Starting phenix.real_space_refine on Wed Jun 18 04:59:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kff_9971/06_2025/6kff_9971.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kff_9971/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6kff_9971/06_2025/6kff_9971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kff_9971/06_2025/6kff_9971.map" model { file = "/net/cci-nas-00/data/ceres_data/6kff_9971/06_2025/6kff_9971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kff_9971/06_2025/6kff_9971.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14072 2.51 5 N 3432 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21192 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 6.68, per 1000 atoms: 0.32 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 C 58 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 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: 5.36 Conformation dependent library (CDL) restraints added in 2.5 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 71.7% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 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: 5.99 Time building geometry restraints manager: 6.17 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 39.020 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.480 ------------------------------------------------------------------------------- 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 : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 0.35 % Allowed : 6.96 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 2496 helix: -0.50 (0.11), residues: 1672 sheet: -4.64 (0.29), residues: 80 loop : -4.12 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 68 HIS 0.004 0.001 HIS A 50 PHE 0.023 0.001 PHE D 119 TYR 0.009 0.001 TYR B 110 ARG 0.002 0.000 ARG H 362 Details of bonding type rmsd hydrogen bonds : bond 0.11147 ( 1240) hydrogen bonds : angle 5.43526 ( 3624) SS BOND : bond 0.00094 ( 16) SS BOND : angle 0.56640 ( 32) covalent geometry : bond 0.00356 (21832) covalent geometry : angle 0.60385 (29744) *********************** 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 : 2.298 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: 0.3672 time to fit residues: 504.9244 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 : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain H residue 171 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 0.0870 chunk 232 optimal weight: 5.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.101869 restraints weight = 32340.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.105568 restraints weight = 17482.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.108098 restraints weight = 11701.217| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21848 Z= 0.157 Angle : 0.636 10.177 29776 Z= 0.311 Chirality : 0.042 0.189 3288 Planarity : 0.004 0.034 3632 Dihedral : 4.873 23.566 2798 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.62 % Allowed : 21.81 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2496 helix: 0.58 (0.13), residues: 1688 sheet: -4.13 (0.38), residues: 80 loop : -3.55 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 59 HIS 0.010 0.002 HIS A 50 PHE 0.021 0.001 PHE H 124 TYR 0.019 0.001 TYR D 301 ARG 0.005 0.000 ARG A 244 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 1240) hydrogen bonds : angle 4.40461 ( 3624) SS BOND : bond 0.00227 ( 16) SS BOND : angle 1.17450 ( 32) covalent geometry : bond 0.00361 (21832) covalent geometry : angle 0.63507 (29744) *********************** 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 838 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 779 time to evaluate : 2.392 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 58 CYS cc_start: 0.7274 (m) cc_final: 0.6878 (m) REVERT: A 123 ARG cc_start: 0.8379 (ttm170) cc_final: 0.8001 (ttp-170) REVERT: A 137 LEU cc_start: 0.9321 (tt) cc_final: 0.9095 (tt) REVERT: A 153 ASP cc_start: 0.8599 (m-30) cc_final: 0.7968 (m-30) REVERT: A 157 LYS cc_start: 0.8188 (tptt) cc_final: 0.7526 (ttmm) REVERT: A 208 TYR cc_start: 0.8380 (t80) cc_final: 0.7900 (t80) REVERT: A 310 LYS cc_start: 0.7082 (ttpt) cc_final: 0.6427 (tptm) REVERT: B 65 ASN cc_start: 0.7688 (p0) cc_final: 0.7324 (p0) REVERT: B 146 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8377 (mtm110) REVERT: B 153 ASP cc_start: 0.8780 (m-30) cc_final: 0.8406 (m-30) REVERT: B 158 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8009 (t80) REVERT: B 192 TYR cc_start: 0.9124 (t80) cc_final: 0.8896 (t80) REVERT: B 208 TYR cc_start: 0.8518 (t80) cc_final: 0.8234 (t80) REVERT: B 305 LYS cc_start: 0.8583 (tttm) cc_final: 0.8350 (tmtt) REVERT: B 310 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6541 (tptt) REVERT: B 332 SER cc_start: 0.9076 (t) cc_final: 0.8847 (t) REVERT: B 359 ILE cc_start: 0.9437 (tp) cc_final: 0.9131 (tp) REVERT: C 64 PHE cc_start: 0.8278 (m-80) cc_final: 0.7864 (m-10) REVERT: C 65 ASN cc_start: 0.7561 (p0) cc_final: 0.7098 (p0) REVERT: C 105 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6895 (m-10) REVERT: C 153 ASP cc_start: 0.8840 (m-30) cc_final: 0.8167 (m-30) REVERT: C 154 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8220 (mtpt) REVERT: C 157 LYS cc_start: 0.8212 (tptt) cc_final: 0.7744 (ttpp) REVERT: C 198 TRP cc_start: 0.8731 (t-100) cc_final: 0.8302 (t-100) REVERT: C 208 TYR cc_start: 0.8355 (t80) cc_final: 0.7869 (t80) REVERT: C 271 ILE cc_start: 0.8806 (tt) cc_final: 0.8565 (tt) REVERT: C 310 LYS cc_start: 0.6837 (ttpt) cc_final: 0.6201 (tptt) REVERT: C 322 LYS cc_start: 0.7681 (pttm) cc_final: 0.6606 (mptt) REVERT: C 353 PRO cc_start: 0.9460 (Cg_endo) cc_final: 0.9248 (Cg_exo) REVERT: D 65 ASN cc_start: 0.7713 (p0) cc_final: 0.7276 (p0) REVERT: D 146 ARG cc_start: 0.8979 (ttp80) cc_final: 0.8309 (mtp-110) REVERT: D 153 ASP cc_start: 0.8827 (m-30) cc_final: 0.8360 (m-30) REVERT: D 158 PHE cc_start: 0.8393 (t80) cc_final: 0.8169 (t80) REVERT: D 192 TYR cc_start: 0.9165 (t80) cc_final: 0.8915 (t80) REVERT: D 206 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8508 (mm-40) REVERT: D 310 LYS cc_start: 0.7233 (ttpt) cc_final: 0.6765 (tptt) REVERT: D 332 SER cc_start: 0.9111 (m) cc_final: 0.8870 (t) REVERT: D 359 ILE cc_start: 0.9459 (tp) cc_final: 0.9227 (tp) REVERT: E 65 ASN cc_start: 0.7333 (p0) cc_final: 0.6901 (p0) REVERT: E 157 LYS cc_start: 0.8364 (tptt) cc_final: 0.7866 (ttmm) REVERT: E 206 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8596 (mm-40) REVERT: E 208 TYR cc_start: 0.8190 (t80) cc_final: 0.7705 (t80) REVERT: E 310 LYS cc_start: 0.7211 (ttpt) cc_final: 0.6648 (tptt) REVERT: F 157 LYS cc_start: 0.8187 (tptt) cc_final: 0.7686 (ttmm) REVERT: F 194 LEU cc_start: 0.9196 (mt) cc_final: 0.8867 (mt) REVERT: F 310 LYS cc_start: 0.7375 (ttpt) cc_final: 0.6937 (tptt) REVERT: G 64 PHE cc_start: 0.8193 (m-80) cc_final: 0.7977 (m-10) REVERT: G 65 ASN cc_start: 0.7642 (p0) cc_final: 0.7241 (p0) REVERT: G 67 GLN cc_start: 0.8113 (mt0) cc_final: 0.7800 (mt0) REVERT: G 105 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6917 (m-10) REVERT: G 153 ASP cc_start: 0.8852 (m-30) cc_final: 0.8480 (m-30) REVERT: G 154 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8207 (mtpt) REVERT: G 157 LYS cc_start: 0.8261 (tptt) cc_final: 0.7753 (ttpp) REVERT: G 192 TYR cc_start: 0.9124 (t80) cc_final: 0.8811 (t80) REVERT: G 208 TYR cc_start: 0.8319 (t80) cc_final: 0.7832 (t80) REVERT: G 304 ASN cc_start: 0.8716 (t0) cc_final: 0.8380 (t0) REVERT: G 310 LYS cc_start: 0.6979 (ttpt) cc_final: 0.6294 (tptt) REVERT: G 322 LYS cc_start: 0.7658 (pttm) cc_final: 0.6557 (mptt) REVERT: G 353 PRO cc_start: 0.9464 (Cg_endo) cc_final: 0.9243 (Cg_exo) REVERT: H 146 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8376 (mtp-110) REVERT: H 192 TYR cc_start: 0.9236 (t80) cc_final: 0.9010 (t80) REVERT: H 206 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8562 (mm-40) REVERT: H 310 LYS cc_start: 0.7282 (ttpt) cc_final: 0.6634 (tptt) REVERT: H 313 LYS cc_start: 0.9340 (ttmt) cc_final: 0.9092 (ttmm) outliers start: 59 outliers final: 35 residues processed: 816 average time/residue: 0.3551 time to fit residues: 434.3934 Evaluate side-chains 764 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 726 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 352 ILE 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 105 TYR 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 121 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 201 VAL 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 105 TYR 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 121 ILE Chi-restraints excluded: chain H residue 193 THR 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 71 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN C 363 ASN D 50 HIS D 329 GLN F 206 GLN F 329 GLN G 50 HIS G 206 GLN G 363 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.107814 restraints weight = 31722.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111674 restraints weight = 16882.