttpt) cc_final: 0.6528 (tptt) REVERT: G 322 LYS cc_start: 0.7522 (pttm) cc_final: 0.6695 (mptt) REVERT: G 353 PRO cc_start: 0.9436 (Cg_endo) cc_final: 0.9225 (Cg_exo) REVERT: H 65 ASN cc_start: 0.7493 (p0) cc_final: 0.6975 (p0) REVERT: H 105 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.7282 (m-10) REVERT: H 137 LEU cc_start: 0.9256 (tt) cc_final: 0.9054 (tt) REVERT: H 146 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8373 (mtp-110) REVERT: H 153 ASP cc_start: 0.8692 (m-30) cc_final: 0.8289 (m-30) REVERT: H 157 LYS cc_start: 0.8238 (tptt) cc_final: 0.7897 (ttmm) REVERT: H 206 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8481 (mm-40) REVERT: H 208 TYR cc_start: 0.8560 (t80) cc_final: 0.8248 (t80) REVERT: H 229 ASP cc_start: 0.8597 (m-30) cc_final: 0.8328 (m-30) REVERT: H 305 LYS cc_start: 0.8652 (tttm) cc_final: 0.8341 (tmtt) REVERT: H 310 LYS cc_start: 0.7245 (ttpt) cc_final: 0.6515 (tptt) REVERT: H 313 LYS cc_start: 0.9355 (ttmt) cc_final: 0.9104 (ttmm) REVERT: H 359 ILE cc_start: 0.9475 (tp) cc_final: 0.9110 (tp) outliers start: 117 outliers final: 80 residues processed: 805 average time/residue: 0.1445 time to fit residues: 178.7260 Evaluate side-chains 810 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 715 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 158 PHE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU 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 105 TYR 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 205 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU 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 105 TYR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 263 VAL 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 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 229 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU 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 67 GLN 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 170 SER 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 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 125 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 263 VAL 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 105 TYR 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 263 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 299 ILE 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 162 LEU Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 264 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 107 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 245 optimal weight: 7.9990 chunk 124 optimal weight: 0.0040 chunk 231 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- 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 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS E 67 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS F 206 GLN G 50 HIS H 50 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.123802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.101552 restraints weight = 32365.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.105258 restraints weight = 17449.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.107731 restraints weight = 11600.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.109392 restraints weight = 8791.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.110693 restraints weight = 7224.827| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 21848 Z= 0.217 Angle : 0.646 11.694 29776 Z= 0.316 Chirality : 0.042 0.200 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.694 23.052 2792 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 5.41 % Allowed : 24.96 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.17), residues: 2496 helix: 0.94 (0.13), residues: 1688 sheet: -3.81 (0.40), residues: 80 loop : -3.17 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 362 TYR 0.015 0.002 TYR F 301 PHE 0.018 0.001 PHE H 242 TRP 0.015 0.001 TRP G 59 HIS 0.014 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00505 (21832) covalent geometry : angle 0.64399 (29744) SS BOND : bond 0.00371 ( 16) SS BOND : angle 1.73897 ( 32) hydrogen bonds : bond 0.04250 ( 1240) hydrogen bonds : angle 4.27286 ( 3624) *********************** 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 862 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 740 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.6853 (p0) cc_final: 0.6414 (p0) REVERT: A 68 TRP cc_start: 0.8170 (t-100) cc_final: 0.7938 (t-100) REVERT: A 123 ARG cc_start: 0.8443 (ttm170) cc_final: 0.8033 (ttp-170) REVERT: A 153 ASP cc_start: 0.8769 (m-30) cc_final: 0.8120 (m-30) REVERT: A 154 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8454 (mtpt) REVERT: A 157 LYS cc_start: 0.8196 (tptt) cc_final: 0.7376 (ttpp) REVERT: A 208 TYR cc_start: 0.8335 (t80) cc_final: 0.7647 (t80) REVERT: A 274 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.6070 (mp0) REVERT: A 305 LYS cc_start: 0.8666 (tttm) cc_final: 0.8196 (tmtt) REVERT: A 310 LYS cc_start: 0.7217 (ttpt) cc_final: 0.6451 (tptm) REVERT: B 65 ASN cc_start: 0.7588 (p0) cc_final: 0.7135 (p0) REVERT: B 105 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.7043 (m-10) REVERT: B 146 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8420 (mtm110) REVERT: B 153 ASP cc_start: 0.8794 (m-30) cc_final: 0.8330 (m-30) REVERT: B 158 PHE cc_start: 0.7535 (t80) cc_final: 0.7248 (t80) REVERT: B 208 TYR cc_start: 0.8507 (t80) cc_final: 0.8197 (t80) REVERT: B 236 TRP cc_start: 0.8909 (p90) cc_final: 0.8599 (p-90) REVERT: B 274 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: B 305 LYS cc_start: 0.8688 (tttm) cc_final: 0.8379 (tmtt) REVERT: B 310 LYS cc_start: 0.7304 (ttpt) cc_final: 0.6552 (tptt) REVERT: B 322 LYS cc_start: 0.7845 (pttm) cc_final: 0.7083 (mptt) REVERT: B 359 ILE cc_start: 0.9422 (tp) cc_final: 0.9136 (tp) REVERT: C 64 PHE cc_start: 0.8412 (m-80) cc_final: 0.7988 (m-10) REVERT: C 68 TRP cc_start: 0.8211 (t-100) cc_final: 0.7944 (t-100) REVERT: C 105 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.7141 (m-10) REVERT: C 123 ARG cc_start: 0.8458 (ttm170) cc_final: 0.8088 (ttp-170) REVERT: C 153 ASP cc_start: 0.8801 (m-30) cc_final: 0.8199 (m-30) REVERT: C 154 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8297 (mtpt) REVERT: C 157 LYS cc_start: 0.8301 (tptt) cc_final: 0.7575 (ttpp) REVERT: C 208 TYR cc_start: 0.8364 (t80) cc_final: 0.7599 (t80) REVERT: C 274 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.6272 (mp0) REVERT: C 305 LYS cc_start: 0.8617 (tttm) cc_final: 0.8140 (tmtt) REVERT: C 310 LYS cc_start: 0.7073 (ttpt) cc_final: 0.6322 (tptm) REVERT: C 322 LYS cc_start: 0.7645 (pttm) cc_final: 0.6491 (mptt) REVERT: C 353 PRO cc_start: 0.9445 (Cg_endo) cc_final: 0.9217 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7757 (p0) cc_final: 0.7348 (p0) REVERT: D 105 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.7267 (m-10) REVERT: D 146 ARG cc_start: 0.8967 (ttp80) cc_final: 0.8429 (mtm110) REVERT: D 153 ASP cc_start: 0.8859 (m-30) cc_final: 0.8381 (m-30) REVERT: D 192 TYR cc_start: 0.9077 (t80) cc_final: 0.8805 (t80) REVERT: D 208 TYR cc_start: 0.8485 (t80) cc_final: 0.8147 (t80) REVERT: D 274 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: D 310 LYS cc_start: 0.7225 (ttpt) cc_final: 0.6742 (tptt) REVERT: D 332 SER cc_start: 0.9199 (m) cc_final: 0.8947 (t) REVERT: D 359 ILE cc_start: 0.9449 (tp) cc_final: 0.9153 (tp) REVERT: E 65 ASN cc_start: 0.6763 (p0) cc_final: 0.6316 (p0) REVERT: E 67 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: E 68 TRP cc_start: 0.8187 (t-100) cc_final: 0.7834 (t-100) REVERT: E 153 ASP cc_start: 0.8805 (m-30) cc_final: 0.8177 (m-30) REVERT: E 157 LYS cc_start: 0.8409 (tptt) cc_final: 0.7942 (ttmm) REVERT: E 206 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8273 (mm-40) REVERT: E 208 