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114338 restraints weight = 11157.731| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1947 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= 0.120 Angle : 0.587 8.561 29776 Z= 0.289 Chirality : 0.039 0.150 3288 Planarity : 0.003 0.028 3632 Dihedral : 4.552 21.792 2792 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.88 % Allowed : 24.25 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 2496 helix: 0.93 (0.13), residues: 1688 sheet: -3.96 (0.39), residues: 80 loop : -3.24 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 59 HIS 0.012 0.002 HIS B 50 PHE 0.015 0.001 PHE G 147 TYR 0.014 0.001 TYR F 301 ARG 0.007 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 1240) hydrogen bonds : angle 4.22369 ( 3624) SS BOND : bond 0.00085 ( 16) SS BOND : angle 1.74537 ( 32) covalent geometry : bond 0.00254 (21832) covalent geometry : angle 0.58404 (29744) *********************** 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 855 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 790 time to evaluate : 2.547 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 67 GLN cc_start: 0.8390 (mp10) cc_final: 0.7652 (mp10) REVERT: A 123 ARG cc_start: 0.8341 (ttm170) cc_final: 0.7940 (ttp-170) REVERT: A 137 LEU cc_start: 0.9231 (tt) cc_final: 0.9017 (tt) REVERT: A 153 ASP cc_start: 0.8626 (m-30) cc_final: 0.7300 (m-30) REVERT: A 157 LYS cc_start: 0.8238 (tptt) cc_final: 0.7596 (ttmm) REVERT: A 158 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7084 (t80) REVERT: A 208 TYR cc_start: 0.8313 (t80) cc_final: 0.7621 (t80) REVERT: A 304 ASN cc_start: 0.8762 (t0) cc_final: 0.8306 (t0) REVERT: A 305 LYS cc_start: 0.8570 (tttm) cc_final: 0.8273 (tmtt) REVERT: A 310 LYS cc_start: 0.7115 (ttpt) cc_final: 0.6389 (tptm) REVERT: B 65 ASN cc_start: 0.7758 (p0) cc_final: 0.7272 (p0) REVERT: B 105 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6864 (m-10) REVERT: B 146 ARG cc_start: 0.8897 (ttp80) cc_final: 0.8392 (mtm110) REVERT: B 153 ASP cc_start: 0.8791 (m-30) cc_final: 0.8367 (m-30) REVERT: B 170 SER cc_start: 0.9371 (t) cc_final: 0.9156 (m) REVERT: B 206 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8445 (mm-40) REVERT: B 208 TYR cc_start: 0.8443 (t80) cc_final: 0.8112 (t80) REVERT: B 305 LYS cc_start: 0.8649 (tttm) cc_final: 0.8334 (tmtt) REVERT: B 310 LYS cc_start: 0.7287 (ttpt) cc_final: 0.6612 (tptt) REVERT: B 315 TYR cc_start: 0.8257 (m-10) cc_final: 0.7513 (m-10) REVERT: B 322 LYS cc_start: 0.7849 (pttm) cc_final: 0.7076 (mptt) REVERT: B 332 SER cc_start: 0.9016 (t) cc_final: 0.8789 (t) REVERT: B 359 ILE cc_start: 0.9421 (tp) cc_final: 0.9122 (tp) REVERT: C 105 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.7113 (m-10) REVERT: C 123 ARG cc_start: 0.8434 (ttm170) cc_final: 0.8059 (ttp-170) REVERT: C 153 ASP cc_start: 0.8779 (m-30) cc_final: 0.8136 (m-30) REVERT: C 154 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8191 (mtpt) REVERT: C 157 LYS cc_start: 0.8240 (tptt) cc_final: 0.7615 (ttpp) REVERT: C 158 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7854 (t80) REVERT: C 198 TRP cc_start: 0.8704 (t-100) cc_final: 0.8278 (t-100) REVERT: C 208 TYR cc_start: 0.8374 (t80) cc_final: 0.7911 (t80) REVERT: C 267 LEU cc_start: 0.9187 (mp) cc_final: 0.8801 (mp) REVERT: C 305 LYS cc_start: 0.8425 (tttm) cc_final: 0.8015 (tmtt) REVERT: C 310 LYS cc_start: 0.6805 (ttpt) cc_final: 0.5994 (tptm) REVERT: C 322 LYS cc_start: 0.7501 (pttm) cc_final: 0.6677 (mptt) REVERT: C 353 PRO cc_start: 0.9387 (Cg_endo) cc_final: 0.9178 (Cg_exo) REVERT: D 64 PHE cc_start: 0.8438 (m-10) cc_final: 0.8230 (m-10) REVERT: D 65 ASN cc_start: 0.7668 (p0) cc_final: 0.7152 (p0) REVERT: D 67 GLN cc_start: 0.8686 (mt0) cc_final: 0.8484 (mt0) REVERT: D 146 ARG cc_start: 0.8945 (ttp80) cc_final: 0.8273 (mtp-110) REVERT: D 153 ASP cc_start: 0.8848 (m-30) cc_final: 0.8384 (m-30) REVERT: D 192 TYR cc_start: 0.9105 (t80) cc_final: 0.8843 (t80) REVERT: D 206 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8466 (mm-40) REVERT: D 275 LYS cc_start: 0.8779 (mptt) cc_final: 0.8570 (mmtt) REVERT: D 310 LYS cc_start: 0.7216 (ttpt) cc_final: 0.6757 (tptt) REVERT: D 322 LYS cc_start: 0.7634 (pttm) cc_final: 0.6900 (mptt) REVERT: D 332 SER cc_start: 0.9161 (m) cc_final: 0.8942 (t) REVERT: D 359 ILE cc_start: 0.9382 (tp) cc_final: 0.9115 (tp) REVERT: E 65 ASN cc_start: 0.7171 (p0) cc_final: 0.6299 (p0) REVERT: E 157 LYS cc_start: 0.8356 (tptt) cc_final: 0.7874 (ttmm) REVERT: E 175 ASP cc_start: 0.8096 (m-30) cc_final: 0.7407 (m-30) REVERT: E 206 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8354 (mm-40) REVERT: E 208 TYR cc_start: 0.8241 (t80) cc_final: 0.7765 (t80) REVERT: E 310 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6630 (tptt) REVERT: E 322 LYS cc_start: 0.7507 (pttm) cc_final: 0.6479 (mptt) REVERT: E 353 PRO cc_start: 0.9339 (Cg_endo) cc_final: 0.9132 (Cg_exo) REVERT: F 157 LYS cc_start: 0.8162 (tptt) cc_final: 0.7555 (ttmm) REVERT: F 158 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7728 (t80) REVERT: F 275 LYS cc_start: 0.8734 (mptt) cc_final: 0.8526 (mmtt) REVERT: F 304 ASN cc_start: 0.8581 (t0) cc_final: 0.7927 (t0) REVERT: F 310 LYS cc_start: 0.7333 (ttpt) cc_final: 0.6884 (tptt) REVERT: G 65 ASN cc_start: 0.7395 (p0) cc_final: 0.6824 (p0) REVERT: G 105 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.7093 (m-10) REVERT: G 123 ARG cc_start: 0.8411 (ttm170) cc_final: 0.8059 (ttp-170) REVERT: G 153 ASP cc_start: 0.8846 (m-30) cc_final: 0.8476 (m-30) REVERT: G 154 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8276 (mtpt) REVERT: G 157 LYS cc_start: 0.8313 (tptt) cc_final: 0.7657 (ttpp) REVERT: G 158 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7851 (t80) REVERT: G 208 TYR cc_start: 0.8315 (t80) cc_final: 0.7862 (t80) REVERT: G 267 LEU cc_start: 0.9195 (mp) cc_final: 0.8806 (mp) REVERT: G 305 LYS cc_start: 0.8428 (tttm) cc_final: 0.7980 (tmtt) REVERT: G 310 LYS cc_start: 0.7145 (ttpt) cc_final: 0.6464 (tptt) REVERT: G 322 LYS cc_start: 0.7404 (pttm) cc_final: 0.6557 (mptt) REVERT: G 353 PRO cc_start: 0.9399 (Cg_endo) cc_final: 0.9199 (Cg_exo) REVERT: H 47 LEU cc_start: 0.9438 (mm) cc_final: 0.9223 (mm) REVERT: H 146 ARG cc_start: 0.8947 (ttp80) cc_final: 0.8211 (mtp-110) REVERT: H 157 LYS cc_start: 0.8217 (tptt) cc_final: 0.7884 (ttmm) REVERT: H 206 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8545 (mm-40) REVERT: H 229 ASP cc_start: 0.8605 (m-30) cc_final: 0.8342 (m-30) REVERT: H 275 LYS cc_start: 0.8655 (mptt) cc_final: 0.8396 (mmtm) REVERT: H 310 LYS cc_start: 0.7275 (ttpt) cc_final: 0.6680 (tptt) REVERT: H 313 LYS cc_start: 0.9328 (ttmt) cc_final: 0.9053 (ttmm) REVERT: H 315 TYR cc_start: 0.8320 (m-10) cc_final: 0.7492 (m-10) REVERT: H 322 LYS cc_start: 0.7807 (pttm) cc_final: 0.7030 (mptt) outliers start: 65 outliers final: 42 residues processed: 812 average time/residue: 0.3373 time to fit residues: 413.6921 Evaluate side-chains 780 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 731 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 360 SER 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 205 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 360 SER 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 158 PHE 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 50 HIS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 360 SER 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 51 PHE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 360 SER 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 299 ILE Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 332 SER 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 206 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 199 optimal weight: 0.4980 chunk 254 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 C 50 HIS C 206 GLN E 50 HIS E 67 GLN F 50 HIS H 50 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.109469 restraints weight = 32261.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.113299 restraints weight = 17130.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115954 restraints weight = 11319.617| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21848 Z= 0.146 Angle : 0.590 7.905 29776 Z= 0.290 Chirality : 0.040 0.147 3288 Planarity : 0.003 0.031 3632 Dihedral : 4.501 23.458 2792 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.65 % Allowed : 25.00 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2496 helix: 1.04 (0.13), residues: 1696 sheet: -3.87 (0.38), residues: 80 loop : -3.17 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 59 HIS 0.014 0.002 HIS G 50 PHE 0.034 0.001 PHE B 242 TYR 0.016 0.001 TYR F 301 ARG 0.009 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 1240) hydrogen bonds : angle 4.17420 ( 3624) SS BOND : bond 0.00314 ( 16) SS BOND : angle 1.83752 ( 32) covalent geometry : bond 0.00335 (21832) covalent geometry : angle 0.58761 (29744) *********************** 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 860 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 755 time to evaluate : 2.388 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 68 TRP cc_start: 0.8167 (t-100) cc_final: 0.7955 (t-100) REVERT: A 123 ARG cc_start: 0.8365 (ttm170) cc_final: 0.7976 (ttp-170) REVERT: A 137 LEU cc_start: 0.9261 (tt) cc_final: 0.9056 (tt) REVERT: A 153 ASP cc_start: 0.8622 (m-30) cc_final: 0.8229 (m-30) REVERT: A 157 LYS cc_start: 0.8159 (tptt) cc_final: 0.7138 (ttmm) REVERT: A 158 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7185 (t80) REVERT: A 170 SER cc_start: 0.9468 (OUTLIER) cc_final: 0.9129 (m) REVERT: A 208 TYR cc_start: 0.8333 (t80) cc_final: 0.7636 (t80) REVERT: A 304 ASN cc_start: 0.8749 (t0) cc_final: 0.8320 (t0) REVERT: A 305 LYS cc_start: 0.8571 (tttm) cc_final: 0.8346 (tmtt) REVERT: A 310 LYS cc_start: 0.7162 (ttpt) cc_final: 0.6445 (tptm) REVERT: B 65 ASN cc_start: 0.7629 (p0) cc_final: 0.7050 (p0) REVERT: B 105 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6776 (m-10) REVERT: B 146 ARG cc_start: 0.8930 (ttp80) cc_final: 0.8432 (mtm110) REVERT: B 153 ASP cc_start: 0.8770 (m-30) cc_final: 0.8366 (m-30) REVERT: B 158 PHE cc_start: 0.7387 (t80) cc_final: 0.7027 (t80) REVERT: B 170 SER cc_start: 0.9348 (t) cc_final: 0.9122 (m) REVERT: B 208 TYR cc_start: 0.8483 (t80) cc_final: 0.8147 (t80) REVERT: B 305 LYS cc_start: 0.8660 (tttm) cc_final: 0.8359 (tmtt) REVERT: B 310 LYS cc_start: 0.7259 (ttpt) cc_final: 0.6530 (tptt) REVERT: B 322 LYS cc_start: 0.7845 (pttm) cc_final: 0.7090 (mptt) REVERT: B 332 SER cc_start: 0.9048 (t) cc_final: 0.8838 (t) REVERT: B 359 ILE cc_start: 0.9483 (tp) cc_final: 0.9203 (tp) REVERT: C 105 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.7063 (m-10) REVERT: C 123 ARG cc_start: 0.8451 (ttm170) cc_final: 0.8056 (ttp-170) REVERT: C 153 ASP cc_start: 0.8755 (m-30) cc_final: 0.8112 (m-30) REVERT: C 154 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8216 (mtpt) REVERT: C 157 LYS cc_start: 0.8215 (tptt) cc_final: 0.7654 (ttpp) REVERT: C 158 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7787 (t80) REVERT: C 208 TYR cc_start: 0.8382 (t80) cc_final: 0.7931 (t80) REVERT: C 267 LEU cc_start: 0.9216 (mp) cc_final: 0.8846 (mp) REVERT: C 274 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.6179 (mp0) REVERT: C 305 LYS cc_start: 0.8438 (tttm) cc_final: 0.8072 (tmtt) REVERT: C 310 LYS cc_start: 0.6844 (ttpt) cc_final: 0.6052 (tptm) REVERT: C 322 LYS cc_start: 0.7508 (pttm) cc_final: 0.6703 (mptt) REVERT: D 65 ASN cc_start: 0.7524 (p0) cc_final: 0.7122 (p0) REVERT: D 105 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7284 (m-10) REVERT: D 146 ARG cc_start: 0.8976 (ttp80) cc_final: 0.8417 (mtm110) REVERT: D 153 ASP cc_start: 0.8827 (m-30) cc_final: 0.8370 (m-30) REVERT: D 192 TYR cc_start: 0.9093 (t80) cc_final: 0.8827 (t80) REVERT: D 206 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8444 (mm-40) REVERT: D 208 TYR cc_start: 0.8508 (t80) cc_final: 0.8183 (t80) REVERT: D 274 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: D 275 LYS cc_start: 0.8774 (mptt) cc_final: 0.8569 (mmtm) REVERT: D 310 LYS cc_start: 0.7266 (ttpt) cc_final: 0.6795 (tptt) REVERT: D 322 LYS cc_start: 0.7684 (pttm) cc_final: 0.6937 (mptt) REVERT: D 332 SER cc_start: 0.9194 (m) cc_final: 0.8948 (t) REVERT: D 359 ILE cc_start: 0.9433 (tp) cc_final: 0.9157 (tp) REVERT: E 65 ASN cc_start: 0.6955 (p0) cc_final: 0.6206 (p0) REVERT: E 67 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8100 (mp10) REVERT: E 129 MET cc_start: 0.8136 (tpp) cc_final: 0.7887 (tpp) REVERT: E 153 ASP cc_start: 0.8772 (m-30) cc_final: 0.8125 (m-30) REVERT: E 157 LYS cc_start: 0.8299 (tptt) cc_final: 0.7829 (ttmm) REVERT: E 170 SER cc_start: 0.9510 (OUTLIER) cc_final: 0.9074 (m) REVERT: E 206 GLN cc_start: 0.9255 (mm-40) cc_final: 0.8347 (mm-40) REVERT: E 208 TYR cc_start: 0.8127 (t80) cc_final: 0.7626 (t80) REVERT: E 274 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.6220 (mp0) REVERT: E 310 LYS cc_start: 0.7202 (ttpt) cc_final: 0.6671 (tptt) REVERT: E 322 LYS cc_start: 0.7472 (pttm) cc_final: 0.6374 (mptt) REVERT: E 353 PRO cc_start: 0.9423 (Cg_endo) cc_final: 0.9207 (Cg_exo) REVERT: F 137 LEU cc_start: 0.9216 (tt) cc_final: 0.8985 (tt) REVERT: F 157 LYS cc_start: 0.8132 (tptt) cc_final: 0.7513 (ttmm) REVERT: F 158 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7572 (t80) REVERT: F 304 ASN cc_start: 0.8577 (t0) cc_final: 0.7960 (t0) REVERT: F 310 LYS cc_start: 0.7343 (ttpt) cc_final: 0.6875 (tptt) REVERT: F 322 LYS cc_start: 0.7722 (pttm) cc_final: 0.6990 (mptt) REVERT: G 67 GLN cc_start: 0.8553 (mp10) cc_final: 0.8305 (mp10) REVERT: G 70 ASN cc_start: 0.8955 (t0) cc_final: 0.8625 (t0) REVERT: G 105 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.7033 (m-10) REVERT: G 123 ARG cc_start: 0.8470 (ttm170) cc_final: 0.8162 (ttp-170) REVERT: G 153 ASP cc_start: 0.8793 (m-30) cc_final: 0.8475 (m-30) REVERT: G 154 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8289 (mtpt) REVERT: G 157 LYS cc_start: 0.8320 (tptt) cc_final: 0.7568 (ttpp) REVERT: G 158 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7900 (t80) REVERT: G 170 SER cc_start: 0.9441 (OUTLIER) cc_final: 0.8949 (m) REVERT: G 208 TYR cc_start: 0.8280 (t80) cc_final: 0.7590 (t80) REVERT: G 267 LEU cc_start: 0.9198 (mp) cc_final: 0.8828 (mp) REVERT: G 274 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.6305 (mp0) REVERT: G 304 ASN cc_start: 0.8639 (t0) cc_final: 0.8336 (t0) REVERT: G 305 LYS cc_start: 0.8633 (tttm) cc_final: 0.8357 (tmtt) REVERT: G 310 LYS cc_start: 0.7165 (ttpt) cc_final: 0.6502 (tptt) REVERT: G 322 LYS cc_start: 0.7410 (pttm) cc_final: 0.6592 (mptt) REVERT: H 47 LEU cc_start: 0.9536 (mm) cc_final: 0.9319 (mm) REVERT: H 65 ASN cc_start: 0.7447 (p0) cc_final: 0.6961 (p0) REVERT: H 105 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7459 (m-10) REVERT: H 137 LEU cc_start: 0.9260 (tt) cc_final: 0.9033 (tt) REVERT: H 153 ASP cc_start: 0.8698 (m-30) cc_final: 0.8311 (m-30) REVERT: H 157 LYS cc_start: 0.8082 (tptt) cc_final: 0.7790 (ttmm) REVERT: H 158 PHE cc_start: 0.7906 (t80) cc_final: 0.7649 (t80) REVERT: H 206 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8520 (mm-40) REVERT: H 229 ASP cc_start: 0.8609 (m-30) cc_final: 0.8338 (m-30) REVERT: H 305 LYS cc_start: 0.8654 (tttm) cc_final: 0.8333 (tmtt) REVERT: H 310 LYS cc_start: 0.7313 (ttpt) cc_final: 0.6621 (tptt) REVERT: H 313 LYS cc_start: 0.9345 (ttmt) cc_final: 0.9096 (ttmm) REVERT: H 322 LYS cc_start: 0.7815 (pttm) cc_final: 0.7064 (mptt) REVERT: H 359 ILE cc_start: 0.9482 (tp) cc_final: 0.9126 (tp) outliers start: 105 outliers final: 71 residues processed: 811 average time/residue: 0.3286 time to fit residues: 406.1584 Evaluate side-chains 809 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 721 time to evaluate : 2.313 ------------------------------------------------------------------------------- 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 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 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 158 PHE 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 351 ASP 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 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 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 360 SER 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 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 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 158 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE 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 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 170 SER 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 360 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 HIS 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 264 LEU Chi-restraints excluded: chain H residue 332 SER 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 202 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 79 HIS B 50 HIS B 206 GLN D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS E 67 GLN G 50 HIS G 206 GLN H 50 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.108703 restraints weight = 31791.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.112669 restraints weight = 16715.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.115370 restraints weight = 10943.032| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21848 Z= 0.118 Angle : 0.577 11.757 29776 Z= 0.281 Chirality : 0.039 0.188 3288 Planarity : 0.003 0.035 3632 Dihedral : 4.349 27.420 2792 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.50 % Allowed : 26.33 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2496 helix: 1.16 (0.13), residues: 1696 sheet: -3.75 (0.39), residues: 80 loop : -3.07 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 68 HIS 0.015 0.002 HIS H 50 PHE 0.041 0.001 PHE B 242 TYR 0.015 0.001 TYR F 301 ARG 0.010 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 1240) hydrogen bonds : angle 4.13082 ( 3624) SS BOND : bond 0.00205 ( 16) SS BOND : angle 1.28343 ( 32) covalent geometry : bond 0.00255 (21832) covalent geometry : angle 0.57609 (29744) *********************** 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 845 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 766 time to evaluate : 2.489 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 68 TRP cc_start: 0.8183 (t-100) cc_final: 0.7938 (t-100) REVERT: A 123 ARG cc_start: 0.8340 (ttm170) cc_final: 0.7936 (ttp-170) REVERT: A 153 ASP cc_start: 0.8583 (m-30) cc_final: 0.8224 (m-30) REVERT: A 154 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8440 (mtpt) REVERT: A 157 LYS cc_start: 0.8151 (tptt) cc_final: 0.7271 (ttpp) REVERT: A 158 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7107 (t80) REVERT: A 170 SER cc_start: 0.9443 (OUTLIER) cc_final: 0.9111 (m) REVERT: A 208 TYR cc_start: 0.8301 (t80) cc_final: 0.7825 (t80) REVERT: A 274 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.6062 (mp0) REVERT: A 304 ASN cc_start: 0.8711 (t0) cc_final: 0.8299 (t0) REVERT: A 305 LYS cc_start: 0.8684 (tttm) cc_final: 0.8366 (tmtt) REVERT: A 310 LYS cc_start: 0.7147 (ttpt) cc_final: 0.6437 (tptm) REVERT: A 345 MET cc_start: 0.9361 (tpp) cc_final: 0.8982 (tpp) REVERT: B 47 LEU cc_start: 0.9456 (mm) cc_final: 0.9255 (mm) REVERT: B 65 ASN cc_start: 0.7581 (p0) cc_final: 0.7007 (p0) REVERT: B 105 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6727 (m-10) REVERT: B 146 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8380 (mtm110) REVERT: B 153 ASP cc_start: 0.8742 (m-30) cc_final: 0.8306 (m-30) REVERT: B 158 PHE cc_start: 0.7637 (t80) cc_final: 0.7119 (t80) REVERT: B 170 SER cc_start: 0.9287 (t) cc_final: 0.9079 (m) REVERT: B 206 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8417 (mm-40) REVERT: B 208 TYR cc_start: 0.8440 (t80) cc_final: 0.8142 (t80) REVERT: B 305 LYS cc_start: 0.8660 (tttm) cc_final: 0.8385 (tmtt) REVERT: B 310 LYS cc_start: 0.7336 (ttpt) cc_final: 0.6566 (tptm) REVERT: B 315 TYR cc_start: 0.8274 (m-10) cc_final: 0.7537 (m-10) REVERT: B 322 LYS cc_start: 0.7800 (pttm) cc_final: 0.7062 (mptt) REVERT: B 332 SER cc_start: 0.9086 (t) cc_final: 0.8884 (t) REVERT: B 359 ILE cc_start: 0.9454 (tp) cc_final: 0.9166 (tp) REVERT: C 123 ARG cc_start: 0.8446 (ttm170) cc_final: 0.8125 (ttp-170) REVERT: C 153 ASP cc_start: 0.8712 (m-30) cc_final: 0.8224 (m-30) REVERT: C 154 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8198 (mtpt) REVERT: C 157 LYS cc_start: 0.8258 (tptt) cc_final: 0.7624 (ttpp) REVERT: C 158 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7784 (t80) REVERT: C 208 TYR cc_start: 0.8354 (t80) cc_final: 0.7886 (t80) REVERT: C 274 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.6194 (mp0) REVERT: C 305 LYS cc_start: 0.8668 (tttm) cc_final: 0.8206 (tmtt) REVERT: C 310 LYS cc_start: 0.7200 (ttpt) cc_final: 0.6361 (tptm) REVERT: C 322 LYS cc_start: 0.7367 (pttm) cc_final: 0.6580 (mptt) REVERT: D 28 ASP cc_start: 0.7205 (m-30) cc_final: 0.7002 (m-30) REVERT: D 65 ASN cc_start: 0.7440 (p0) cc_final: 0.7083 (p0) REVERT: D 153 ASP cc_start: 0.8758 (m-30) cc_final: 0.8252 (m-30) REVERT: D 192 TYR cc_start: 0.9058 (t80) cc_final: 0.8845 (t80) REVERT: D 206 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8556 (mm-40) REVERT: D 208 TYR cc_start: 0.8447 (t80) cc_final: 0.8081 (t80) REVERT: D 274 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.6303 (mp0) REVERT: D 310 LYS cc_start: 0.7384 (ttpt) cc_final: 0.6927 (tptt) REVERT: D 322 LYS cc_start: 0.7600 (pttm) cc_final: 0.6889 (mptt) REVERT: D 332 SER cc_start: 0.9175 (m) cc_final: 0.8950 (t) REVERT: D 359 ILE cc_start: 0.9444 (tp) cc_final: 0.9146 (tp) REVERT: E 59 TRP cc_start: 0.8029 (t-100) cc_final: 0.7609 (t-100) REVERT: E 153 ASP cc_start: 0.8771 (m-30) cc_final: 0.8468 (m-30) REVERT: E 157 LYS cc_start: 0.8266 (tptt) cc_final: 0.7660 (ttmm) REVERT: E 175 ASP cc_start: 0.8117 (m-30) cc_final: 0.7532 (m-30) REVERT: E 206 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8350 (mm-40) REVERT: E 208 TYR cc_start: 0.8284 (t80) cc_final: 0.7783 (t80) REVERT: E 274 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: E 305 LYS cc_start: 0.8543 (tttm) cc_final: 0.8037 (tmtt) REVERT: E 310 LYS cc_start: 0.7153 (ttpt) cc_final: 0.6550 (tptt) REVERT: E 322 LYS cc_start: 0.7387 (pttm) cc_final: 0.6597 (mptt) REVERT: E 353 PRO cc_start: 0.9374 (Cg_endo) cc_final: 0.9159 (Cg_exo) REVERT: F 157 LYS cc_start: 0.8104 (tptt) cc_final: 0.7533 (ttmm) REVERT: F 158 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7605 (t80) REVERT: F 206 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8581 (mm-40) REVERT: F 274 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: F 304 ASN cc_start: 0.8604 (t0) cc_final: 0.8032 (t0) REVERT: F 310 LYS cc_start: 0.7308 (ttpt) cc_final: 0.6856 (tptt) REVERT: F 322 LYS cc_start: 0.7574 (pttm) cc_final: 0.6880 (mptt) REVERT: G 70 ASN cc_start: 0.8906 (t0) cc_final: 0.8588 (t0) REVERT: G 105 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.7112 (m-10) REVERT: G 123 ARG cc_start: 0.8422 (ttm170) cc_final: 0.8078 (ttp-170) REVERT: G 153 ASP cc_start: 0.8741 (m-30) cc_final: 0.8465 (m-30) REVERT: G 154 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8303 (mtpt) REVERT: G 157 LYS cc_start: 0.8323 (tptt) cc_final: 0.7562 (ttpp) REVERT: G 158 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7802 (t80) REVERT: G 170 SER cc_start: 0.9440 (OUTLIER) cc_final: 0.9002 (m) REVERT: G 208 TYR cc_start: 0.8306 (t80) cc_final: 0.7850 (t80) REVERT: G 267 LEU cc_start: 0.9224 (mp) cc_final: 0.8988 (mp) REVERT: G 274 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: G 304 ASN cc_start: 0.8612 (t0) cc_final: 0.8319 (t0) REVERT: G 310 LYS cc_start: 0.7133 (ttpt) cc_final: 0.6390 (tptm) REVERT: G 322 LYS cc_start: 0.7351 (pttm) cc_final: 0.6634 (mptt) REVERT: H 47 LEU cc_start: 0.9456 (mm) cc_final: 0.9229 (mm) REVERT: H 65 ASN cc_start: 0.7370 (p0) cc_final: 0.6838 (p0) REVERT: H 105 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7459 (m-10) REVERT: H 153 ASP cc_start: 0.8658 (m-30) cc_final: 0.8248 (m-30) REVERT: H 157 LYS cc_start: 0.8186 (tptt) cc_final: 0.7703 (ttmm) REVERT: H 158 PHE cc_start: 0.8001 (t80) cc_final: 0.7646 (t80) REVERT: H 229 ASP cc_start: 0.8609 (m-30) cc_final: 0.8337 (m-30) REVERT: H 274 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: H 305 LYS cc_start: 0.8612 (tttm) cc_final: 0.8305 (tmtt) REVERT: H 310 LYS cc_start: 0.7345 (ttpt) cc_final: 0.6589 (tptm) REVERT: H 313 LYS cc_start: 0.9346 (ttmt) cc_final: 0.9101 (ttmm) REVERT: H 315 TYR cc_start: 0.8327 (m-10) cc_final: 0.7614 (m-10) REVERT: H 322 LYS cc_start: 0.7799 (pttm) cc_final: 0.7086 (mptt) REVERT: H 331 PHE cc_start: 0.9020 (m-10) cc_final: 0.8739 (m-10) REVERT: H 359 ILE cc_start: 0.9455 (tp) cc_final: 0.9104 (tp) outliers start: 79 outliers final: 47 residues processed: 802 average time/residue: 0.3300 time to fit residues: 404.4908 Evaluate side-chains 787 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 724 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE 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 50 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 199 GLN 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 351 ASP Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 81 THR 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 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 299 ILE Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 162 LEU 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 360 SER Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 360 SER 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 170 SER 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 H residue 105 TYR 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 274 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 90 optimal weight: 0.4980 chunk 147 optimal weight: 0.0980 chunk 200 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 123 optimal weight: 0.0980 chunk 116 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 52 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 246 optimal weight: 7.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 50 HIS F 67 GLN G 79 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 = 0.3463 r_free = 0.3463 target = 0.133724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.111402 restraints weight = 31403.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.115387 restraints weight = 16549.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.118128 restraints weight = 10843.221| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21848 Z= 0.112 Angle : 0.578 12.581 29776 Z= 0.281 Chirality : 0.038 0.203 3288 Planarity : 0.003 0.037 3632 Dihedral : 4.225 27.878 2792 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.41 % Allowed : 27.48 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2496 helix: 1.26 (0.13), residues: 1712 sheet: -3.74 (0.40), residues: 80 loop : -2.97 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 68 HIS 0.013 0.002 HIS G 50 PHE 0.028 0.001 PHE B 242 TYR 0.016 0.001 TYR F 301 ARG 0.013 0.000 ARG G 362 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 1240) hydrogen bonds : angle 4.07045 ( 3624) SS BOND : bond 0.00212 ( 16) SS BOND : angle 1.48826 ( 32) covalent geometry : bond 0.00234 (21832) covalent geometry : angle 0.57600 (29744) *********************** 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 852 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 775 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8158 (t-100) cc_final: 0.7829 (t-100) REVERT: A 123 ARG cc_start: 0.8313 (ttm170) cc_final: 0.7970 (ttp-170) REVERT: A 153 ASP cc_start: 0.8582 (m-30) cc_final: 0.8239 (m-30) REVERT: A 154 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8497 (mtpt) REVERT: A 157 LYS cc_start: 0.8136 (tptt) cc_final: 0.7226 (ttpp) REVERT: A 158 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6999 (t80) REVERT: A 175 ASP cc_start: 0.7973 (m-30) cc_final: 0.7438 (m-30) REVERT: A 208 TYR cc_start: 0.8249 (t80) cc_final: 0.7855 (t80) REVERT: A 236 TRP cc_start: 0.8694 (p-90) cc_final: 0.8332 (p-90) REVERT: A 274 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: A 304 ASN cc_start: 0.8656 (t0) cc_final: 0.8261 (t0) REVERT: A 310 LYS cc_start: 0.7106 (ttpt) cc_final: 0.6476 (tptm) REVERT: A 345 MET cc_start: 0.9358 (tpp) cc_final: 0.9077 (tpp) REVERT: B 59 TRP cc_start: 0.7877 (t-100) cc_final: 0.7009 (t-100) REVERT: B 65 ASN cc_start: 0.7488 (p0) cc_final: 0.6884 (p0) REVERT: B 105 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6705 (m-10) REVERT: B 146 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8359 (mtm110) REVERT: B 153 ASP cc_start: 0.8741 (m-30) cc_final: 0.8343 (m-30) REVERT: B 158 PHE cc_start: 0.7561 (t80) cc_final: 0.7069 (t80) REVERT: B 206 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8407 (mm-40) REVERT: B 208 TYR cc_start: 0.8419 (t80) cc_final: 0.8101 (t80) REVERT: B 305 LYS cc_start: 0.8641 (tttm) cc_final: 0.8396 (tmtt) REVERT: B 310 LYS cc_start: 0.7340 (ttpt) cc_final: 0.6626 (tptm) REVERT: B 315 TYR cc_start: 0.8228 (m-10) cc_final: 0.7559 (m-10) REVERT: B 322 LYS cc_start: 0.7775 (pttm) cc_final: 0.7038 (mptt) REVERT: B 359 ILE cc_start: 0.9394 (tp) cc_final: 0.9088 (tp) REVERT: C 123 ARG cc_start: 0.8415 (ttm170) cc_final: 0.8084 (ttp-170) REVERT: C 153 ASP cc_start: 0.8693 (m-30) cc_final: 0.8249 (m-30) REVERT: C 154 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8285 (mtpt) REVERT: C 157 LYS cc_start: 0.8266 (tptt) cc_final: 0.7539 (ttpp) REVERT: C 158 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7808 (t80) REVERT: C 208 TYR cc_start: 0.8326 (t80) cc_final: 0.7807 (t80) REVERT: C 274 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: C 305 LYS cc_start: 0.8578 (tttm) cc_final: 0.8249 (tmtt) REVERT: C 310 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6337 (tptm) REVERT: C 322 LYS cc_start: 0.7300 (pttm) cc_final: 0.6503 (tttm) REVERT: D 65 ASN cc_start: 0.7585 (p0) cc_final: 0.7079 (p0) REVERT: D 153 ASP cc_start: 0.8751 (m-30) cc_final: 0.8290 (m-30) REVERT: D 183 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8762 (ttpt) REVERT: D 206 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8532 (mm-40) REVERT: D 208 TYR cc_start: 0.8373 (t80) cc_final: 0.7960 (t80) REVERT: D 274 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: D 310 LYS cc_start: 0.7376 (ttpt) cc_final: 0.6903 (tptt) REVERT: D 315 TYR cc_start: 0.8321 (m-10) cc_final: 0.7680 (m-10) REVERT: D 322 LYS cc_start: 0.7557 (pttm) cc_final: 0.6848 (mptt) REVERT: D 332 SER cc_start: 0.9165 (m) cc_final: 0.8821 (p) REVERT: D 359 ILE cc_start: 0.9369 (tp) cc_final: 0.9052 (tp) REVERT: E 59 TRP cc_start: 0.8041 (t-100) cc_final: 0.7728 (t-100) REVERT: E 153 ASP cc_start: 0.8730 (m-30) cc_final: 0.8436 (m-30) REVERT: E 157 LYS cc_start: 0.8239 (tptt) cc_final: 0.7596 (ttmm) REVERT: E 175 ASP cc_start: 0.8126 (m-30) cc_final: 0.7574 (m-30) REVERT: E 206 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8401 (mm-40) REVERT: E 208 TYR cc_start: 0.8272 (t80) cc_final: 0.7867 (t80) REVERT: E 274 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.6315 (mp0) REVERT: E 305 LYS cc_start: 0.8509 (tttm) cc_final: 0.8067 (tmtt) REVERT: E 310 LYS cc_start: 0.7127 (ttpt) cc_final: 0.6531 (tptt) REVERT: E 322 LYS cc_start: 0.7234 (pttm) cc_final: 0.6394 (tttm) REVERT: E 345 MET cc_start: 0.9262 (tpp) cc_final: 0.9032 (mpp) REVERT: F 59 TRP cc_start: 0.7757 (t-100) cc_final: 0.7339 (t-100) REVERT: F 67 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: F 157 LYS cc_start: 0.8072 (tptt) cc_final: 0.7699 (ttmm) REVERT: F 158 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7567 (t80) REVERT: F 183 LYS cc_start: 0.9025 (ttpt) cc_final: 0.8818 (ttpt) REVERT: F 199 GLN cc_start: 0.8047 (tp40) cc_final: 0.7755 (tt0) REVERT: F 206 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8569 (mm-40) REVERT: F 274 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: F 304 ASN cc_start: 0.8596 (t0) cc_final: 0.8108 (t0) REVERT: F 310 LYS cc_start: 0.7357 (ttpt) cc_final: 0.6915 (tptt) REVERT: F 322 LYS cc_start: 0.7508 (pttm) cc_final: 0.6827 (mptt) REVERT: G 70 ASN cc_start: 0.8943 (t0) cc_final: 0.8655 (t0) REVERT: G 123 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8065 (ttp-170) REVERT: G 153 ASP cc_start: 0.8723 (m-30) cc_final: 0.8412 (m-30) REVERT: G 154 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8317 (mtpt) REVERT: G 157 LYS cc_start: 0.8306 (tptt) cc_final: 0.7495 (ttpp) REVERT: G 158 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7635 (t80) REVERT: G 208 TYR cc_start: 0.8277 (t80) cc_final: 0.7790 (t80) REVERT: G 274 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: G 310 LYS cc_start: 0.7096 (ttpt) cc_final: 0.6407 (tptm) REVERT: G 322 LYS cc_start: 0.7265 (pttm) cc_final: 0.6400 (tttm) REVERT: H 47 LEU cc_start: 0.9503 (mm) cc_final: 0.9285 (mm) REVERT: H 105 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7444 (m-10) REVERT: H 153 ASP cc_start: 0.8664 (m-30) cc_final: 0.8305 (m-30) REVERT: H 157 LYS cc_start: 0.8152 (tptt) cc_final: 0.7624 (ttmm) REVERT: H 158 PHE cc_start: 0.8122 (t80) cc_final: 0.7747 (t80) REVERT: H 208 TYR cc_start: 0.8445 (t80) cc_final: 0.8184 (t80) REVERT: H 229 ASP cc_start: 0.8595 (m-30) cc_final: 0.8352 (m-30) REVERT: H 274 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.6228 (mp0) REVERT: H 305 LYS cc_start: 0.8531 (tttm) cc_final: 0.8255 (tmtt) REVERT: H 310 LYS cc_start: 0.7394 (ttpt) cc_final: 0.6645 (tptm) REVERT: H 313 LYS cc_start: 0.9331 (ttmt) cc_final: 0.9087 (ttmm) REVERT: H 315 TYR cc_start: 0.8293 (m-10) cc_final: 0.7644 (m-10) REVERT: H 322 LYS cc_start: 0.7742 (pttm) cc_final: 0.7069 (mptt) REVERT: H 359 ILE cc_start: 0.9436 (tp) cc_final: 0.9093 (tp) outliers start: 77 outliers final: 44 residues processed: 812 average time/residue: 0.3187 time to fit residues: 396.2010 Evaluate side-chains 783 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 725 time to evaluate : 2.353 ------------------------------------------------------------------------------- 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 B residue 50 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 199 GLN 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 264 LEU Chi-restraints excluded: chain D residue 274 GLU 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 274 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 274 GLU 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 125 ILE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 332 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 12 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 63 optimal weight: 0.0980 chunk 251 optimal weight: 0.0000 chunk 46 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 195 optimal weight: 0.0270 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS D 50 HIS D 63 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN E 79 HIS F 50 HIS F 67 GLN G 50 HIS G 206 GLN H 67 GLN H 79 HIS H 115 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.114327 restraints weight = 31230.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118394 restraints weight = 16297.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.121144 restraints weight = 10593.400| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21848 Z= 0.112 Angle : 0.585 12.928 29776 Z= 0.283 Chirality : 0.038 0.175 3288 Planarity : 0.003 0.033 3632 Dihedral : 4.130 29.700 2792 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.24 % Allowed : 29.08 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2496 helix: 1.25 (0.13), residues: 1728 sheet: -3.77 (0.39), residues: 80 loop : -2.97 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 59 HIS 0.015 0.001 HIS F 50 PHE 0.017 0.001 PHE E 330 TYR 0.018 0.001 TYR F 301 ARG 0.013 0.000 ARG C 362 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 1240) hydrogen bonds : angle 3.99456 ( 3624) SS BOND : bond 0.00222 ( 16) SS BOND : angle 1.32155 ( 32) covalent geometry : bond 0.00238 (21832) covalent geometry : angle 0.58352 (29744) *********************** 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 807 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 734 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8081 (t-100) cc_final: 0.7876 (t-100) REVERT: A 123 ARG cc_start: 0.8344 (ttm170) cc_final: 0.7998 (ttp-170) REVERT: A 153 ASP cc_start: 0.8581 (m-30) cc_final: 0.8270 (m-30) REVERT: A 154 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8504 (mtpt) REVERT: A 157 LYS cc_start: 0.8128 (tptt) cc_final: 0.7206 (ttpp) REVERT: A 158 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7045 (t80) REVERT: A 175 ASP cc_start: 0.7954 (m-30) cc_final: 0.7430 (m-30) REVERT: A 208 TYR cc_start: 0.8348 (t80) cc_final: 0.7876 (t80) REVERT: A 236 TRP cc_start: 0.8667 (p-90) cc_final: 0.8283 (p-90) REVERT: A 274 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.6101 (mp0) REVERT: A 310 LYS cc_start: 0.7135 (ttpt) cc_final: 0.6430 (tptm) REVERT: A 322 LYS cc_start: 0.7208 (pttm) cc_final: 0.6394 (tttm) REVERT: B 65 ASN cc_start: 0.7303 (p0) cc_final: 0.6702 (p0) REVERT: B 105 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6726 (m-10) REVERT: B 146 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8441 (mtm110) REVERT: B 153 ASP cc_start: 0.8712 (m-30) cc_final: 0.8340 (m-30) REVERT: B 158 PHE cc_start: 0.7510 (t80) cc_final: 0.7062 (t80) REVERT: B 206 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8388 (mm-40) REVERT: B 208 TYR cc_start: 0.8359 (t80) cc_final: 0.8032 (t80) REVERT: B 310 LYS cc_start: 0.7420 (ttpt) cc_final: 0.6703 (tptm) REVERT: B 315 TYR cc_start: 0.8217 (m-10) cc_final: 0.7587 (m-10) REVERT: B 322 LYS cc_start: 0.7742 (pttm) cc_final: 0.7046 (mptt) REVERT: B 359 ILE cc_start: 0.9372 (tp) cc_final: 0.9068 (tp) REVERT: C 105 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.7054 (m-10) REVERT: C 123 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8076 (ttp-170) REVERT: C 153 ASP cc_start: 0.8637 (m-30) cc_final: 0.8073 (m-30) REVERT: C 154 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8288 (mtpt) REVERT: C 157 LYS cc_start: 0.8275 (tptt) cc_final: 0.7559 (ttpp) REVERT: C 158 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7769 (t80) REVERT: C 206 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8693 (mm-40) REVERT: C 208 TYR cc_start: 0.8372 (t80) cc_final: 0.7845 (t80) REVERT: C 236 TRP cc_start: 0.8602 (p-90) cc_final: 0.8210 (p-90) REVERT: C 274 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: C 305 LYS cc_start: 0.8562 (tttm) cc_final: 0.8336 (tmtt) REVERT: C 310 LYS cc_start: 0.7157 (ttpt) cc_final: 0.6264 (tptm) REVERT: C 322 LYS cc_start: 0.7275 (pttm) cc_final: 0.6443 (tttm) REVERT: D 65 ASN cc_start: 0.7546 (p0) cc_final: 0.6966 (p0) REVERT: D 153 ASP cc_start: 0.8740 (m-30) cc_final: 0.8287 (m-30) REVERT: D 206 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8542 (mm-40) REVERT: D 208 TYR cc_start: 0.8350 (t80) cc_final: 0.7908 (t80) REVERT: D 274 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: D 310 LYS cc_start: 0.7384 (ttpt) cc_final: 0.6929 (tptt) REVERT: D 315 TYR cc_start: 0.8291 (m-10) cc_final: 0.7701 (m-10) REVERT: D 322 LYS cc_start: 0.7537 (pttm) cc_final: 0.6857 (mptt) REVERT: D 332 SER cc_start: 0.9148 (m) cc_final: 0.8861 (p) REVERT: D 359 ILE cc_start: 0.9358 (tp) cc_final: 0.9001 (tp) REVERT: E 59 TRP cc_start: 0.7934 (t-100) cc_final: 0.7671 (t-100) REVERT: E 153 ASP cc_start: 0.8721 (m-30) cc_final: 0.8439 (m-30) REVERT: E 157 LYS cc_start: 0.8162 (tptt) cc_final: 0.7765 (ttmm) REVERT: E 158 PHE cc_start: 0.7288 (t80) cc_final: 0.7030 (t80) REVERT: E 175 ASP cc_start: 0.8154 (m-30) cc_final: 0.7620 (m-30) REVERT: E 206 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8397 (mm-40) REVERT: E 208 TYR cc_start: 0.8345 (t80) cc_final: 0.7852 (t80) REVERT: E 274 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: E 305 LYS cc_start: 0.8452 (tttm) cc_final: 0.8166 (tmtt) REVERT: E 310 LYS cc_start: 0.7124 (ttpt) cc_final: 0.6570 (tptt) REVERT: E 322 LYS cc_start: 0.7165 (pttm) cc_final: 0.6507 (tttm) REVERT: F 153 ASP cc_start: 0.8616 (m-30) cc_final: 0.8232 (m-30) REVERT: F 157 LYS cc_start: 0.8062 (tptt) cc_final: 0.7705 (ttmm) REVERT: F 158 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7502 (t80) REVERT: F 206 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8597 (mm-40) REVERT: F 274 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: F 304 ASN cc_start: 0.8577 (t0) cc_final: 0.8124 (t0) REVERT: F 310 LYS cc_start: 0.7402 (ttpt) cc_final: 0.6975 (tptt) REVERT: F 315 TYR cc_start: 0.8318 (m-10) cc_final: 0.7661 (m-10) REVERT: F 322 LYS cc_start: 0.7427 (pttm) cc_final: 0.6745 (mptt) REVERT: G 70 ASN cc_start: 0.8913 (t0) cc_final: 0.8642 (t0) REVERT: G 123 ARG cc_start: 0.8376 (ttm170) cc_final: 0.8051 (ttp-170) REVERT: G 153 ASP cc_start: 0.8684 (m-30) cc_final: 0.8408 (m-30) REVERT: G 154 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8332 (mtpt) REVERT: G 157 LYS cc_start: 0.8288 (tptt) cc_final: 0.7487 (ttpp) REVERT: G 158 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7506 (t80) REVERT: G 208 TYR cc_start: 0.8316 (t80) cc_final: 0.7814 (t80) REVERT: G 236 TRP cc_start: 0.8601 (p-90) cc_final: 0.8236 (p-90) REVERT: G 274 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.6319 (mp0) REVERT: G 310 LYS cc_start: 0.7205 (ttpt) cc_final: 0.6527 (tptm) REVERT: G 322 LYS cc_start: 0.7268 (pttm) cc_final: 0.6442 (tttm) REVERT: H 47 LEU cc_start: 0.9484 (mm) cc_final: 0.9267 (mm) REVERT: H 105 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7419 (m-10) REVERT: H 153 ASP cc_start: 0.8640 (m-30) cc_final: 0.8329 (m-30) REVERT: H 157 LYS cc_start: 0.8116 (tptt) cc_final: 0.7620 (ttmm) REVERT: H 158 PHE cc_start: 0.7939 (t80) cc_final: 0.7568 (t80) REVERT: H 208 TYR cc_start: 0.8447 (t80) cc_final: 0.8121 (t80) REVERT: H 229 ASP cc_start: 0.8592 (m-30) cc_final: 0.8356 (m-30) REVERT: H 274 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.6124 (mp0) REVERT: H 305 LYS cc_start: 0.8541 (tttm) cc_final: 0.8271 (tmtt) REVERT: H 310 LYS cc_start: 0.7406 (ttpt) cc_final: 0.6707 (tptm) REVERT: H 313 LYS cc_start: 0.9313 (ttmt) cc_final: 0.9066 (ttmm) REVERT: H 315 TYR cc_start: 0.8240 (m-10) cc_final: 0.7604 (m-10) REVERT: H 316 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8543 (mm) REVERT: H 322 LYS cc_start: 0.7708 (pttm) cc_final: 0.6910 (tttm) REVERT: H 359 ILE cc_start: 0.9435 (tp) cc_final: 0.9093 (tp) outliers start: 73 outliers final: 42 residues processed: 766 average time/residue: 0.3378 time to fit residues: 398.8649 Evaluate side-chains 767 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 710 time to evaluate : 2.333 ------------------------------------------------------------------------------- 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 B residue 50 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 199 GLN 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 81 THR 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 299 ILE 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 170 SER Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 332 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 231 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 220 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 124 optimal weight: 0.0570 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 50 HIS F 79 HIS H 67 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113669 restraints weight = 31402.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.117657 restraints weight = 16581.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120331 restraints weight = 10854.097| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2890 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= 0.114 Angle : 0.588 12.809 29776 Z= 0.284 Chirality : 0.038 0.170 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.104 28.006 2792 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.28 % Allowed : 28.99 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2496 helix: 1.33 (0.13), residues: 1712 sheet: -3.81 (0.38), residues: 80 loop : -2.90 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 236 HIS 0.013 0.002 HIS B 50 PHE 0.014 0.001 PHE A 330 TYR 0.018 0.001 TYR F 301 ARG 0.012 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 1240) hydrogen bonds : angle 3.97170 ( 3624) SS BOND : bond 0.00204 ( 16) SS BOND : angle 1.19232 ( 32) covalent geometry : bond 0.00251 (21832) covalent geometry : angle 0.58711 (29744) *********************** 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 822 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 748 time to evaluate : 2.206 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 123 ARG cc_start: 0.8330 (ttm170) cc_final: 0.7985 (ttp-170) REVERT: A 153 ASP cc_start: 0.8572 (m-30) cc_final: 0.8271 (m-30) REVERT: A 154 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8455 (mtpt) REVERT: A 157 LYS cc_start: 0.8110 (tptt) cc_final: 0.7170 (ttpp) REVERT: A 158 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7016 (t80) REVERT: A 175 ASP cc_start: 0.7970 (m-30) cc_final: 0.7446 (m-30) REVERT: A 206 GLN cc_start: 0.8857 (mm110) cc_final: 0.8326 (mm-40) REVERT: A 208 TYR cc_start: 0.8319 (t80) cc_final: 0.7851 (t80) REVERT: A 236 TRP cc_start: 0.8635 (p-90) cc_final: 0.8309 (p-90) REVERT: A 274 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: A 310 LYS cc_start: 0.7116 (ttpt) cc_final: 0.6414 (tptm) REVERT: A 322 LYS cc_start: 0.7231 (pttm) cc_final: 0.6409 (tttm) REVERT: B 105 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: B 146 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8466 (mtm110) REVERT: B 153 ASP cc_start: 0.8708 (m-30) cc_final: 0.8375 (m-30) REVERT: B 158 PHE cc_start: 0.7608 (t80) cc_final: 0.7233 (t80) REVERT: B 199 GLN cc_start: 0.8191 (tp40) cc_final: 0.7888 (tt0) REVERT: B 206 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8375 (mm-40) REVERT: B 208 TYR cc_start: 0.8368 (t80) cc_final: 0.8046 (t80) REVERT: B 236 TRP cc_start: 0.8927 (p-90) cc_final: 0.8631 (p-90) REVERT: B 310 LYS cc_start: 0.7360 (ttpt) cc_final: 0.6700 (tptm) REVERT: B 315 TYR cc_start: 0.8231 (m-10) cc_final: 0.7577 (m-10) REVERT: B 322 LYS cc_start: 0.7741 (pttm) cc_final: 0.7055 (mptt) REVERT: B 359 ILE cc_start: 0.9374 (tp) cc_final: 0.9069 (tp) REVERT: C 105 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.7174 (m-10) REVERT: C 123 ARG cc_start: 0.8388 (ttm170) cc_final: 0.8061 (ttp-170) REVERT: C 153 ASP cc_start: 0.8630 (m-30) cc_final: 0.8075 (m-30) REVERT: C 154 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8295 (mtpt) REVERT: C 157 LYS cc_start: 0.8230 (tptt) cc_final: 0.7510 (ttpp) REVERT: C 158 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7685 (t80) REVERT: C 178 ARG cc_start: 0.9119 (ttp-110) cc_final: 0.8888 (ttp80) REVERT: C 206 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8581 (mm-40) REVERT: C 208 TYR cc_start: 0.8384 (t80) cc_final: 0.7853 (t80) REVERT: C 236 TRP cc_start: 0.8635 (p-90) cc_final: 0.8268 (p-90) REVERT: C 274 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: C 304 ASN cc_start: 0.8602 (t0) cc_final: 0.8340 (t0) REVERT: C 310 LYS cc_start: 0.7167 (ttpt) cc_final: 0.6283 (tptm) REVERT: C 322 LYS cc_start: 0.7256 (pttm) cc_final: 0.6457 (tttm) REVERT: D 65 ASN cc_start: 0.7448 (p0) cc_final: 0.6947 (p0) REVERT: D 105 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: D 153 ASP cc_start: 0.8720 (m-30) cc_final: 0.8298 (m-30) REVERT: D 206 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8493 (mm-40) REVERT: D 208 TYR cc_start: 0.8367 (t80) cc_final: 0.7939 (t80) REVERT: D 274 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.6055 (mp0) REVERT: D 305 LYS cc_start: 0.8583 (tttm) cc_final: 0.8240 (tmtt) REVERT: D 310 LYS cc_start: 0.7409 (ttpt) cc_final: 0.6936 (tptt) REVERT: D 315 TYR cc_start: 0.8312 (m-10) cc_final: 0.7703 (m-10) REVERT: D 322 LYS cc_start: 0.7428 (pttm) cc_final: 0.6774 (mptt) REVERT: D 332 SER cc_start: 0.9158 (m) cc_final: 0.8861 (p) REVERT: D 359 ILE cc_start: 0.9391 (tp) cc_final: 0.9078 (tp) REVERT: E 59 TRP cc_start: 0.7933 (t-100) cc_final: 0.7728 (t-100) REVERT: E 153 ASP cc_start: 0.8694 (m-30) cc_final: 0.8447 (m-30) REVERT: E 157 LYS cc_start: 0.8163 (tptt) cc_final: 0.7746 (ttmm) REVERT: E 175 ASP cc_start: 0.8158 (m-30) cc_final: 0.7634 (m-30) REVERT: E 206 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8414 (mm-40) REVERT: E 208 TYR cc_start: 0.8347 (t80) cc_final: 0.7812 (t80) REVERT: E 236 TRP cc_start: 0.8769 (p-90) cc_final: 0.8371 (p-90) REVERT: E 274 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: E 305 LYS cc_start: 0.8450 (tttm) cc_final: 0.8153 (tmtt) REVERT: E 310 LYS cc_start: 0.7256 (ttpt) cc_final: 0.6666 (tptt) REVERT: E 322 LYS cc_start: 0.7190 (pttm) cc_final: 0.6423 (tttm) REVERT: F 153 ASP cc_start: 0.8607 (m-30) cc_final: 0.8257 (m-30) REVERT: F 157 LYS cc_start: 0.8080 (tptt) cc_final: 0.7698 (ttmm) REVERT: F 158 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7529 (t80) REVERT: F 183 LYS cc_start: 0.9022 (ttpt) cc_final: 0.8807 (ttpt) REVERT: F 206 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8596 (mm-40) REVERT: F 208 TYR cc_start: 0.8378 (t80) cc_final: 0.8107 (t80) REVERT: F 274 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.6206 (mp0) REVERT: F 304 ASN cc_start: 0.8455 (t0) cc_final: 0.8058 (t0) REVERT: F 310 LYS cc_start: 0.7501 (ttpt) cc_final: 0.6991 (tptt) REVERT: F 315 TYR cc_start: 0.8332 (m-10) cc_final: 0.7693 (m-10) REVERT: F 322 LYS cc_start: 0.7417 (pttm) cc_final: 0.6731 (mptt) REVERT: F 332 SER cc_start: 0.9214 (m) cc_final: 0.8952 (t) REVERT: G 70 ASN cc_start: 0.8925 (t0) cc_final: 0.8654 (t0) REVERT: G 105 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.7272 (m-10) REVERT: G 123 ARG cc_start: 0.8363 (ttm170) cc_final: 0.8040 (ttp-170) REVERT: G 153 ASP cc_start: 0.8678 (m-30) cc_final: 0.8399 (m-30) REVERT: G 154 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8267 (mtpt) REVERT: G 157 LYS cc_start: 0.8248 (tptt) cc_final: 0.7458 (ttpp) REVERT: G 158 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7472 (t80) REVERT: G 206 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8663 (mm-40) REVERT: G 208 TYR cc_start: 0.8321 (t80) cc_final: 0.7791 (t80) REVERT: G 236 TRP cc_start: 0.8613 (p-90) cc_final: 0.8258 (p-90) REVERT: G 271 ILE cc_start: 0.8774 (tt) cc_final: 0.8521 (tt) REVERT: G 274 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: G 310 LYS cc_start: 0.7135 (ttpt) cc_final: 0.6460 (tptm) REVERT: G 322 LYS cc_start: 0.7255 (pttm) cc_final: 0.6593 (mptt) REVERT: H 47 LEU cc_start: 0.9437 (mm) cc_final: 0.9209 (mm) REVERT: H 65 ASN cc_start: 0.7283 (p0) cc_final: 0.6697 (p0) REVERT: H 105 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7435 (m-10) REVERT: H 153 ASP cc_start: 0.8642 (m-30) cc_final: 0.8331 (m-30) REVERT: H 158 PHE cc_start: 0.7959 (t80) cc_final: 0.7579 (t80) REVERT: H 199 GLN cc_start: 0.8146 (tp40) cc_final: 0.7924 (tt0) REVERT: H 208 TYR cc_start: 0.8427 (t80) cc_final: 0.8080 (t80) REVERT: H 274 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.6055 (mp0) REVERT: H 305 LYS cc_start: 0.8505 (tttm) cc_final: 0.8271 (tmtt) REVERT: H 310 LYS cc_start: 0.7430 (ttpt) cc_final: 0.6726 (tptm) REVERT: H 313 LYS cc_start: 0.9315 (ttmt) cc_final: 0.9073 (ttmm) REVERT: H 315 TYR cc_start: 0.8250 (m-10) cc_final: 0.7536 (m-10) REVERT: H 316 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8540 (mm) REVERT: H 322 LYS cc_start: 0.7700 (pttm) cc_final: 0.7069 (mptt) REVERT: H 359 ILE cc_start: 0.9435 (tp) cc_final: 0.9097 (tp) outliers start: 74 outliers final: 45 residues processed: 782 average time/residue: 0.3208 time to fit residues: 384.2336 Evaluate side-chains 786 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 724 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 274 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 199 GLN 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 81 THR Chi-restraints excluded: chain D residue 105 TYR 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 299 ILE Chi-restraints excluded: chain E residue 50 HIS 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 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 158 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU 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 170 SER Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 332 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 221 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 220 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 149 optimal weight: 0.0770 chunk 142 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN B 50 HIS D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN G 50 HIS H 67 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.134881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.112513 restraints weight = 31213.