TYR cc_start: 0.8221 (t80) cc_final: 0.7580 (t80) REVERT: E 274 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: E 305 LYS cc_start: 0.8572 (tttm) cc_final: 0.8074 (tmtt) REVERT: E 310 LYS cc_start: 0.7234 (ttpt) cc_final: 0.6674 (tptt) REVERT: E 322 LYS cc_start: 0.7613 (pttm) cc_final: 0.6445 (mptt) REVERT: E 353 PRO cc_start: 0.9467 (Cg_endo) cc_final: 0.9250 (Cg_exo) REVERT: F 59 TRP cc_start: 0.7986 (t-100) cc_final: 0.7335 (t-100) REVERT: F 65 ASN cc_start: 0.7429 (p0) cc_final: 0.6970 (p0) REVERT: F 153 ASP cc_start: 0.8794 (m-30) cc_final: 0.8361 (m-30) REVERT: F 157 LYS cc_start: 0.8174 (tptt) cc_final: 0.7806 (ttmm) REVERT: F 274 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: F 310 LYS cc_start: 0.7366 (ttpt) cc_final: 0.6899 (tptt) REVERT: G 68 TRP cc_start: 0.8232 (t-100) cc_final: 0.7865 (t-100) REVERT: G 105 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6998 (m-10) REVERT: G 123 ARG cc_start: 0.8456 (ttm170) cc_final: 0.8090 (ttp-170) REVERT: G 153 ASP cc_start: 0.8803 (m-30) cc_final: 0.8506 (m-30) REVERT: G 154 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8240 (mtpt) REVERT: G 157 LYS cc_start: 0.8314 (tptt) cc_final: 0.7565 (ttpp) REVERT: G 158 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7765 (t80) REVERT: G 208 TYR cc_start: 0.8290 (t80) cc_final: 0.7550 (t80) REVERT: G 271 ILE cc_start: 0.8910 (tt) cc_final: 0.8695 (tt) REVERT: G 274 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: G 304 ASN cc_start: 0.8674 (t0) cc_final: 0.8379 (t0) REVERT: G 310 LYS cc_start: 0.7155 (ttpt) cc_final: 0.6528 (tptt) REVERT: G 322 LYS cc_start: 0.7594 (pttm) cc_final: 0.6443 (mptt) REVERT: G 353 PRO cc_start: 0.9430 (Cg_endo) cc_final: 0.9228 (Cg_exo) REVERT: H 65 ASN cc_start: 0.7539 (p0) cc_final: 0.7032 (p0) REVERT: H 105 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7228 (m-10) REVERT: H 137 LEU cc_start: 0.9283 (tt) cc_final: 0.9061 (tt) REVERT: H 146 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8489 (mtp-110) REVERT: H 153 ASP cc_start: 0.8683 (m-30) cc_final: 0.8260 (m-30) REVERT: H 158 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7681 (t80) REVERT: H 206 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8462 (mm-40) REVERT: H 208 TYR cc_start: 0.8567 (t80) cc_final: 0.8243 (t80) REVERT: H 229 ASP cc_start: 0.8599 (m-30) cc_final: 0.8328 (m-30) REVERT: H 274 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: H 305 LYS cc_start: 0.8663 (tttm) cc_final: 0.8331 (tmtt) REVERT: H 310 LYS cc_start: 0.7279 (ttpt) cc_final: 0.6533 (tptt) REVERT: H 313 LYS cc_start: 0.9358 (ttmt) cc_final: 0.9106 (ttmm) REVERT: H 353 PRO cc_start: 0.9608 (Cg_endo) cc_final: 0.9375 (Cg_exo) REVERT: H 359 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.9120 (tp) outliers start: 122 outliers final: 89 residues processed: 804 average time/residue: 0.1468 time to fit residues: 181.2666 Evaluate side-chains 839 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 733 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 274 GLU 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 105 TYR 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 263 VAL 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 105 TYR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 263 VAL 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 50 HIS Chi-restraints excluded: chain D residue 56 ILE 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 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 229 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU 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 67 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 170 SER 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 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 177 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 263 VAL 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 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 105 TYR 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 263 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER 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 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 177 ILE 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 332 SER Chi-restraints excluded: chain H residue 359 ILE 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 33 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 50 HIS B 67 GLN C 50 HIS C 206 GLN D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN E 67 GLN ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN G 50 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.107452 restraints weight = 31814.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.111339 restraints weight = 16871.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114027 restraints weight = 11090.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115743 restraints weight = 8271.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.117121 restraints weight = 6748.369| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21848 Z= 0.133 Angle : 0.596 12.112 29776 Z= 0.291 Chirality : 0.040 0.213 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.517 22.193 2792 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 5.23 % Allowed : 25.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.18), residues: 2496 helix: 1.10 (0.13), residues: 1696 sheet: -3.91 (0.38), residues: 80 loop : -3.13 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 362 TYR 0.018 0.001 TYR B 300 PHE 0.017 0.001 PHE H 124 TRP 0.013 0.001 TRP G 59 HIS 0.016 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00299 (21832) covalent geometry : angle 0.59378 (29744) SS BOND : bond 0.00155 ( 16) SS BOND : angle 1.61973 ( 32) hydrogen bonds : bond 0.03908 ( 1240) hydrogen bonds : angle 4.18202 ( 3624) *********************** 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 873 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 755 time to evaluate : 0.786 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 68 TRP cc_start: 0.8131 (t-100) cc_final: 0.7892 (t-100) REVERT: A 123 ARG cc_start: 0.8429 (ttm170) cc_final: 0.8013 (ttp-170) REVERT: A 153 ASP cc_start: 0.8721 (m-30) cc_final: 0.7516 (m-30) REVERT: A 154 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8449 (mtpt) REVERT: A 157 LYS cc_start: 0.8211 (tptt) cc_final: 0.7359 (ttpp) REVERT: A 208 TYR cc_start: 0.8295 (t80) cc_final: 0.7608 (t80) REVERT: A 305 LYS cc_start: 0.8673 (tttm) cc_final: 0.8218 (tmtt) REVERT: A 310 LYS cc_start: 0.7218 (ttpt) cc_final: 0.6497 (tptm) REVERT: B 65 ASN cc_start: 0.7516 (p0) cc_final: 0.7071 (p0) REVERT: B 105 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.7004 (m-10) REVERT: B 146 ARG cc_start: 0.8886 (ttp80) cc_final: 0.8366 (mtm110) REVERT: B 153 ASP cc_start: 0.8746 (m-30) cc_final: 0.8312 (m-30) REVERT: B 158 PHE cc_start: 0.7645 (t80) cc_final: 0.7247 (t80) REVERT: B 206 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8219 (mm-40) REVERT: B 208 TYR cc_start: 0.8562 (t80) cc_final: 0.8240 (t80) REVERT: B 274 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: B 305 LYS cc_start: 0.8665 (tttm) cc_final: 0.8360 (tmtt) REVERT: B 310 LYS cc_start: 0.7255 (ttpt) cc_final: 0.6544 (tptt) REVERT: B 315 TYR cc_start: 0.8320 (m-10) cc_final: 0.7558 (m-10) REVERT: B 322 LYS cc_start: 0.7874 (pttm) cc_final: 0.7081 (mptt) REVERT: B 359 ILE cc_start: 0.9440 (tp) cc_final: 0.9145 (tp) REVERT: C 68 TRP cc_start: 0.8142 (t-100) cc_final: 0.7865 (t-100) REVERT: C 105 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.7140 (m-10) REVERT: C 123 ARG cc_start: 0.8449 (ttm170) cc_final: 0.8095 (ttp-170) REVERT: C 153 ASP cc_start: 0.8737 (m-30) cc_final: 0.8153 (m-30) REVERT: C 154 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8297 (mtpt) REVERT: C 157 LYS cc_start: 0.8291 (tptt) cc_final: 0.7553 (ttpp) REVERT: C 208 TYR cc_start: 0.8342 (t80) cc_final: 0.7620 (t80) REVERT: C 267 LEU cc_start: 0.9195 (mp) cc_final: 0.8893 (mp) REVERT: C 274 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.6231 (mp0) REVERT: C 305 LYS cc_start: 0.8456 (tttm) cc_final: 0.8145 (tmtt) REVERT: C 310 LYS cc_start: 0.7018 (ttpt) cc_final: 0.6305 (tptm) REVERT: C 322 LYS cc_start: 0.7566 (pttm) cc_final: 0.6524 (mptt) REVERT: C 353 PRO cc_start: 0.9380 (Cg_endo) cc_final: 0.9138 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7564 (p0) cc_final: 0.7218 (p0) REVERT: D 105 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: D 146 ARG cc_start: 0.8954 (ttp80) cc_final: 0.8307 (mtp-110) REVERT: D 153 ASP cc_start: 0.8822 (m-30) cc_final: 0.8385 (m-30) REVERT: D 192 TYR cc_start: 0.9025 (t80) cc_final: 0.8801 (t80) REVERT: D 206 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8645 (mm-40) REVERT: D 208 TYR cc_start: 0.8451 (t80) cc_final: 0.8119 (t80) REVERT: D 274 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.6211 (mp0) REVERT: D 310 LYS cc_start: 0.7294 (ttpt) cc_final: 0.6820 (tptt) REVERT: D 315 TYR cc_start: 0.8375 (m-10) cc_final: 0.7597 (m-10) REVERT: D 322 LYS cc_start: 0.7678 (pttm) cc_final: 0.6950 (mptt) REVERT: D 359 ILE cc_start: 0.9398 (tp) cc_final: 0.9135 (tp) REVERT: E 68 TRP cc_start: 0.8156 (t-100) cc_final: 0.7882 (t-100) REVERT: E 107 TRP cc_start: 0.8370 (m100) cc_final: 0.7669 (m-10) REVERT: E 129 MET cc_start: 0.8131 (tpp) cc_final: 0.7881 (tpp) REVERT: E 153 ASP cc_start: 0.8797 (m-30) cc_final: 0.7672 (m-30) REVERT: E 157 LYS cc_start: 0.8411 (tptt) cc_final: 0.7923 (ttmm) REVERT: E 206 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8338 (mm-40) REVERT: E 208 TYR cc_start: 0.8262 (t80) cc_final: 0.7757 (t80) REVERT: E 274 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.6275 (mp0) REVERT: E 305 LYS cc_start: 0.8530 (tttm) cc_final: 0.8063 (tmtt) REVERT: E 310 LYS cc_start: 0.7164 (ttpt) cc_final: 0.6663 (tptt) REVERT: E 322 LYS cc_start: 0.7441 (pttm) cc_final: 0.6391 (mptt) REVERT: E 353 PRO cc_start: 0.9392 (Cg_endo) cc_final: 0.9159 (Cg_exo) REVERT: F 59 TRP cc_start: 0.7985 (t-100) cc_final: 0.7299 (t-100) REVERT: F 153 ASP cc_start: 0.8790 (m-30) cc_final: 0.8347 (m-30) REVERT: F 157 LYS cc_start: 0.8218 (tptt) cc_final: 0.7848 (ttmm) REVERT: F 158 PHE cc_start: 0.8158 (t80) cc_final: 0.7779 (t80) REVERT: F 274 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.6232 (mp0) REVERT: F 310 LYS cc_start: 0.7326 (ttpt) cc_final: 0.6867 (tptt) REVERT: F 322 LYS cc_start: 0.7808 (pttm) cc_final: 0.7099 (mptt) REVERT: F 332 SER cc_start: 0.9218 (m) cc_final: 0.8918 (t) REVERT: G 68 TRP cc_start: 0.8163 (t-100) cc_final: 0.7894 (t-100) REVERT: G 105 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6935 (m-10) REVERT: G 123 ARG cc_start: 0.8413 (ttm170) cc_final: 0.8061 (ttp-170) REVERT: G 153 ASP cc_start: 0.8737 (m-30) cc_final: 0.8435 (m-30) REVERT: G 154 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8259 (mtpt) REVERT: G 157 LYS cc_start: 0.8302 (tptt) cc_final: 0.7540 (ttpp) REVERT: G 158 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7669 (t80) REVERT: G 208 TYR cc_start: 0.8267 (t80) cc_final: 0.7820 (t80) REVERT: G 236 TRP cc_start: 0.8798 (p-90) cc_final: 0.8546 (p-90) REVERT: G 267 LEU cc_start: 0.9185 (mp) cc_final: 0.8795 (mp) REVERT: G 271 ILE cc_start: 0.8867 (tt) cc_final: 0.8583 (tt) REVERT: G 274 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: G 304 ASN cc_start: 0.8674 (t0) cc_final: 0.8384 (t0) REVERT: G 310 LYS cc_start: 0.7154 (ttpt) cc_final: 0.6453 (tptm) REVERT: G 322 LYS cc_start: 0.7441 (pttm) cc_final: 0.6670 (mptt) REVERT: G 353 PRO cc_start: 0.9377 (Cg_endo) cc_final: 0.9149 (Cg_exo) REVERT: H 65 ASN cc_start: 0.7545 (p0) cc_final: 0.7071 (p0) REVERT: H 105 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.7184 (m-10) REVERT: H 137 LEU cc_start: 0.9239 (tt) cc_final: 0.9025 (tt) REVERT: H 146 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8179 (mtp-110) REVERT: H 153 ASP cc_start: 0.8669 (m-30) cc_final: 0.8296 (m-30) REVERT: H 158 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7658 (t80) REVERT: H 206 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8469 (mm-40) REVERT: H 208 TYR cc_start: 0.8545 (t80) cc_final: 0.8211 (t80) REVERT: H 229 ASP cc_start: 0.8594 (m-30) cc_final: 0.8336 (m-30) REVERT: H 274 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: H 305 LYS cc_start: 0.8620 (tttm) cc_final: 0.8314 (tmtt) REVERT: H 310 LYS cc_start: 0.7290 (ttpt) cc_final: 0.6609 (tptt) REVERT: H 313 LYS cc_start: 0.9332 (ttmt) cc_final: 0.9038 (ttmm) REVERT: H 315 TYR cc_start: 0.8352 (m-10) cc_final: 0.7576 (m-10) REVERT: H 322 LYS cc_start: 0.7872 (pttm) cc_final: 0.7136 (mptt) REVERT: H 359 ILE cc_start: 0.9452 (tp) cc_final: 0.9117 (tp) outliers start: 118 outliers final: 77 residues processed: 822 average time/residue: 0.1413 time to fit residues: 178.0018 Evaluate side-chains 811 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 720 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 105 TYR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 VAL 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 105 TYR 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 205 ILE Chi-restraints excluded: chain B residue 263 VAL 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 50 HIS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 263 VAL 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 50 HIS 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 162 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 201 VAL 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 263 VAL 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 50 HIS Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 226 ILE 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 37 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 GLU 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 105 TYR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER 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 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 162 LEU Chi-restraints excluded: chain H residue 177 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 285 VAL Chi-restraints excluded: chain H residue 332 SER 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 195 optimal weight: 0.0670 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS B 50 HIS C 50 HIS D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN E 79 HIS F 206 GLN G 50 HIS G 79 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.128620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.106332 restraints weight = 31885.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.110214 restraints weight = 16818.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.112897 restraints weight = 11047.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.114595 restraints weight = 8213.