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116531 restraints weight = 16529.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119281 restraints weight = 10828.644| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21848 Z= 0.113 Angle : 0.597 12.153 29776 Z= 0.288 Chirality : 0.038 0.158 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.089 26.647 2792 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.37 % Allowed : 29.52 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2496 helix: 1.37 (0.13), residues: 1712 sheet: -3.79 (0.39), residues: 80 loop : -2.83 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 68 HIS 0.011 0.001 HIS F 50 PHE 0.028 0.001 PHE H 124 TYR 0.018 0.001 TYR D 301 ARG 0.010 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 1240) hydrogen bonds : angle 3.93363 ( 3624) SS BOND : bond 0.00180 ( 16) SS BOND : angle 1.15593 ( 32) covalent geometry : bond 0.00245 (21832) covalent geometry : angle 0.59566 (29744) *********************** 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 823 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 747 time to evaluate : 2.416 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 123 ARG cc_start: 0.8318 (ttm170) cc_final: 0.7975 (ttp-170) REVERT: A 153 ASP cc_start: 0.8478 (m-30) cc_final: 0.8216 (m-30) REVERT: A 157 LYS cc_start: 0.8035 (tptt) cc_final: 0.7090 (ttpp) REVERT: A 158 PHE cc_start: 0.7779 (t80) cc_final: 0.7053 (t80) REVERT: A 175 ASP cc_start: 0.7969 (m-30) cc_final: 0.7448 (m-30) REVERT: A 206 GLN cc_start: 0.8771 (mm110) cc_final: 0.8387 (mm-40) REVERT: A 208 TYR cc_start: 0.8316 (t80) cc_final: 0.7843 (t80) REVERT: A 236 TRP cc_start: 0.8625 (p-90) cc_final: 0.8284 (p-90) REVERT: A 270 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8831 (t0) REVERT: A 274 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: A 310 LYS cc_start: 0.7159 (ttpt) cc_final: 0.6465 (tptm) REVERT: A 322 LYS cc_start: 0.7247 (pttm) cc_final: 0.6526 (tttm) REVERT: A 345 MET cc_start: 0.9304 (tpp) cc_final: 0.8905 (tpp) REVERT: B 105 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6797 (m-10) REVERT: B 146 ARG cc_start: 0.8869 (ttp80) cc_final: 0.8458 (mtm110) REVERT: B 153 ASP cc_start: 0.8658 (m-30) cc_final: 0.8357 (m-30) REVERT: B 158 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7258 (t80) REVERT: B 199 GLN cc_start: 0.8205 (tp40) cc_final: 0.7908 (tt0) REVERT: B 206 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8374 (mm-40) REVERT: B 208 TYR cc_start: 0.8320 (t80) cc_final: 0.8006 (t80) REVERT: B 310 LYS cc_start: 0.7362 (ttpt) cc_final: 0.6709 (tptm) REVERT: B 315 TYR cc_start: 0.8230 (m-10) cc_final: 0.7598 (m-10) REVERT: B 322 LYS cc_start: 0.7733 (pttm) cc_final: 0.7083 (mptt) REVERT: B 359 ILE cc_start: 0.9390 (tp) cc_final: 0.9075 (tp) REVERT: C 105 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.7175 (m-10) REVERT: C 123 ARG cc_start: 0.8372 (ttm170) cc_final: 0.8047 (ttp-170) REVERT: C 153 ASP cc_start: 0.8632 (m-30) cc_final: 0.8121 (m-30) REVERT: C 154 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8289 (mtpt) REVERT: C 157 LYS cc_start: 0.8219 (tptt) cc_final: 0.7483 (ttpp) REVERT: C 158 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7649 (t80) REVERT: C 178 ARG cc_start: 0.9125 (ttp-110) cc_final: 0.8860 (ttp80) REVERT: C 206 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8543 (mm-40) REVERT: C 208 TYR cc_start: 0.8373 (t80) cc_final: 0.7931 (t80) REVERT: C 236 TRP cc_start: 0.8604 (p-90) cc_final: 0.8209 (p-90) REVERT: C 274 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.6323 (mp0) REVERT: C 304 ASN cc_start: 0.8616 (t0) cc_final: 0.8257 (t0) REVERT: C 310 LYS cc_start: 0.7126 (ttpt) cc_final: 0.6294 (tptm) REVERT: C 322 LYS cc_start: 0.7242 (pttm) cc_final: 0.6546 (mptt) REVERT: D 65 ASN cc_start: 0.7422 (p0) cc_final: 0.6878 (p0) REVERT: D 153 ASP cc_start: 0.8707 (m-30) cc_final: 0.8341 (m-30) REVERT: D 206 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8471 (mm-40) REVERT: D 208 TYR cc_start: 0.8356 (t80) cc_final: 0.7899 (t80) REVERT: D 274 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.6016 (mp0) REVERT: D 305 LYS cc_start: 0.8587 (tttm) cc_final: 0.8258 (tmtt) REVERT: D 310 LYS cc_start: 0.7485 (ttpt) cc_final: 0.6932 (tptt) REVERT: D 315 TYR cc_start: 0.8310 (m-10) cc_final: 0.7696 (m-10) REVERT: D 322 LYS cc_start: 0.7440 (pttm) cc_final: 0.6790 (mptt) REVERT: D 359 ILE cc_start: 0.9354 (tp) cc_final: 0.9016 (tp) REVERT: E 59 TRP cc_start: 0.7982 (t-100) cc_final: 0.7763 (t-100) REVERT: E 107 TRP cc_start: 0.8223 (m100) cc_final: 0.7360 (m-10) REVERT: E 153 ASP cc_start: 0.8650 (m-30) cc_final: 0.8411 (m-30) REVERT: E 157 LYS cc_start: 0.8256 (tptt) cc_final: 0.7761 (ttmm) REVERT: E 175 ASP cc_start: 0.8165 (m-30) cc_final: 0.7632 (m-30) REVERT: E 206 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8389 (mm-40) REVERT: E 208 TYR cc_start: 0.8356 (t80) cc_final: 0.7816 (t80) REVERT: E 236 TRP cc_start: 0.8741 (p-90) cc_final: 0.8306 (p-90) REVERT: E 274 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.6201 (mp0) REVERT: E 305 LYS cc_start: 0.8477 (tttm) cc_final: 0.8173 (tmtt) REVERT: E 310 LYS cc_start: 0.7268 (ttpt) cc_final: 0.6579 (tptt) REVERT: E 322 LYS cc_start: 0.7163 (pttm) cc_final: 0.6568 (mptt) REVERT: F 153 ASP cc_start: 0.8662 (m-30) cc_final: 0.8312 (m-30) REVERT: F 157 LYS cc_start: 0.8075 (tptt) cc_final: 0.7688 (ttmm) REVERT: F 158 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7491 (t80) REVERT: F 206 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8584 (mm-40) REVERT: F 208 TYR cc_start: 0.8375 (t80) cc_final: 0.8088 (t80) REVERT: F 274 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: F 304 ASN cc_start: 0.8481 (t0) cc_final: 0.8060 (t0) REVERT: F 310 LYS cc_start: 0.7494 (ttpt) cc_final: 0.6988 (tptt) REVERT: F 315 TYR cc_start: 0.8355 (m-10) cc_final: 0.7709 (m-10) REVERT: F 322 LYS cc_start: 0.7395 (pttm) cc_final: 0.6724 (mptt) REVERT: F 332 SER cc_start: 0.9216 (m) cc_final: 0.8969 (t) REVERT: G 105 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.7202 (m-10) REVERT: G 123 ARG cc_start: 0.8354 (ttm170) cc_final: 0.8028 (ttp-170) REVERT: G 153 ASP cc_start: 0.8683 (m-30) cc_final: 0.8437 (m-30) REVERT: G 154 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8291 (mtpt) REVERT: G 157 LYS cc_start: 0.8241 (tptt) cc_final: 0.7420 (ttpp) REVERT: G 158 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7542 (t80) REVERT: G 206 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8640 (mm-40) REVERT: G 208 TYR cc_start: 0.8329 (t80) cc_final: 0.7887 (t80) REVERT: G 236 TRP cc_start: 0.8611 (p-90) cc_final: 0.8242 (p-90) REVERT: G 271 ILE cc_start: 0.8754 (tt) cc_final: 0.8486 (tt) REVERT: G 274 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: G 310 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6421 (tptm) REVERT: G 322 LYS cc_start: 0.7285 (pttm) cc_final: 0.6601 (mptt) REVERT: H 47 LEU cc_start: 0.9403 (mm) cc_final: 0.9177 (mm) REVERT: H 65 ASN cc_start: 0.7384 (p0) cc_final: 0.6980 (p0) REVERT: H 105 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.7453 (m-10) REVERT: H 158 PHE cc_start: 0.7935 (t80) cc_final: 0.7564 (t80) REVERT: H 208 TYR cc_start: 0.8409 (t80) cc_final: 0.8074 (t80) REVERT: H 274 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.6020 (mp0) REVERT: H 305 LYS cc_start: 0.8530 (tttm) cc_final: 0.8287 (tmtt) REVERT: H 310 LYS cc_start: 0.7442 (ttpt) cc_final: 0.6747 (tptm) REVERT: H 313 LYS cc_start: 0.9313 (ttmt) cc_final: 0.9076 (ttmm) REVERT: H 315 TYR cc_start: 0.8245 (m-10) cc_final: 0.7549 (m-10) REVERT: H 316 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8523 (mm) REVERT: H 322 LYS cc_start: 0.7684 (pttm) cc_final: 0.7052 (mptt) REVERT: H 359 ILE cc_start: 0.9422 (tp) cc_final: 0.9084 (tp) outliers start: 76 outliers final: 52 residues processed: 786 average time/residue: 0.3134 time to fit residues: 377.2595 Evaluate side-chains 804 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 735 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 270 ASN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 199 GLN 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 81 THR 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 299 ILE 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 170 SER Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 351 ASP 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 158 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 351 ASP 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 162 LEU Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 332 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 45 optimal weight: 0.8980 chunk 236 optimal weight: 9.9990 chunk 39 optimal weight: 0.0060 chunk 44 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 228 optimal weight: 0.5980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS C 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 50 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.136729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.114530 restraints weight = 31265.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.118512 restraints weight = 16522.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.121294 restraints weight = 10811.202| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21848 Z= 0.115 Angle : 0.597 9.487 29776 Z= 0.290 Chirality : 0.038 0.183 3288 Planarity : 0.003 0.034 3632 Dihedral : 4.088 28.170 2792 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.97 % Allowed : 30.05 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2496 helix: 1.40 (0.13), residues: 1712 sheet: -3.87 (0.38), residues: 80 loop : -2.76 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 59 HIS 0.016 0.002 HIS G 50 PHE 0.021 0.001 PHE D 330 TYR 0.018 0.001 TYR D 301 ARG 0.011 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 1240) hydrogen bonds : angle 3.90455 ( 3624) SS BOND : bond 0.00358 ( 16) SS BOND : angle 1.26575 ( 32) covalent geometry : bond 0.00253 (21832) covalent geometry : angle 0.59589 (29744) ********************** 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 809 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 742 time to evaluate : 2.429 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 123 ARG cc_start: 0.8322 (ttm170) cc_final: 0.7978 (ttp-170) REVERT: A 153 ASP cc_start: 0.8487 (m-30) cc_final: 0.8238 (m-30) REVERT: A 157 LYS cc_start: 0.8000 (tptt) cc_final: 0.6812 (ttmm) REVERT: A 158 PHE cc_start: 0.7777 (t80) cc_final: 0.7035 (t80) REVERT: A 175 ASP cc_start: 0.7974 (m-30) cc_final: 0.7446 (m-30) REVERT: A 206 GLN cc_start: 0.8748 (mm110) cc_final: 0.8345 (mm-40) REVERT: A 208 TYR cc_start: 0.8319 (t80) cc_final: 0.7846 (t80) REVERT: A 236 TRP cc_start: 0.8604 (p-90) cc_final: 0.8312 (p-90) REVERT: A 274 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.5891 (mp0) REVERT: A 310 LYS cc_start: 0.7128 (ttpt) cc_final: 0.6450 (tptm) REVERT: A 322 LYS cc_start: 0.7280 (pttm) cc_final: 0.6654 (mptt) REVERT: A 345 MET cc_start: 0.9305 (tpp) cc_final: 0.8900 (tpp) REVERT: B 105 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.6916 (m-10) REVERT: B 146 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8460 (mtm110) REVERT: B 153 ASP cc_start: 0.8626 (m-30) cc_final: 0.8321 (m-30) REVERT: B 158 PHE cc_start: 0.7350 (t80) cc_final: 0.6938 (t80) REVERT: B 199 GLN cc_start: 0.8225 (tp40) cc_final: 0.7940 (tt0) REVERT: B 208 TYR cc_start: 0.8325 (t80) cc_final: 0.7971 (t80) REVERT: B 310 LYS cc_start: 0.7367 (ttpt) cc_final: 0.6717 (tptm) REVERT: B 315 TYR cc_start: 0.8225 (m-10) cc_final: 0.7586 (m-10) REVERT: B 322 LYS cc_start: 0.7691 (pttm) cc_final: 0.7099 (mptt) REVERT: B 359 ILE cc_start: 0.9398 (tp) cc_final: 0.9077 (tp) REVERT: C 105 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.7161 (m-10) REVERT: C 123 ARG cc_start: 0.8364 (ttm170) cc_final: 0.8039 (ttp-170) REVERT: C 153 ASP cc_start: 0.8630 (m-30) cc_final: 0.8112 (m-30) REVERT: C 154 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8306 (mtpt) REVERT: C 157 LYS cc_start: 0.8220 (tptt) cc_final: 0.7475 (ttpp) REVERT: C 158 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7613 (t80) REVERT: C 206 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8525 (mm-40) REVERT: C 208 TYR cc_start: 0.8431 (t80) cc_final: 0.7916 (t80) REVERT: C 236 TRP cc_start: 0.8605 (p-90) cc_final: 0.8175 (p-90) REVERT: C 274 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.6305 (mp0) REVERT: C 304 ASN cc_start: 0.8626 (t0) cc_final: 0.8263 (t0) REVERT: C 310 LYS cc_start: 0.7126 (ttpt) cc_final: 0.6290 (tptm) REVERT: C 322 LYS cc_start: 0.7233 (pttm) cc_final: 0.6549 (mptt) REVERT: D 65 ASN cc_start: 0.7388 (p0) cc_final: 0.6866 (p0) REVERT: D 153 ASP cc_start: 0.8717 (m-30) cc_final: 0.8368 (m-30) REVERT: D 199 GLN cc_start: 0.8163 (tp40) cc_final: 0.7866 (tt0) REVERT: D 208 TYR cc_start: 0.8371 (t80) cc_final: 0.7919 (t80) REVERT: D 274 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: D 305 LYS cc_start: 0.8605 (tttm) cc_final: 0.8395 (tmtt) REVERT: D 310 LYS cc_start: 0.7517 (ttpt) cc_final: 0.6970 (tptt) REVERT: D 315 TYR cc_start: 0.8312 (m-10) cc_final: 0.7680 (m-10) REVERT: D 322 LYS cc_start: 0.7426 (pttm) cc_final: 0.6822 (mptt) REVERT: D 359 ILE cc_start: 0.9353 (tp) cc_final: 0.9025 (tp) REVERT: E 107 TRP cc_start: 0.8239 (m100) cc_final: 0.7366 (m-10) REVERT: E 153 ASP cc_start: 0.8646 (m-30) cc_final: 0.8413 (m-30) REVERT: E 157 LYS cc_start: 0.8252 (tptt) cc_final: 0.7762 (ttmm) REVERT: E 175 ASP cc_start: 0.8160 (m-30) cc_final: 0.7629 (m-30) REVERT: E 206 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8387 (mm-40) REVERT: E 208 TYR cc_start: 0.8363 (t80) cc_final: 0.7824 (t80) REVERT: E 236 TRP cc_start: 0.8741 (p-90) cc_final: 0.8285 (p-90) REVERT: E 274 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.6206 (mp0) REVERT: E 305 LYS cc_start: 0.8474 (tttm) cc_final: 0.8178 (tmtt) REVERT: E 310 LYS cc_start: 0.7344 (ttpt) cc_final: 0.6632 (tptt) REVERT: E 322 LYS cc_start: 0.7141 (pttm) cc_final: 0.6560 (mptt) REVERT: E 345 MET cc_start: 0.9288 (tpp) cc_final: 0.8928 (tpp) REVERT: F 157 LYS cc_start: 0.7987 (tptt) cc_final: 0.7615 (ttmm) REVERT: F 158 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7481 (t80) REVERT: F 206 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8593 (mm-40) REVERT: F 208 TYR cc_start: 0.8369 (t80) cc_final: 0.8068 (t80) REVERT: F 274 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: F 304 ASN cc_start: 0.8485 (t0) cc_final: 0.8069 (t0) REVERT: F 310 LYS cc_start: 0.7576 (ttpt) cc_final: 0.7047 (tptt) REVERT: F 315 TYR cc_start: 0.8377 (m-10) cc_final: 0.7720 (m-10) REVERT: F 322 LYS cc_start: 0.7372 (pttm) cc_final: 0.6726 (mptt) REVERT: F 332 SER cc_start: 0.9203 (m) cc_final: 0.8962 (t) REVERT: G 105 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: G 123 ARG cc_start: 0.8343 (ttm170) cc_final: 0.8024 (ttp-170) REVERT: G 153 ASP cc_start: 0.8670 (m-30) cc_final: 0.8430 (m-30) REVERT: G 154 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8287 (mtpt) REVERT: G 157 LYS cc_start: 0.8167 (tptt) cc_final: 0.7336 (ttpp) REVERT: G 158 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7495 (t80) REVERT: G 206 GLN cc_start: 0.9182 (mm-40) cc_final: 0.8705 (mm-40) REVERT: G 208 TYR cc_start: 0.8396 (t80) cc_final: 0.7879 (t80) REVERT: G 236 TRP cc_start: 0.8595 (p-90) cc_final: 0.8203 (p-90) REVERT: G 271 ILE cc_start: 0.8701 (tt) cc_final: 0.8448 (tt) REVERT: G 274 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: G 310 LYS cc_start: 0.7219 (ttpt) cc_final: 0.6445 (tptm) REVERT: G 322 LYS cc_start: 0.7270 (pttm) cc_final: 0.6595 (mptt) REVERT: H 47 LEU cc_start: 0.9385 (mm) cc_final: 0.9181 (mm) REVERT: H 65 ASN cc_start: 0.7461 (p0) cc_final: 0.6914 (p0) REVERT: H 105 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7446 (m-10) REVERT: H 158 PHE cc_start: 0.7905 (t80) cc_final: 0.7525 (t80) REVERT: H 208 TYR cc_start: 0.8412 (t80) cc_final: 0.8081 (t80) REVERT: H 274 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.6008 (mp0) REVERT: H 305 LYS cc_start: 0.8520 (tttm) cc_final: 0.8274 (tmtt) REVERT: H 310 LYS cc_start: 0.7455 (ttpt) cc_final: 0.6767 (tptm) REVERT: H 313 LYS cc_start: 0.9315 (ttmt) cc_final: 0.9084 (ttmm) REVERT: H 315 TYR cc_start: 0.8248 (m-10) cc_final: 0.7540 (m-10) REVERT: H 316 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8450 (mm) REVERT: H 322 LYS cc_start: 0.7647 (pttm) cc_final: 0.7066 (mptt) REVERT: H 359 ILE cc_start: 0.9421 (tp) cc_final: 0.9083 (tp) outliers start: 67 outliers final: 49 residues processed: 776 average time/residue: 0.3313 time to fit residues: 395.3697 Evaluate side-chains 795 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 731 time to evaluate : 2.202 ------------------------------------------------------------------------------- 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 332 SER Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 199 GLN 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 81 THR 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 299 ILE Chi-restraints excluded: chain E residue 50 HIS 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 351 ASP 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 158 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 GLU 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 170 SER Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 351 ASP 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 162 LEU Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 332 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 220 optimal weight: 0.9980 chunk 226 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 187 optimal weight: 0.0870 chunk 139 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS D 50 HIS D 67 GLN E 67 GLN F 50 HIS G 50 HIS G 79 HIS H 67 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113890 restraints weight = 31263.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117904 restraints weight = 16525.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.120598 restraints weight = 10774.786| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21848 Z= 0.115 Angle : 0.603 11.376 29776 Z= 0.294 Chirality : 0.038 0.203 3288 Planarity : 0.004 0.046 3632 Dihedral : 4.095 27.985 2792 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.15 % Allowed : 29.92 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2496 helix: 1.43 (0.13), residues: 1712 sheet: -3.95 (0.38), residues: 80 loop : -2.70 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 59 HIS 0.017 0.002 HIS B 50 PHE 0.028 0.001 PHE F 330 TYR 0.018 0.001 TYR D 301 ARG 0.010 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 1240) hydrogen bonds : angle 3.89628 ( 3624) SS BOND : bond 0.00472 ( 16) SS BOND : angle 1.49638 ( 32) covalent geometry : bond 0.00253 (21832) covalent geometry : angle 0.60162 (29744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8180.95 seconds wall clock time: 141 minutes 52.20 seconds (8512.20 seconds total)