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115953 restraints weight = 6689.389| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21848 Z= 0.135 Angle : 0.604 12.382 29776 Z= 0.293 Chirality : 0.040 0.181 3288 Planarity : 0.003 0.042 3632 Dihedral : 4.450 21.968 2792 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.10 % Allowed : 26.51 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.18), residues: 2496 helix: 1.12 (0.13), residues: 1712 sheet: -4.03 (0.37), residues: 80 loop : -3.06 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 362 TYR 0.021 0.001 TYR B 300 PHE 0.016 0.001 PHE A 64 TRP 0.031 0.001 TRP C 236 HIS 0.015 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00306 (21832) covalent geometry : angle 0.60157 (29744) SS BOND : bond 0.00265 ( 16) SS BOND : angle 1.68250 ( 32) hydrogen bonds : bond 0.03818 ( 1240) hydrogen bonds : angle 4.15193 ( 3624) *********************** 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 849 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 734 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8127 (t-100) cc_final: 0.7911 (t-100) REVERT: A 107 TRP cc_start: 0.8182 (m100) cc_final: 0.7418 (m-10) REVERT: A 123 ARG cc_start: 0.8412 (ttm170) cc_final: 0.8006 (ttp-170) REVERT: A 153 ASP cc_start: 0.8685 (m-30) cc_final: 0.7526 (m-30) REVERT: A 157 LYS cc_start: 0.8207 (tptt) cc_final: 0.7360 (ttpp) REVERT: A 208 TYR cc_start: 0.8334 (t80) cc_final: 0.7636 (t80) REVERT: A 236 TRP cc_start: 0.8660 (p-90) cc_final: 0.8459 (p-90) REVERT: A 274 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: A 305 LYS cc_start: 0.8624 (tttm) cc_final: 0.8186 (tmtt) REVERT: A 310 LYS cc_start: 0.7177 (ttpt) cc_final: 0.6487 (tptm) REVERT: A 345 MET cc_start: 0.9383 (tpp) cc_final: 0.8974 (tpp) REVERT: B 65 ASN cc_start: 0.7578 (p0) cc_final: 0.6997 (p0) REVERT: B 146 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8362 (mtm110) REVERT: B 153 ASP cc_start: 0.8730 (m-30) cc_final: 0.8319 (m-30) REVERT: B 158 PHE cc_start: 0.7682 (t80) cc_final: 0.7329 (t80) REVERT: B 206 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8217 (mm-40) REVERT: B 208 TYR cc_start: 0.8547 (t80) cc_final: 0.8232 (t80) REVERT: B 274 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: B 305 LYS cc_start: 0.8668 (tttm) cc_final: 0.8408 (tmtt) REVERT: B 310 LYS cc_start: 0.7261 (ttpt) cc_final: 0.6566 (tptt) REVERT: B 315 TYR cc_start: 0.8317 (m-10) cc_final: 0.7578 (m-10) REVERT: B 322 LYS cc_start: 0.7850 (pttm) cc_final: 0.7080 (mptt) REVERT: B 359 ILE cc_start: 0.9444 (tp) cc_final: 0.9149 (tp) REVERT: C 68 TRP cc_start: 0.8146 (t-100) cc_final: 0.7852 (t-100) REVERT: C 105 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.7136 (m-10) REVERT: C 123 ARG cc_start: 0.8448 (ttm170) cc_final: 0.8097 (ttp-170) REVERT: C 153 ASP cc_start: 0.8735 (m-30) cc_final: 0.8187 (m-30) REVERT: C 154 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8310 (mtpt) REVERT: C 157 LYS cc_start: 0.8290 (tptt) cc_final: 0.7538 (ttpp) REVERT: C 206 GLN cc_start: 0.9264 (mm-40) cc_final: 0.8496 (mm-40) REVERT: C 208 TYR cc_start: 0.8338 (t80) cc_final: 0.7852 (t80) REVERT: C 236 TRP cc_start: 0.8651 (p-90) cc_final: 0.8225 (p-90) REVERT: C 267 LEU cc_start: 0.9157 (mp) cc_final: 0.8840 (mp) REVERT: C 274 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: C 305 LYS cc_start: 0.8480 (tttm) cc_final: 0.8153 (tmtt) REVERT: C 310 LYS cc_start: 0.7010 (ttpt) cc_final: 0.6336 (tptm) REVERT: C 322 LYS cc_start: 0.7474 (pttm) cc_final: 0.6606 (tmtt) REVERT: C 353 PRO cc_start: 0.9367 (Cg_endo) cc_final: 0.9149 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7623 (p0) cc_final: 0.7147 (p0) REVERT: D 146 ARG cc_start: 0.8942 (ttp80) cc_final: 0.8259 (mtp-110) REVERT: D 153 ASP cc_start: 0.8756 (m-30) cc_final: 0.8298 (m-30) REVERT: D 183 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8834 (ttpt) REVERT: D 192 TYR cc_start: 0.9020 (t80) cc_final: 0.8808 (t80) REVERT: D 206 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8589 (mm-40) REVERT: D 208 TYR cc_start: 0.8458 (t80) cc_final: 0.8092 (t80) REVERT: D 274 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.6152 (mp0) REVERT: D 310 LYS cc_start: 0.7305 (ttpt) cc_final: 0.6832 (tptt) REVERT: D 315 TYR cc_start: 0.8358 (m-10) cc_final: 0.7580 (m-10) REVERT: D 322 LYS cc_start: 0.7664 (pttm) cc_final: 0.6936 (mptt) REVERT: D 332 SER cc_start: 0.9240 (m) cc_final: 0.8975 (t) REVERT: D 359 ILE cc_start: 0.9423 (tp) cc_final: 0.9134 (tp) REVERT: E 68 TRP cc_start: 0.8135 (t-100) cc_final: 0.7767 (t-100) REVERT: E 107 TRP cc_start: 0.8228 (m100) cc_final: 0.7507 (m-10) REVERT: E 129 MET cc_start: 0.8130 (tpp) cc_final: 0.7891 (tpp) REVERT: E 153 ASP cc_start: 0.8786 (m-30) cc_final: 0.7648 (m-30) REVERT: E 157 LYS cc_start: 0.8434 (tptt) cc_final: 0.7947 (ttmm) REVERT: E 206 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8284 (mm-40) REVERT: E 208 TYR cc_start: 0.8267 (t80) cc_final: 0.7772 (t80) REVERT: E 274 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.6404 (mp0) REVERT: E 305 LYS cc_start: 0.8522 (tttm) cc_final: 0.8078 (tmtt) REVERT: E 310 LYS cc_start: 0.7169 (ttpt) cc_final: 0.6560 (tptt) REVERT: E 322 LYS cc_start: 0.7409 (pttm) cc_final: 0.6381 (mptt) REVERT: E 353 PRO cc_start: 0.9352 (Cg_endo) cc_final: 0.9132 (Cg_exo) REVERT: F 59 TRP cc_start: 0.7980 (t-100) cc_final: 0.7218 (t-100) REVERT: F 153 ASP cc_start: 0.8715 (m-30) cc_final: 0.8267 (m-30) REVERT: F 157 LYS cc_start: 0.8235 (tptt) cc_final: 0.7893 (ttmm) REVERT: F 158 PHE cc_start: 0.8166 (t80) cc_final: 0.7785 (t80) REVERT: F 274 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.6214 (mp0) REVERT: F 310 LYS cc_start: 0.7335 (ttpt) cc_final: 0.6871 (tptt) REVERT: F 315 TYR cc_start: 0.8403 (m-10) cc_final: 0.7598 (m-10) REVERT: F 322 LYS cc_start: 0.7779 (pttm) cc_final: 0.7083 (mptt) REVERT: F 332 SER cc_start: 0.9220 (m) cc_final: 0.8929 (t) REVERT: G 68 TRP cc_start: 0.8166 (t-100) cc_final: 0.7863 (t-100) REVERT: G 105 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6953 (m-10) REVERT: G 123 ARG cc_start: 0.8456 (ttm170) cc_final: 0.8060 (ttp-170) REVERT: G 153 ASP cc_start: 0.8728 (m-30) cc_final: 0.8451 (m-30) REVERT: G 154 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8262 (mtpt) REVERT: G 157 LYS cc_start: 0.8312 (tptt) cc_final: 0.7538 (ttpp) REVERT: G 158 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7685 (t80) REVERT: G 208 TYR cc_start: 0.8269 (t80) cc_final: 0.7806 (t80) REVERT: G 236 TRP cc_start: 0.8791 (p-90) cc_final: 0.8542 (p-90) REVERT: G 267 LEU cc_start: 0.9214 (mp) cc_final: 0.8816 (mp) REVERT: G 271 ILE cc_start: 0.8883 (tt) cc_final: 0.8586 (tt) REVERT: G 274 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.6369 (mp0) REVERT: G 304 ASN cc_start: 0.8691 (t0) cc_final: 0.8387 (t0) REVERT: G 310 LYS cc_start: 0.7139 (ttpt) cc_final: 0.6470 (tptm) REVERT: G 322 LYS cc_start: 0.7359 (pttm) cc_final: 0.6576 (mptt) REVERT: G 353 PRO cc_start: 0.9340 (Cg_endo) cc_final: 0.9140 (Cg_exo) REVERT: H 65 ASN cc_start: 0.7533 (p0) cc_final: 0.7042 (p0) REVERT: H 105 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7179 (m-10) REVERT: H 137 LEU cc_start: 0.9233 (tt) cc_final: 0.9023 (tt) REVERT: H 146 ARG cc_start: 0.8942 (ttp80) cc_final: 0.8304 (mtp-110) REVERT: H 153 ASP cc_start: 0.8664 (m-30) cc_final: 0.8289 (m-30) REVERT: H 158 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7679 (t80) REVERT: H 206 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8611 (mm-40) REVERT: H 208 TYR cc_start: 0.8539 (t80) cc_final: 0.8211 (t80) REVERT: H 229 ASP cc_start: 0.8605 (m-30) cc_final: 0.8368 (m-30) REVERT: H 274 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: H 305 LYS cc_start: 0.8513 (tttm) cc_final: 0.8249 (tmtt) REVERT: H 310 LYS cc_start: 0.7294 (ttpt) cc_final: 0.6642 (tptt) REVERT: H 315 TYR cc_start: 0.8350 (m-10) cc_final: 0.7584 (m-10) REVERT: H 316 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8444 (mm) REVERT: H 322 LYS cc_start: 0.7846 (pttm) cc_final: 0.7123 (mptt) REVERT: H 359 ILE cc_start: 0.9462 (tp) cc_final: 0.9122 (tp) outliers start: 115 outliers final: 85 residues processed: 797 average time/residue: 0.1423 time to fit residues: 174.0470 Evaluate side-chains 813 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 714 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 105 TYR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 284 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 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 263 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU 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 105 TYR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 263 VAL 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 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 51 PHE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 201 VAL 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 263 VAL 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 39 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 332 SER 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 125 ILE 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 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 105 TYR 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 263 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER 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 105 TYR 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 177 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 316 LEU Chi-restraints excluded: chain H residue 332 SER 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 207 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 154 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 232 optimal weight: 0.7980 chunk 187 optimal weight: 0.0070 chunk 140 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN C 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111807 restraints weight = 31605.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115731 restraints weight = 16676.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.118385 restraints weight = 10919.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.120298 restraints weight = 8139.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121661 restraints weight = 6513.305| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21848 Z= 0.118 Angle : 0.595 12.916 29776 Z= 0.288 Chirality : 0.039 0.175 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.308 21.005 2792 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.08 % Allowed : 27.88 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.18), residues: 2496 helix: 1.19 (0.13), residues: 1728 sheet: -3.99 (0.37), residues: 80 loop : -2.92 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 362 TYR 0.019 0.001 TYR B 300 PHE 0.019 0.001 PHE E 64 TRP 0.021 0.001 TRP C 236 HIS 0.019 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00250 (21832) covalent geometry : angle 0.59274 (29744) SS BOND : bond 0.00242 ( 16) SS BOND : angle 1.56213 ( 32) hydrogen bonds : bond 0.03540 ( 1240) hydrogen bonds : angle 4.09505 ( 3624) *********************** 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 855 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 763 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8090 (t-100) cc_final: 0.7843 (t-100) REVERT: A 123 ARG cc_start: 0.8387 (ttm170) cc_final: 0.7990 (ttp-170) REVERT: A 153 ASP cc_start: 0.8631 (m-30) cc_final: 0.8327 (m-30) REVERT: A 157 LYS cc_start: 0.8152 (tptt) cc_final: 0.7303 (ttpp) REVERT: A 158 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7262 (t80) REVERT: A 208 TYR cc_start: 0.8326 (t80) cc_final: 0.7839 (t80) REVERT: A 274 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: A 305 LYS cc_start: 0.8507 (tttm) cc_final: 0.8176 (tmtt) REVERT: A 310 LYS cc_start: 0.7160 (ttpt) cc_final: 0.6498 (tptm) REVERT: A 345 MET cc_start: 0.9346 (tpp) cc_final: 0.8927 (tpp) REVERT: B 65 ASN cc_start: 0.7365 (p0) cc_final: 0.6791 (p0) REVERT: B 146 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8236 (mtp-110) REVERT: B 153 ASP cc_start: 0.8714 (m-30) cc_final: 0.8319 (m-30) REVERT: B 158 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7433 (t80) REVERT: B 206 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8176 (mm-40) REVERT: B 208 TYR cc_start: 0.8522 (t80) cc_final: 0.8193 (t80) REVERT: B 274 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: B 305 LYS cc_start: 0.8553 (tttm) cc_final: 0.8330 (tmtt) REVERT: B 310 LYS cc_start: 0.7340 (ttpt) cc_final: 0.6662 (tptt) REVERT: B 315 TYR cc_start: 0.8275 (m-10) cc_final: 0.7567 (m-10) REVERT: B 322 LYS cc_start: 0.7801 (pttm) cc_final: 0.7046 (mptt) REVERT: B 359 ILE cc_start: 0.9399 (tp) cc_final: 0.9076 (tp) REVERT: C 68 TRP cc_start: 0.8120 (t-100) cc_final: 0.7832 (t-100) REVERT: C 105 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.7071 (m-10) REVERT: C 123 ARG cc_start: 0.8449 (ttm170) cc_final: 0.8063 (ttp-170) REVERT: C 153 ASP cc_start: 0.8697 (m-30) cc_final: 0.7527 (m-30) REVERT: C 154 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8268 (mtpt) REVERT: C 157 LYS cc_start: 0.8294 (tptt) cc_final: 0.7543 (ttpp) REVERT: C 206 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8444 (mm-40) REVERT: C 208 TYR cc_start: 0.8321 (t80) cc_final: 0.7800 (t80) REVERT: C 236 TRP cc_start: 0.8699 (p-90) cc_final: 0.8208 (p-90) REVERT: C 267 LEU cc_start: 0.9128 (mp) cc_final: 0.8867 (mp) REVERT: C 274 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: C 304 ASN cc_start: 0.8630 (t0) cc_final: 0.8359 (t0) REVERT: C 310 LYS cc_start: 0.7109 (ttpt) cc_final: 0.6434 (tptm) REVERT: C 322 LYS cc_start: 0.7292 (pttm) cc_final: 0.6505 (tmtt) REVERT: C 353 PRO cc_start: 0.9278 (Cg_endo) cc_final: 0.9075 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7603 (p0) cc_final: 0.7109 (p0) REVERT: D 153 ASP cc_start: 0.8739 (m-30) cc_final: 0.8342 (m-30) REVERT: D 183 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8828 (ttpt) REVERT: D 206 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8566 (mm-40) REVERT: D 208 TYR cc_start: 0.8429 (t80) cc_final: 0.8033 (t80) REVERT: D 274 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.6222 (mp0) REVERT: D 310 LYS cc_start: 0.7327 (ttpt) cc_final: 0.6838 (tptt) REVERT: D 315 TYR cc_start: 0.8321 (m-10) cc_final: 0.7593 (m-10) REVERT: D 322 LYS cc_start: 0.7558 (pttm) cc_final: 0.6856 (mptt) REVERT: D 332 SER cc_start: 0.9228 (m) cc_final: 0.8852 (p) REVERT: D 359 ILE cc_start: 0.9410 (tp) cc_final: 0.9124 (tp) REVERT: E 68 TRP cc_start: 0.8133 (t-100) cc_final: 0.7814 (t-100) REVERT: E 153 ASP cc_start: 0.8709 (m-30) cc_final: 0.8446 (m-30) REVERT: E 157 LYS cc_start: 0.8281 (tptt) cc_final: 0.7834 (ttmm) REVERT: E 175 ASP cc_start: 0.8149 (m-30) cc_final: 0.7610 (m-30) REVERT: E 206 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8373 (mm-40) REVERT: E 208 TYR cc_start: 0.8278 (t80) cc_final: 0.7786 (t80) REVERT: E 274 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.6366 (mp0) REVERT: E 305 LYS cc_start: 0.8466 (tttm) cc_final: 0.8176 (tmtt) REVERT: E 310 LYS cc_start: 0.7166 (ttpt) cc_final: 0.6576 (tptt) REVERT: E 322 LYS cc_start: 0.7295 (pttm) cc_final: 0.6541 (tttm) REVERT: E 353 PRO cc_start: 0.9302 (Cg_endo) cc_final: 0.9080 (Cg_exo) REVERT: F 59 TRP cc_start: 0.7869 (t-100) cc_final: 0.7191 (t-100) REVERT: F 67 GLN cc_start: 0.7623 (mp10) cc_final: 0.7389 (mp10) REVERT: F 153 ASP cc_start: 0.8698 (m-30) cc_final: 0.8312 (m-30) REVERT: F 157 LYS cc_start: 0.8161 (tptt) cc_final: 0.7678 (ttmm) REVERT: F 158 PHE cc_start: 0.8050 (t80) cc_final: 0.7762 (t80) REVERT: F 274 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.6154 (mp0) REVERT: F 310 LYS cc_start: 0.7394 (ttpt) cc_final: 0.6918 (tptt) REVERT: F 315 TYR cc_start: 0.8355 (m-10) cc_final: 0.7599 (m-10) REVERT: F 322 LYS cc_start: 0.7521 (pttm) cc_final: 0.6843 (mptt) REVERT: F 332 SER cc_start: 0.9209 (m) cc_final: 0.8923 (t) REVERT: F 359 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9206 (tp) REVERT: G 68 TRP cc_start: 0.8142 (t-100) cc_final: 0.7819 (t-100) REVERT: G 105 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6919 (m-10) REVERT: G 123 ARG cc_start: 0.8426 (ttm170) cc_final: 0.8107 (ttp-170) REVERT: G 153 ASP cc_start: 0.8696 (m-30) cc_final: 0.8412 (m-30) REVERT: G 154 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8296 (mtpt) REVERT: G 157 LYS cc_start: 0.8300 (tptt) cc_final: 0.7533 (ttpp) REVERT: G 158 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7495 (t80) REVERT: G 208 TYR cc_start: 0.8244 (t80) cc_final: 0.7776 (t80) REVERT: G 267 LEU cc_start: 0.9179 (mp) cc_final: 0.8829 (mp) REVERT: G 271 ILE cc_start: 0.8832 (tt) cc_final: 0.8552 (tt) REVERT: G 274 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: G 304 ASN cc_start: 0.8657 (t0) cc_final: 0.8325 (t0) REVERT: G 310 LYS cc_start: 0.7080 (ttpt) cc_final: 0.6430 (tptm) REVERT: G 322 LYS cc_start: 0.7266 (pttm) cc_final: 0.6421 (tttm) REVERT: G 353 PRO cc_start: 0.9270 (Cg_endo) cc_final: 0.9047 (Cg_exo) REVERT: H 105 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.7176 (m-10) REVERT: H 137 LEU cc_start: 0.9187 (tt) cc_final: 0.8975 (tt) REVERT: H 153 ASP cc_start: 0.8649 (m-30) cc_final: 0.8310 (m-30) REVERT: H 158 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7565 (t80) REVERT: H 206 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8577 (mm-40) REVERT: H 208 TYR cc_start: 0.8507 (t80) cc_final: 0.8176 (t80) REVERT: H 227 LEU cc_start: 0.8219 (mm) cc_final: 0.7944 (mm) REVERT: H 274 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.6122 (mp0) REVERT: H 305 LYS cc_start: 0.8502 (tttm) cc_final: 0.8283 (tmtt) REVERT: H 310 LYS cc_start: 0.7343 (ttpt) cc_final: 0.6712 (tptt) REVERT: H 315 TYR cc_start: 0.8332 (m-10) cc_final: 0.7602 (m-10) REVERT: H 316 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8393 (mm) REVERT: H 322 LYS cc_start: 0.7757 (pttm) cc_final: 0.7097 (mptt) REVERT: H 359 ILE cc_start: 0.9438 (tp) cc_final: 0.9108 (tp) outliers start: 92 outliers final: 60 residues processed: 814 average time/residue: 0.1442 time to fit residues: 182.0210 Evaluate side-chains 818 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 741 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 274 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 125 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 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 332 SER Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 ILE 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 299 ILE Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 177 ILE 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 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 226 ILE 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 50 HIS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 177 ILE 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 359 ILE Chi-restraints excluded: chain G residue 105 TYR 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 263 VAL 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 H residue 50 HIS 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 162 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 332 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 70 optimal weight: 0.0770 chunk 32 optimal weight: 20.0000 chunk 185 optimal weight: 0.2980 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS C 50 HIS D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 79 HIS G 50 HIS H 79 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.132083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.109879 restraints weight = 31439.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113811 restraints weight = 16622.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116522 restraints weight = 10869.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118392 restraints weight = 8090.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.119582 restraints weight = 6526.200| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21848 Z= 0.116 Angle : 0.613 12.818 29776 Z= 0.294 Chirality : 0.039 0.175 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.199 20.743 2792 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.81 % Allowed : 29.12 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.18), residues: 2496 helix: 1.25 (0.13), residues: 1728 sheet: -3.96 (0.38), residues: 80 loop : -2.90 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 362 TYR 0.018 0.001 TYR B 300 PHE 0.021 0.001 PHE E 330 TRP 0.046 0.001 TRP A 236 HIS 0.021 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00252 (21832) covalent geometry : angle 0.61149 (29744) SS BOND : bond 0.00265 ( 16) SS BOND : angle 1.57686 ( 32) hydrogen bonds : bond 0.03327 ( 1240) hydrogen bonds : angle 4.03640 ( 3624) *********************** 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 837 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 751 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8051 (t-100) cc_final: 0.7784 (t-100) REVERT: A 123 ARG cc_start: 0.8369 (ttm170) cc_final: 0.8046 (ttp-170) REVERT: A 153 ASP cc_start: 0.8551 (m-30) cc_final: 0.8257 (m-30) REVERT: A 157 LYS cc_start: 0.8154 (tptt) cc_final: 0.7274 (ttpp) REVERT: A 158 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7232 (t80) REVERT: A 208 TYR cc_start: 0.8313 (t80) cc_final: 0.7819 (t80) REVERT: A 236 TRP cc_start: 0.8449 (p-90) cc_final: 0.7924 (p-90) REVERT: A 274 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.6272 (mp0) REVERT: A 304 ASN cc_start: 0.8663 (t0) cc_final: 0.8321 (t0) REVERT: A 310 LYS cc_start: 0.7158 (ttpt) cc_final: 0.6458 (tptm) REVERT: A 322 LYS cc_start: 0.7345 (pttm) cc_final: 0.6431 (tttm) REVERT: B 153 ASP cc_start: 0.8728 (m-30) cc_final: 0.8363 (m-30) REVERT: B 158 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7513 (t80) REVERT: B 206 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8276 (mm-40) REVERT: B 208 TYR cc_start: 0.8502 (t80) cc_final: 0.8146 (t80) REVERT: B 274 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.6068 (mp0) REVERT: B 305 LYS cc_start: 0.8524 (tttm) cc_final: 0.8320 (tmtt) REVERT: B 310 LYS cc_start: 0.7350 (ttpt) cc_final: 0.6659 (tptm) REVERT: B 315 TYR cc_start: 0.8244 (m-10) cc_final: 0.7559 (m-10) REVERT: B 322 LYS cc_start: 0.7733 (pttm) cc_final: 0.7046 (mptt) REVERT: B 359 ILE cc_start: 0.9377 (tp) cc_final: 0.9011 (tp) REVERT: C 68 TRP cc_start: 0.8166 (t-100) cc_final: 0.7861 (t-100) REVERT: C 123 ARG cc_start: 0.8405 (ttm170) cc_final: 0.8089 (ttp-170) REVERT: C 153 ASP cc_start: 0.8661 (m-30) cc_final: 0.8421 (m-30) REVERT: C 157 LYS cc_start: 0.8226 (tptt) cc_final: 0.7337 (ttmm) REVERT: C 206 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8450 (mm-40) REVERT: C 208 TYR cc_start: 0.8283 (t80) cc_final: 0.7761 (t80) REVERT: C 236 TRP cc_start: 0.8630 (p-90) cc_final: 0.8177 (p-90) REVERT: C 267 LEU cc_start: 0.9144 (mp) cc_final: 0.8880 (mp) REVERT: C 274 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: C 304 ASN cc_start: 0.8638 (t0) cc_final: 0.8294 (t0) REVERT: C 310 LYS cc_start: 0.7047 (ttpt) cc_final: 0.6405 (tptm) REVERT: C 322 LYS cc_start: 0.7282 (pttm) cc_final: 0.6491 (tmtt) REVERT: C 353 PRO cc_start: 0.9287 (Cg_endo) cc_final: 0.9070 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7550 (p0) cc_final: 0.7027 (p0) REVERT: D 153 ASP cc_start: 0.8734 (m-30) cc_final: 0.8362 (m-30) REVERT: D 206 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8559 (mm-40) REVERT: D 208 TYR cc_start: 0.8425 (t80) cc_final: 0.8043 (t80) REVERT: D 274 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.6076 (mp0) REVERT: D 310 LYS cc_start: 0.7344 (ttpt) cc_final: 0.6877 (tptt) REVERT: D 315 TYR cc_start: 0.8305 (m-10) cc_final: 0.7616 (m-10) REVERT: D 322 LYS cc_start: 0.7539 (pttm) cc_final: 0.6840 (mptt) REVERT: D 332 SER cc_start: 0.9220 (m) cc_final: 0.8975 (t) REVERT: D 359 ILE cc_start: 0.9383 (tp) cc_final: 0.9075 (tp) REVERT: E 59 TRP cc_start: 0.7962 (t-100) cc_final: 0.7505 (t-100) REVERT: E 68 TRP cc_start: 0.8101 (t-100) cc_final: 0.7795 (t-100) REVERT: E 153 ASP cc_start: 0.8711 (m-30) cc_final: 0.8444 (m-30) REVERT: E 157 LYS cc_start: 0.8293 (tptt) cc_final: 0.7846 (ttmm) REVERT: E 175 ASP cc_start: 0.8168 (m-30) cc_final: 0.7614 (m-30) REVERT: E 206 GLN cc_start: 0.9260 (mm-40) cc_final: 0.8384 (mm-40) REVERT: E 208 TYR cc_start: 0.8278 (t80) cc_final: 0.7820 (t80) REVERT: E 274 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: E 305 LYS cc_start: 0.8446 (tttm) cc_final: 0.8160 (tmtt) REVERT: E 310 LYS cc_start: 0.7135 (ttpt) cc_final: 0.6534 (tptt) REVERT: E 322 LYS cc_start: 0.7259 (pttm) cc_final: 0.6473 (tttm) REVERT: E 331 PHE cc_start: 0.9023 (m-10) cc_final: 0.8812 (m-10) REVERT: E 353 PRO cc_start: 0.9252 (Cg_endo) cc_final: 0.9032 (Cg_exo) REVERT: F 59 TRP cc_start: 0.7868 (t-100) cc_final: 0.7188 (t-100) REVERT: F 67 GLN cc_start: 0.7386 (mp10) cc_final: 0.7130 (mp10) REVERT: F 153 ASP cc_start: 0.8706 (m-30) cc_final: 0.8334 (m-30) REVERT: F 157 LYS cc_start: 0.8164 (tptt) cc_final: 0.7662 (ttmm) REVERT: F 158 PHE cc_start: 0.7908 (t80) cc_final: 0.7645 (t80) REVERT: F 274 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: F 310 LYS cc_start: 0.7453 (ttpt) cc_final: 0.6955 (tptt) REVERT: F 315 TYR cc_start: 0.8330 (m-10) cc_final: 0.7625 (m-10) REVERT: F 322 LYS cc_start: 0.7443 (pttm) cc_final: 0.6749 (mptt) REVERT: F 332 SER cc_start: 0.9201 (m) cc_final: 0.8928 (t) REVERT: F 359 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9205 (tp) REVERT: G 68 TRP cc_start: 0.8205 (t-100) cc_final: 0.7859 (t-100) REVERT: G 105 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.7028 (m-10) REVERT: G 123 ARG cc_start: 0.8411 (ttm170) cc_final: 0.8092 (ttp-170) REVERT: G 153 ASP cc_start: 0.8696 (m-30) cc_final: 0.8409 (m-30) REVERT: G 154 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8276 (mtpt) REVERT: G 157 LYS cc_start: 0.8285 (tptt) cc_final: 0.7484 (ttpp) REVERT: G 158 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7506 (t80) REVERT: G 208 TYR cc_start: 0.8230 (t80) cc_final: 0.7773 (t80) REVERT: G 236 TRP cc_start: 0.8472 (p-90) cc_final: 0.7988 (p-90) REVERT: G 267 LEU cc_start: 0.9138 (mp) cc_final: 0.8792 (mp) REVERT: G 274 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: G 310 LYS cc_start: 0.7191 (ttpt) cc_final: 0.6514 (tptm) REVERT: G 322 LYS cc_start: 0.7213 (pttm) cc_final: 0.6430 (tttm) REVERT: G 353 PRO cc_start: 0.9224 (Cg_endo) cc_final: 0.9013 (Cg_exo) REVERT: H 105 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.7290 (m-10) REVERT: H 137 LEU cc_start: 0.9144 (tt) cc_final: 0.8932 (tt) REVERT: H 153 ASP cc_start: 0.8622 (m-30) cc_final: 0.8332 (m-30) REVERT: H 158 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7680 (t80) REVERT: H 199 GLN cc_start: 0.8260 (tp40) cc_final: 0.7889 (tt0) REVERT: H 208 TYR cc_start: 0.8508 (t80) cc_final: 0.8177 (t80) REVERT: H 227 LEU cc_start: 0.8148 (mm) cc_final: 0.7941 (mm) REVERT: H 274 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.6002 (mp0) REVERT: H 305 LYS cc_start: 0.8532 (tttm) cc_final: 0.8284 (tmtt) REVERT: H 310 LYS cc_start: 0.7365 (ttpt) cc_final: 0.6746 (tptt) REVERT: H 315 TYR cc_start: 0.8316 (m-10) cc_final: 0.7636 (m-10) REVERT: H 316 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8369 (mm) REVERT: H 322 LYS cc_start: 0.7719 (pttm) cc_final: 0.6907 (tttm) REVERT: H 359 ILE cc_start: 0.9432 (tp) cc_final: 0.9098 (tp) outliers start: 86 outliers final: 59 residues processed: 797 average time/residue: 0.1572 time to fit residues: 192.9580 Evaluate side-chains 804 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 729 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 274 GLU Chi-restraints excluded: chain A residue 285 VAL 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 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 332 SER Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 263 VAL 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 D residue 50 HIS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 177 ILE 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 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 170 SER 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 360 SER Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 162 LEU 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 359 ILE Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 105 TYR 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 263 VAL Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 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 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 212 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 50 HIS C 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN G 50 HIS H 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.131568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.109186 restraints weight = 31606.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113075 restraints weight = 16872.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115781 restraints weight = 11125.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117608 restraints weight = 8299.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118915 restraints weight = 6722.801| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21848 Z= 0.129 Angle : 0.622 12.383 29776 Z= 0.301 Chirality : 0.039 0.194 3288 Planarity : 0.004 0.035 3632 Dihedral : 4.219 21.894 2792 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.46 % Allowed : 29.70 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.17), residues: 2496 helix: 1.28 (0.13), residues: 1720 sheet: None (None), residues: 0 loop : -2.82 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 362 TYR 0.024 0.001 TYR F 300 PHE 0.019 0.001 PHE G 330 TRP 0.040 0.001 TRP A 236 HIS 0.016 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00293 (21832) covalent geometry : angle 0.62029 (29744) SS BOND : bond 0.00237 ( 16) SS BOND : angle 1.68684 ( 32) hydrogen bonds : bond 0.03363 ( 1240) hydrogen bonds : angle 4.02308 ( 3624) ********************** 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 810 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 732 time to evaluate : 0.843 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 68 TRP cc_start: 0.8088 (t-100) cc_final: 0.7794 (t-100) REVERT: A 123 ARG cc_start: 0.8376 (ttm170) cc_final: 0.8055 (ttp-170) REVERT: A 153 ASP cc_start: 0.8527 (m-30) cc_final: 0.8243 (m-30) REVERT: A 157 LYS cc_start: 0.8122 (tptt) cc_final: 0.7261 (ttpp) REVERT: A 208 TYR cc_start: 0.8282 (t80) cc_final: 0.7786 (t80) REVERT: A 236 TRP cc_start: 0.8396 (p-90) cc_final: 0.7825 (p-90) REVERT: A 274 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.6319 (mp0) REVERT: A 310 LYS cc_start: 0.7173 (ttpt) cc_final: 0.6480 (tptm) REVERT: A 322 LYS cc_start: 0.7354 (pttm) cc_final: 0.6445 (tttm) REVERT: A 345 MET cc_start: 0.9326 (tpp) cc_final: 0.8969 (tpp) REVERT: B 146 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8384 (mtp-110) REVERT: B 153 ASP cc_start: 0.8708 (m-30) cc_final: 0.8359 (m-30) REVERT: B 158 PHE cc_start: 0.7591 (t80) cc_final: 0.7291 (t80) REVERT: B 206 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8179 (mm-40) REVERT: B 208 TYR cc_start: 0.8508 (t80) cc_final: 0.8158 (t80) REVERT: B 274 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: B 310 LYS cc_start: 0.7360 (ttpt) cc_final: 0.6683 (tptm) REVERT: B 315 TYR cc_start: 0.8249 (m-10) cc_final: 0.7558 (m-10) REVERT: B 322 LYS cc_start: 0.7732 (pttm) cc_final: 0.7061 (mptt) REVERT: B 359 ILE cc_start: 0.9421 (tp) cc_final: 0.9088 (tp) REVERT: C 68 TRP cc_start: 0.8174 (t-100) cc_final: 0.7876 (t-100) REVERT: C 107 TRP cc_start: 0.8332 (m100) cc_final: 0.7516 (m-10) REVERT: C 123 ARG cc_start: 0.8444 (ttm170) cc_final: 0.8122 (ttp-170) REVERT: C 153 ASP cc_start: 0.8650 (m-30) cc_final: 0.7755 (m-30) REVERT: C 154 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8301 (mtpt) REVERT: C 157 LYS cc_start: 0.8210 (tptt) cc_final: 0.7458 (ttpp) REVERT: C 206 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8426 (mm-40) REVERT: C 208 TYR cc_start: 0.8283 (t80) cc_final: 0.7757 (t80) REVERT: C 236 TRP cc_start: 0.8643 (p-90) cc_final: 0.8173 (p-90) REVERT: C 274 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.6181 (mp0) REVERT: C 304 ASN cc_start: 0.8649 (t0) cc_final: 0.8301 (t0) REVERT: C 310 LYS cc_start: 0.7075 (ttpt) cc_final: 0.6436 (tptm) REVERT: C 322 LYS cc_start: 0.7249 (pttm) cc_final: 0.6506 (tmtt) REVERT: C 353 PRO cc_start: 0.9304 (Cg_endo) cc_final: 0.9097 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7523 (p0) cc_final: 0.7028 (p0) REVERT: D 153 ASP cc_start: 0.8717 (m-30) cc_final: 0.8365 (m-30) REVERT: D 158 PHE cc_start: 0.8144 (t80) cc_final: 0.7773 (t80) REVERT: D 206 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8556 (mm-40) REVERT: D 208 TYR cc_start: 0.8436 (t80) cc_final: 0.8052 (t80) REVERT: D 274 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.6095 (mp0) REVERT: D 305 LYS cc_start: 0.8607 (tttm) cc_final: 0.8360 (tmtt) REVERT: D 310 LYS cc_start: 0.7354 (ttpt) cc_final: 0.6893 (tptt) REVERT: D 315 TYR cc_start: 0.8304 (m-10) cc_final: 0.7610 (m-10) REVERT: D 322 LYS cc_start: 0.7538 (pttm) cc_final: 0.6864 (mptt) REVERT: D 332 SER cc_start: 0.9214 (m) cc_final: 0.8856 (p) REVERT: D 359 ILE cc_start: 0.9403 (tp) cc_final: 0.9081 (tp) REVERT: E 68 TRP cc_start: 0.8130 (t-100) cc_final: 0.7851 (t-100) REVERT: E 153 ASP cc_start: 0.8659 (m-30) cc_final: 0.8412 (m-30) REVERT: E 157 LYS cc_start: 0.8275 (tptt) cc_final: 0.7811 (ttmm) REVERT: E 175 ASP cc_start: 0.8177 (m-30) cc_final: 0.7629 (m-30) REVERT: E 206 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8373 (mm-40) REVERT: E 208 TYR cc_start: 0.8351 (t80) cc_final: 0.7822 (t80) REVERT: E 274 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.6231 (mp0) REVERT: E 305 LYS cc_start: 0.8442 (tttm) cc_final: 0.8166 (tmtt) REVERT: E 310 LYS cc_start: 0.7235 (ttpt) cc_final: 0.6613 (tptt) REVERT: E 322 LYS cc_start: 0.7257 (pttm) cc_final: 0.6486 (tttm) REVERT: E 331 PHE cc_start: 0.9018 (m-10) cc_final: 0.8780 (m-10) REVERT: F 59 TRP cc_start: 0.7897 (t-100) cc_final: 0.7265 (t-100) REVERT: F 153 ASP cc_start: 0.8684 (m-30) cc_final: 0.8331 (m-30) REVERT: F 157 LYS cc_start: 0.8168 (tptt) cc_final: 0.7668 (ttmm) REVERT: F 158 PHE cc_start: 0.7967 (t80) cc_final: 0.7716 (t80) REVERT: F 274 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.6007 (mp0) REVERT: F 310 LYS cc_start: 0.7471 (ttpt) cc_final: 0.6974 (tptt) REVERT: F 315 TYR cc_start: 0.8355 (m-10) cc_final: 0.7623 (m-10) REVERT: F 322 LYS cc_start: 0.7438 (pttm) cc_final: 0.6747 (mptt) REVERT: F 332 SER cc_start: 0.9202 (m) cc_final: 0.8945 (t) REVERT: F 359 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9212 (tp) REVERT: G 68 TRP cc_start: 0.8240 (t-100) cc_final: 0.7896 (t-100) REVERT: G 105 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.7032 (m-10) REVERT: G 123 ARG cc_start: 0.8422 (ttm170) cc_final: 0.8102 (ttp-170) REVERT: G 153 ASP cc_start: 0.8689 (m-30) cc_final: 0.8419 (m-30) REVERT: G 154 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8219 (mtpt) REVERT: G 157 LYS cc_start: 0.8287 (tptt) cc_final: 0.7492 (ttpp) REVERT: G 158 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7499 (t80) REVERT: G 208 TYR cc_start: 0.8244 (t80) cc_final: 0.7755 (t80) REVERT: G 236 TRP cc_start: 0.8422 (p-90) cc_final: 0.7836 (p-90) REVERT: G 267 LEU cc_start: 0.9144 (mp) cc_final: 0.8791 (mp) REVERT: G 274 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: G 310 LYS cc_start: 0.7231 (ttpt) cc_final: 0.6571 (tptm) REVERT: G 322 LYS cc_start: 0.7244 (pttm) cc_final: 0.6434 (tttm) REVERT: G 353 PRO cc_start: 0.9242 (Cg_endo) cc_final: 0.9034 (Cg_exo) REVERT: H 105 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7311 (m-10) REVERT: H 137 LEU cc_start: 0.9196 (tt) cc_final: 0.8985 (tt) REVERT: H 153 ASP cc_start: 0.8623 (m-30) cc_final: 0.8331 (m-30) REVERT: H 158 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7555 (t80) REVERT: H 199 GLN cc_start: 0.8279 (tp40) cc_final: 0.7908 (tt0) REVERT: H 208 TYR cc_start: 0.8501 (t80) cc_final: 0.8167 (t80) REVERT: H 227 LEU cc_start: 0.8102 (mm) cc_final: 0.7887 (mm) REVERT: H 274 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.5952 (mp0) REVERT: H 305 LYS cc_start: 0.8548 (tttm) cc_final: 0.8309 (tmtt) REVERT: H 310 LYS cc_start: 0.7394 (ttpt) cc_final: 0.6767 (tptt) REVERT: H 315 TYR cc_start: 0.8329 (m-10) cc_final: 0.7613 (m-10) REVERT: H 316 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8390 (mm) REVERT: H 322 LYS cc_start: 0.7691 (pttm) cc_final: 0.7095 (mptt) REVERT: H 359 ILE cc_start: 0.9446 (tp) cc_final: 0.9118 (tp) outliers start: 78 outliers final: 59 residues processed: 779 average time/residue: 0.1559 time to fit residues: 187.4703 Evaluate side-chains 793 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 720 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 285 VAL 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 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 332 SER Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 263 VAL 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 D residue 50 HIS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 177 ILE 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 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 170 SER 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 360 SER Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 162 LEU 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 359 ILE Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 105 TYR 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 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 50 HIS 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 177 ILE Chi-restraints excluded: chain H residue 262 THR 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 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 134 optimal weight: 0.0870 chunk 250 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 254 optimal weight: 0.3980 chunk 132 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 176 optimal weight: 0.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- 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** C 50 HIS D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN G 50 HIS H 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.111018 restraints weight = 31447.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.114957 restraints weight = 16665.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117698 restraints weight = 10941.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.119609 restraints weight = 8137.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120929 restraints weight = 6550.795| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21848 Z= 0.119 Angle : 0.615 12.808 29776 Z= 0.299 Chirality : 0.038 0.154 3288 Planarity : 0.004 0.031 3632 Dihedral : 4.178 21.348 2792 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.15 % Allowed : 30.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2496 helix: 1.31 (0.13), residues: 1720 sheet: None (None), residues: 0 loop : -2.77 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 362 TYR 0.023 0.001 TYR F 300 PHE 0.029 0.001 PHE H 124 TRP 0.033 0.001 TRP A 236 HIS 0.021 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00257 (21832) covalent geometry : angle 0.61331 (29744) SS BOND : bond 0.00261 ( 16) SS BOND : angle 1.65617 ( 32) hydrogen bonds : bond 0.03242 ( 1240) hydrogen bonds : angle 3.97420 ( 3624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3924.37 seconds wall clock time: 68 minutes 17.78 seconds (4097.78 seconds total)